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3D-PDR

View on GitHubGet a ZipGet a Tarball

3D-PDR is a three-dimensional photodissociation region code written in Fortran. It uses the Sundials package (written in C) to solve the set of ordinary differential equations and it is the successor of UCL_PDR, a one-dimensional PDR code written at UCL. Using the HEALpix ray-tracing scheme, 3D-PDR solves a three-dimensional escape probability routine and evaluates the attenuation of the far-ultraviolet radiation in the PDR and the propagation of FIR/submm emission lines out of the PDR.

The code is parallelized (OpenMP) and can be applied to 1D and 3D problems. The GitHub package includes: the 3D-PDR code, three different chemical networks (33, 58, and 128 species) and molecular data, the Sundials solver, and a set of various 1D uniform density clouds and a uniform density spherical distribution to test the 3D version of the code. To `make' 3D-PDR, you will first need to install the Sundials package and link 3D-PDR with the ODE solver. Please see the manual for instructions on how to do this step-by-step.

(Update: 23/04/2019) The file [3dpdr_cr.tar] that can be found in the main tarball, contains a totally new version of 3D-PDR treating cosmic-ray sources. This version was developed by Brandt Gaches [email: gaches .at. ph1.uni-koeln.de] and is presented in Gaches et al. (2019a). The tarball contains a short additional manual. Please contact Brandt Gaches for any question regarding this version.

3D-PDR works with the gfortran version 4.8.4 and the ifort version 14.0.4. Later compiler versions may require adjustments in the code.

Authors, Contributors and Users

Main author: Thomas G. Bisbas (@tbisbas).

Contributors: Serena Viti, Michael J. Barlow, Jeremy Yates, Tom Bell, Brandt Gaches

You are free to download and use the code for your work provided that you will cite the paper by Bisbas et al., 2012, MNRAS, 427, 2100

A number of papers have been using 3D-PDR for studying Photodissociation Regions in 1D and 3D:

Copyright © 2023 Leiden University
- - +
Skip to main content

3D-PDR

View on GitHubGet a ZipGet a Tarball

3D-PDR is a three-dimensional photodissociation region code written in Fortran. It uses the Sundials package (written in C) to solve the set of ordinary differential equations and it is the successor of UCL_PDR, a one-dimensional PDR code written at UCL. Using the HEALpix ray-tracing scheme, 3D-PDR solves a three-dimensional escape probability routine and evaluates the attenuation of the far-ultraviolet radiation in the PDR and the propagation of FIR/submm emission lines out of the PDR.

The code is parallelized (OpenMP) and can be applied to 1D and 3D problems. The GitHub package includes: the 3D-PDR code, three different chemical networks (33, 58, and 128 species) and molecular data, the Sundials solver, and a set of various 1D uniform density clouds and a uniform density spherical distribution to test the 3D version of the code. To `make' 3D-PDR, you will first need to install the Sundials package and link 3D-PDR with the ODE solver. Please see the manual for instructions on how to do this step-by-step.

(Update: 23/04/2019) The file [3dpdr_cr.tar] that can be found in the main tarball, contains a totally new version of 3D-PDR treating cosmic-ray sources. This version was developed by Brandt Gaches [email: gaches .at. ph1.uni-koeln.de] and is presented in Gaches et al. (2019a). The tarball contains a short additional manual. Please contact Brandt Gaches for any question regarding this version.

3D-PDR works with the gfortran version 4.8.4 and the ifort version 14.0.4. Later compiler versions may require adjustments in the code.

Authors, Contributors and Users

Main author: Thomas G. Bisbas (@tbisbas).

Contributors: Serena Viti, Michael J. Barlow, Jeremy Yates, Tom Bell, Brandt Gaches

You are free to download and use the code for your work provided that you will cite the paper by Bisbas et al., 2012, MNRAS, 427, 2100

A number of papers have been using 3D-PDR for studying Photodissociation Regions in 1D and 3D:

+ + \ No newline at end of file diff --git a/404.html b/404.html index 99445f17..38de1ecb 100644 --- a/404.html +++ b/404.html @@ -13,13 +13,13 @@ - - + +
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mathnormal"},"i"),(0,n.kt)("span",{parentName:"span",className:"mclose"},")")))),(0,n.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,n.kt)("span",{parentName:"span",className:"vlist-r"},(0,n.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8360000000000001em"}},(0,n.kt)("span",{parentName:"span"}))))),(0,n.kt)("span",{parentName:"span",className:"mclose nulldelimiter"}))))))),(0,n.kt)("p",null,"where the first two terms give the total rate of surface to bulk transfer and the final fraction divides this amongst the species on the surface. We subtract this ODE from each surface species and add it to the equivalent bulk species. If the rate of change of the surface is negative, the bulk is transferred to the surface."),(0,n.kt)("h2",{id:"individual-swapping"},"Individual Swapping"),(0,n.kt)("p",null,"Any species in the bulk has the possibilty of diffusing to the surface. It will then displace a surface particle (which will join the bulk) and become part of the surface. 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Furthermore, since H3O+ was increased in abundance by increasing CRIR and SO was destroyed, their ratio was extremely sensitive to the rate. "),(0,m.kt)("p",null,"In the work, we present the plot below which shows how the equilibrium abundance of each species changes with the CRIR as well as the ratio. We plot this for a range of temperatures to show that this behaviour is not particularly sensitive to the gas temperature."),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"crir_h3o_so_example",src:t(8715).Z,width:"1600",height:"1067"})),(0,m.kt)("p",null,"In a sense, this is all the information we need. A complex array of reactions all compete and contribute to produce the outcome of the model. Whatever they are, we see the abundance of these species are very sensitive to the CR over a wide range of temperature and density. 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Hopefully, we'll see the same reactions are most important to the abundance of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," and SO at all densities and tempertures. If we don't find that that's the case, then the chemistry is these species is fairly complex and perhaps trying to present a simple cause for the CRIR dependence is not a good idea."),(0,m.kt)("p",null,"So, let's analyse the outputs!"),(0,m.kt)("h4",{id:"21-h_3o"},"2.1 ",(0,m.kt)("span",{parentName:"h4",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))),(0,m.kt)("p",null,(0,m.kt)("inlineCode",{parentName:"p"},"analysis()")," takes three arguments: the species, the output file to analyse, and a file to store the analsis output. Let's run it for every model in our little grid so we can inspect the outputs."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'outputs=glob("../output/[0-9]*.csv") #all files that start with a number\nfor output in outputs:\n \n analysis_output="../output/H3O-analysis-"+output[10:]\n uclchem.analysis.analysis("H3O+",output,analysis_output)\n')),(0,m.kt)("p",null,"This will produce one file per model output with lists of the most important reactions at each time step. Analysis will only print a time step when the most important reactions change from the previous one so we often see many fewer steps than in the full output. Let's look at the low temperature, low density, low zeta case:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 7.90e+05 years\nFormation = 1.92e-18 from:\nH2 + H2O+ -> H3O+ + H : 78.49%\nH2O + HCO+ -> CO + H3O+ : 17.68%\nH3+ + H2O -> H3O+ + H2 : 3.40%\n\nDestruction = -1.92e-18 from:\nH3O+ + E- -> OH + H + H : 65.43%\nH3O+ + E- -> H2O + H : 15.21%\nH3O+ + E- -> OH + H2 : 11.52%\nH3O+ + H2S -> H3S+ + H2O : 5.17%\nH3O+ + E- -> O + H2 + H : 1.20%\nH3O+ + HCN -> HCNH+ + H2O : 0.33%\nH3O+ + SIO -> SIOH+ + H2O : 0.33%\n")),(0,m.kt)("p",null,"What this shows is the reactions that cause 99.9% of the formation and 99.9% of the destruction of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," at a time step. The total rate of formation and destruction in units of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"s"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"1")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"s^{-1}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"s"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"1")))))))))))))," is given as well the percentage of the total that each reaction contributes. "),(0,m.kt)("p",null,"What we need to find is a pattern in these reactions which holds across time and across different densities and temperatures. It actually turns out that the reactions printed above are the dominate formation and destruction routes of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," for all parameters for all times. For example, at high temperature, high density and high zeta, we get:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.00e+04 years\nFormation = 2.03e-14 from:\nH2 + H2O+ -> H3O+ + H : 95.47%\nH3+ + H2O -> H3O+ + H2 : 3.14%\nH2O + HCO+ -> CO + H3O+ : 1.05%\n\nDestruction = -2.03e-14 from:\nH3O+ + E- -> OH + H + H : 69.82%\nH3O+ + E- -> H2O + H : 16.23%\nH3O+ + E- -> OH + H2 : 12.29%\nH3O+ + E- -> O + H2 + H : 1.28%\n")),(0,m.kt)("p",null,"The sole difference being that the formation rate is much higher. Since equilibrium is reached, the destruction rate is also higher and so we need to use the fact we know the ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord 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with CRIR to infer that the destruction rate is only faster because there is more ",(0,m.kt)("span",{parentName:"p",className:"math 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destroy."),(0,m.kt)("p",null,"However, there are some problems here! Why does ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"}))))))))))," + ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," become so efficient at high CRIR? We know the rate of a two body reaction does not depend on CRIR (",(0,m.kt)("a",{parentName:"p",href:"/docs/gas"},"see the chemistry docs"),") so it must be that ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is increasing in abundance. We can run analysis on ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," to see what is driving that. In fact, as we report in the paper, following this thread we find that a chain of hydrogenations starting from ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mi",{parentName:"mrow"},"O"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"H"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"OH^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is the overall route of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," formation and that this chain starts with small ions that are primarly formed through cosmic ray reactions. ",(0,m.kt)("em",{parentName:"p"},"It will very often be the case that analysing one species requires you to run analysis on another.")),(0,m.kt)("h4",{id:"22-so"},"2.2 SO"),(0,m.kt)("p",null,"With a strong explanation for ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+")))))))))))),", we can now look at SO. We start by running analysis again and then by looking at the reactions as before."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'outputs=glob("../output/[0-9]*.csv") #won\'t pick up H3O+ analysis because it\'s not a number\nfor output in outputs:\n \n analysis_output="../output/SO-analysis-"+output[10:]\n uclchem.analysis.analysis("SO",output,analysis_output)\n')),(0,m.kt)("p",null,"Again, let's start by looking at the low temperature, high density, low zeta case:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.31e+04 years\nFormation = 3.67e-22 from:\n#SO + THERM -> SO : 68.11%\nHSO+ + E- -> SO + H : 21.04%\n#SO + DEUVCR -> SO : 9.87%\n\nDestruction = -3.78e-22 from:\nSO + FREEZE -> #SO : 78.04%\nHCO+ + SO -> HSO+ + CO : 20.97%\n")),(0,m.kt)("p",null,"An interesting point here is that equilbrium is reached at around ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1.31"),(0,m.kt)("mo",{parentName:"mrow"},"\xd7"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mn",{parentName:"msup"},"4"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"1.31 \\times 10^4")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.72777em",verticalAlign:"-0.08333em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},"."),(0,m.kt)("span",{parentName:"span",className:"mord"},"3"),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2222222222222222em"}}),(0,m.kt)("span",{parentName:"span",className:"mbin"},"\xd7"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2222222222222222em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4"))))))))))))," yr in this model. Since ",(0,m.kt)("inlineCode",{parentName:"p"},"analysis()")," only prints a time step when the most important reactions are different to the last one, this time step is the last output from the analysis. We can see that we broadly reach an equilibrium between thermal desorption and freeze out of SO, with some formation and destruction via ions. "),(0,m.kt)("p",null,"This doesn't hold up at lower densities or higher temperatures, looking at the high temperature, low density, low zeta case, we see a second pattern of reactions:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 9.50e+05 years\nFormation = 1.05e-20 from:\nO2 + S -> SO + O : 98.10%\nO + NS -> SO + N : 1.48%\n\nDestruction = -1.02e-20 from:\nC + SO -> CS + O : 39.10%\nC + SO -> S + CO : 39.10%\nC+ + SO -> SO+ + C : 4.33%\nC+ + SO -> CS+ + O : 4.33%\nC+ + SO -> S+ + CO : 4.33%\nC+ + SO -> S + CO+ : 4.33%\nN + SO -> S + NO : 3.46%\nH+ + SO -> SO+ + H : 0.28%\n")),(0,m.kt)("p",null,"However, it's not so complex. All the low zeta outputs show one of these two sets of reactions. Essentially, higher temperatures are opening up gas phase reaction routes which form and destroy SO. These new routes are not particularly quick with a total rate of change of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"20"))),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"s"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"1")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"10^{-20} s^{-1}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"0"))))))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"s"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"1"))))))))))))),". Note that quite a lot of these are due to reactions with ions."),(0,m.kt)("p",null,"Finally, we look at the high zeta cases and find that no matter the temperature or density, we see the same reactions:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.81e+04 years\nFormation = 5.64e-17 from:\nO2 + S -> SO + O : 85.30%\nHSO+ + E- -> SO + H : 13.19%\nO + NS -> SO + N : 1.19%\n\nDestruction = -5.64e-17 from:\nH+ + SO -> SO+ + H : 13.16%\nC+ + SO -> SO+ + C : 10.52%\nC+ + SO -> CS+ + O : 10.52%\nC+ + SO -> S+ + CO : 10.52%\nC+ + SO -> S + CO+ : 10.52%\nH3+ + SO -> HSO+ + H2 : 9.86%\nC + SO -> CS + O : 8.90%\nC + SO -> S + CO : 8.90%\nSO + CRPHOT -> S + O : 4.11%\nSO + CRPHOT -> SO+ + E- : 4.11%\nHCO+ + SO -> HSO+ + CO : 3.20%\nHE+ + SO -> S+ + O + HE : 1.93%\nHE+ + SO -> S + O+ + HE : 1.93%\nN + SO -> S + NO : 0.87%\n")),(0,m.kt)("p",null,"Ions take over the destruction of SO when the CRIR is high and these reactions are proceeding about 1000 times faster than the low zeta rates. This makes sense as increasing the CRIR will greatly increase the abundances of these simple ionic species."),(0,m.kt)("p",null,"All in all, we can conclude that a range of gas phase reactions control the abundance of SO at low zeta but once the CRIR is high, destruction via ions dominates the SO chemistry leading to the decreasing abundance that we see."),(0,m.kt)("h2",{id:"summary-notes"},"Summary Notes"),(0,m.kt)("p",null,"In this notebook, we've run some representative models to look at why the SO and ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," abundances seem to so heavily depend on the CRIR. We find that a chain of very efficient reactions starting with simple ions comprise the primary formation route of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," so that the total production of this species depends entirely on the abundance of those ions. With high CRIR, those ions become very abundant and we get a lot of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," formation."),(0,m.kt)("p",null,"SO is complex at first glance since the formation routes vary by parameter. However, looking at the destruction routes we can see that it's simply that SO can be easily destroyed by simple ions and, again, these are very abundant in gas exposed to a high CRIR."),(0,m.kt)("p",null,"An interesting note about SO is that we could potentially say that destruction via C",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is the dominant destruction route. However, we would caution users to be careful with that kind of statement. Reactions with H",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+")))))))))))),", HE",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," and other also destroy SO. It could be that if we turned off the C",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," reactions, the SO chemistry would be unchanged as other ions take up the slack. Therefore, unless a single reaction is clearly dominant (as in ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," formation), it is best to test the importance of a reaction by removing it before concluding it is the single most important reaction."),(0,m.kt)("h2",{id:"considerations"},"Considerations"),(0,m.kt)("p",null,(0,m.kt)("inlineCode",{parentName:"p"},"uclchem.analysis.analysis()")," looks at a snapshot of the gas and calculates the instantaneous rate of change of important reactions. However, over the course of a time step, abundances change and reactions rise and fall in importance. More importantly, complex interplay between reactions can contribute to an outcome. 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Defaults to 0.99.")),(0,i.kt)("a",{id:"uclchem.analysis.total_element_abundance"}),(0,i.kt)("h4",{id:"total_element_abundance"},"total","_","element","_","abundance"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def total_element_abundance(element, df)\n")),(0,i.kt)("p",null,"Calculates that the total elemental abundance of a species as a function of time. Allows you to check conservation."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"element")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Name of element"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"df")," ",(0,i.kt)("em",{parentName:"li"},"pandas.DataFrame")," - DataFrame from ",(0,i.kt)("inlineCode",{parentName:"li"},"read_output_file()"))),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"pandas.Series")," - Total abundance of element for all time steps in df.")),(0,i.kt)("a",{id:"uclchem.analysis.check_element_conservation"}),(0,i.kt)("h4",{id:"check_element_conservation"},"check","_","element","_","conservation"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},'def check_element_conservation(df,\n element_list=["H", "N", "C", "O"],\n percent=True)\n')),(0,i.kt)("p",null,"Check the conservation of major element by comparing total abundance at start and end of model"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"df")," ",(0,i.kt)("em",{parentName:"li"},"pandas.DataFrame")," - UCLCHEM output in format from ",(0,i.kt)("inlineCode",{parentName:"li"},"read_output_file")),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"element_list")," ",(0,i.kt)("em",{parentName:"li"},"list, optional")," - List of elements to check. 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Then calculate mass and alert user if it doesn't match\ninput mass."),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.get_n_atoms"}),(0,i.kt)("h4",{id:"get_n_atoms"},"get","_","n","_","atoms"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_n_atoms() -> int\n")),(0,i.kt)("p",null,"Obtain the number of atoms in the molecule"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"int")," - The number of atoms")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.set_n_atoms"}),(0,i.kt)("h4",{id:"set_n_atoms"},"set","_","n","_","atoms"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_n_atoms(new_n_atoms: int) -> None\n")),(0,i.kt)("p",null,"Set the number of atoms"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_n_atoms")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The new number of atoms")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__eq__"}),(0,i.kt)("h4",{id:"__eq__"},"_","_","eq","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __eq__(other)\n")),(0,i.kt)("p",null,"Check for equality based on either a string or another Species instance."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"str, Species")," - Another species")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"NotImplementedError")," - We can only compare between species or strings of species.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if two species are identical.")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__lt__"}),(0,i.kt)("h4",{id:"__lt__"},"_","_","lt","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __lt__(other) -> bool\n")),(0,i.kt)("p",null,"Compare the mass of the species"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - Another species instance")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if less than the other species")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__gt__"}),(0,i.kt)("h4",{id:"__gt__"},"_","_","gt","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __gt__(other) -> bool\n")),(0,i.kt)("p",null,"Compare the mass of the species"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - Another species instance")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if larger than than the other species")),(0,i.kt)("a",{id:"uclchem.makerates"}),(0,i.kt)("h1",{id:"uclchemmakerates"},"uclchem.makerates"),(0,i.kt)("a",{id:"uclchem.makerates.makerates"}),(0,i.kt)("h1",{id:"uclchemmakeratesmakerates"},"uclchem.makerates.makerates"),(0,i.kt)("a",{id:"uclchem.makerates.makerates.run_makerates"}),(0,i.kt)("h4",{id:"run_makerates"},"run","_","makerates"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},'def run_makerates(configuration_file: str = "user_settings.yaml",\n write_files: bool = True) -> Network\n')),(0,i.kt)("p",null,"The main run wrapper for makerates, it loads a configuration, parses it in Network\nand then returns the Network. 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Defaults to None."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"path_to_reaction_file")," ",(0,i.kt)("em",{parentName:"li"},"Union","[str, bytes, os.PathLike]",", optional")," - Path to a reactions.csv in/from the src directory. Defaults to None."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"verbosity")," ",(0,i.kt)("em",{parentName:"li"},"LEVEL, optional")," - The verbosity level as specified in logging. Defaults to None.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - You cannot specify both an input configuration and species+reaction.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Network")," - A chemical reaction network.")),(0,i.kt)("a",{id:"uclchem.makerates.network"}),(0,i.kt)("h1",{id:"uclchemmakeratesnetwork"},"uclchem.makerates.network"),(0,i.kt)("p",null,"This python file contains all functions for de-duplicating species and reaction lists,\nchecking for common errors, and automatic addition of reactions such as freeze out,\ndesorption and bulk reactions for three phase models."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network"}),(0,i.kt)("h2",{id:"network-objects"},"Network Objects"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"class Network()\n")),(0,i.kt)("p",null,"The network class stores all the information about reaction network."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.__init__"}),(0,i.kt)("h4",{id:"__init__-1"},"_","_","init","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __init__(species: list[Species],\n reactions: list[Reaction],\n three_phase: bool = False,\n user_defined_bulk: list = [])\n")),(0,i.kt)("p",null,"A class to store network information such as indices of important reactions."),(0,i.kt)("p",null,"The class fully utilizes getters and setters, which can be used to add/remove\nreactions and the species involved. Important is that you do not directly edit\nthe internal dictionaries that store the species and reactions, unless you\nknow what you are doing. The network by default checks for duplicates in species\nand identical reactions that overlap in temperature ranges, potentially causing\nproblems."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of chemical species that are added to the network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - A list of chemical reactions that are added to the network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool, optional")," - Whether to use a three phase model (gas, surface, bulk). Defaults to False."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"user_defined_bulk")," ",(0,i.kt)("em",{parentName:"li"},"list, optional")," - List of user defined bulk. Defaults to [].")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.find_similar_reactions"}),(0,i.kt)("h4",{id:"find_similar_reactions"},"find","_","similar","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def find_similar_reactions(reaction: Reaction) -> dict[int, Reaction]\n")),(0,i.kt)("p",null,"Reactions are similar if the reaction has the same reactants and products,\nfind all reactions that are similar, returning their index and the reaction itself."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - Reaction with possible identical (but for temperature range) reactions in the network")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[int, Reaction]",": A dict with the identical reactions."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_reaction_by_index"}),(0,i.kt)("h4",{id:"remove_reaction_by_index"},"remove","_","reaction","_","by","_","index"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_reaction_by_index(reaction_idx: int) -> None\n")),(0,i.kt)("p",null,"Remove a reaction by its index in the internal _reactions_dict, this is the only way\nto remove reactions that are defined piecewise across temperature ranges."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - Index of the reaction to remove")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_reaction"}),(0,i.kt)("h4",{id:"remove_reaction"},"remove","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_reaction(reaction: Reaction) -> None\n")),(0,i.kt)("p",null,"Remove the reaction by giving the object itself, this only works if the reaction is\nnot piecewise defined across the temperature ranges."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - The reaction you wish to delete.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction"}),(0,i.kt)("h4",{id:"get_reaction"},"get","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction(reaction_idx: int) -> Reaction\n")),(0,i.kt)("p",null,"Obtain a reaction from the reaction set given an index of the internal _reactions_dict."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The reaction index")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Reaction")," - the desired reaction")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_reaction"}),(0,i.kt)("h4",{id:"set_reaction"},"set","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_reaction(reaction_idx: int, reaction: Reaction) -> None\n")),(0,i.kt)("p",null,"This setter explicitely sets the reaction for a certain index."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The index to be written to"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - The reaction to be added to the index.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction_dict"}),(0,i.kt)("h4",{id:"get_reaction_dict"},"get","_","reaction","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction_dict() -> dict[int, Reaction]\n")),(0,i.kt)("p",null,"Returns the whole internal reaction dictionary."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[int, Reaction]",": A copy of the internal reactions dictionary."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_reaction_dict"}),(0,i.kt)("h4",{id:"set_reaction_dict"},"set","_","reaction","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_reaction_dict(new_dict: dict[int, Reaction]) -> None\n")),(0,i.kt)("p",null,"Override the reactions dictionary with a new dictionar."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_dict")," ",(0,i.kt)("em",{parentName:"li"},"dict","[int, Reaction]")," - The new reactions_dictionary.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction_list"}),(0,i.kt)("h4",{id:"get_reaction_list"},"get","_","reaction","_","list"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction_list() -> list[Reaction]\n")),(0,i.kt)("p",null,"Obtain all the reactions in the Network."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list[Reaction]")," - A list with all the reaction objects")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.sort_reactions"}),(0,i.kt)("h4",{id:"sort_reactions"},"sort","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def sort_reactions() -> None\n")),(0,i.kt)("p",null,"Sort the reaction dictionary by reaction type first and by the first reactant second."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_species"}),(0,i.kt)("h4",{id:"add_species"},"add","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_species(species: Union[Union[Species, str], list[Union[Species,\n str]]])\n")),(0,i.kt)("p",null,"Add species to the network, given a (list of) species. If it is a list of strings,\nit tries to instantiate a species class with it. It also checks for duplicate entries and\nfilters out attempts to add reaction types to the species."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Union[Union","[Species, str]",", list[Union","[Species, str]","]]")," - A (list of) species or strings.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - If we cannot parse the (list of) reactions"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - If an ice specie with binding energy of zero is added.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_species"}),(0,i.kt)("h4",{id:"remove_species"},"remove","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_species(specie_name: str) -> None\n")),(0,i.kt)("p",null,"Remove a specie from the network"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"specie_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Species to remove")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_species_list"}),(0,i.kt)("h4",{id:"get_species_list"},"get","_","species","_","list"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_species_list() -> list[Species]\n")),(0,i.kt)("p",null,"Obtain a list with all the species in the network"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list[Species]")," - A list of all the species in the reaction network")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_species_dict"}),(0,i.kt)("h4",{id:"get_species_dict"},"get","_","species","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_species_dict() -> dict[str, Species]\n")),(0,i.kt)("p",null,"Get the internal dictionary that stores all the species, it consists\nof all species' names as key, with the species object as value."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[str, Species]",": A dictionary with the species"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_specie"}),(0,i.kt)("h4",{id:"get_specie"},"get","_","specie"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_specie(specie_name: str) -> Species\n")),(0,i.kt)("p",null,"Get the species of the reaction network (from the internal dictionary)"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"specie_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - the name of the species as a string")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Species")," - The species object")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_specie"}),(0,i.kt)("h4",{id:"set_specie"},"set","_","specie"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_specie(species_name: str, species: Species) -> None\n")),(0,i.kt)("p",null,"Set the species of the reaction network in the internal dictionary"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - The name of the species as string"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - The Species object to set")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_species_dict"}),(0,i.kt)("h4",{id:"set_species_dict"},"set","_","species","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_species_dict(new_species_dict: dict[str, Species]) -> None\n")),(0,i.kt)("p",null,"Set the internal species dict"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_species_dict")," ",(0,i.kt)("em",{parentName:"li"},"dict","[str, Species]")," - The new dictionary to set")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.sort_species"}),(0,i.kt)("h4",{id:"sort_species"},"sort","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def sort_species() -> None\n")),(0,i.kt)("p",null,"Sort the species based on their mass in ascending order. We always make sure the Electron is last."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_network"}),(0,i.kt)("h4",{id:"check_network"},"check","_","network"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_network() -> None\n")),(0,i.kt)("p",null,"Run through the list of reactions and check for obvious errors such\nas duplicate reactions, multiple freeze out routes (to warn, not necessarily\nan error), etc."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_and_filter_species"}),(0,i.kt)("h4",{id:"check_and_filter_species"},"check","_","and","_","filter","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_and_filter_species() -> None\n")),(0,i.kt)("p",null,"Check every speces in network appears in at least one reaction.\nRemove any that do not and alert user."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_bulk_species"}),(0,i.kt)("h4",{id:"add_bulk_species"},"add","_","bulk","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_bulk_species() -> None\n")),(0,i.kt)("p",null,"For three phase models, MakeRates will produce the version of the species in the bulk\nso that the user doesn't have to endlessly relist the same species"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_freeze_and_desorbs"}),(0,i.kt)("h4",{id:"check_freeze_and_desorbs"},"check","_","freeze","_","and","_","desorbs"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_freeze_and_desorbs() -> None\n")),(0,i.kt)("p",null,(0,i.kt)("inlineCode",{parentName:"p"},"add_freeze_reactions()")," and ",(0,i.kt)("inlineCode",{parentName:"p"},"add_desorb_reactions()")," automatically generate\nall desorption and freeze out reactions. However, user may want to change a species on freeze out\neg C+ becomes ",(0,i.kt)("inlineCode",{parentName:"p"},"C")," rather than ",(0,i.kt)("inlineCode",{parentName:"p"},"C"),"+. This function checks for that and updates species so they'll\nfreeze or desorb correctly when reactions are generated."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_freeze_reactions"}),(0,i.kt)("h4",{id:"add_freeze_reactions"},"add","_","freeze","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_freeze_reactions() -> None\n")),(0,i.kt)("p",null,"Save the user effort by automatically generating freeze out reactions"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_desorb_reactions"}),(0,i.kt)("h4",{id:"add_desorb_reactions"},"add","_","desorb","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_desorb_reactions() -> None\n")),(0,i.kt)("p",null,"Save the user effort by automatically generating desorption reactions"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_chemdes_reactions"}),(0,i.kt)("h4",{id:"add_chemdes_reactions"},"add","_","chemdes","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_chemdes_reactions() -> None\n")),(0,i.kt)("p",null,"We have the user list all Langmuir-Hinshelwood and Eley-Rideal\nreactions once. Then we duplicate so that the reaction branches\nwith products on grain and products desorbing."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_for_excited_species"}),(0,i.kt)("h4",{id:"check_for_excited_species"},"check","_","for","_","excited","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_for_excited_species() -> bool\n")),(0,i.kt)("p",null,"Check if there are any exicted species in the network, true if there are any."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_excited_surface_reactions"}),(0,i.kt)("h4",{id:"add_excited_surface_reactions"},"add","_","excited","_","surface","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_excited_surface_reactions() -> None\n")),(0,i.kt)("p",null,"All excited species will relax to the ground state if they do not react\nthe vibrational frequency of the species is used as a pseudo approximation of the rate coefficient\nWe assume all grain reactions have an excited variant. For example:\n",(0,i.kt)("inlineCode",{parentName:"p"},"A"),", ",(0,i.kt)("inlineCode",{parentName:"p"},"B")," LH ",(0,i.kt)("inlineCode",{parentName:"p"},"C")," will have the variants:\n",(0,i.kt)("inlineCode",{parentName:"p"},"A"),(0,i.kt)("em",{parentName:"p"},", ",(0,i.kt)("inlineCode",{parentName:"em"},"B")," EXSOLID ",(0,i.kt)("inlineCode",{parentName:"em"},"C")," and ",(0,i.kt)("inlineCode",{parentName:"em"},"A"),", ",(0,i.kt)("inlineCode",{parentName:"em"},"B"))," EXSOLID ",(0,i.kt)("inlineCode",{parentName:"p"},"C"),"\nIf only one of the reactants in the base reaction has an excited counterpart then\nonly one excited version of that reaction is created."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_bulk_reactions"}),(0,i.kt)("h4",{id:"add_bulk_reactions"},"add","_","bulk","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_bulk_reactions() -> None\n")),(0,i.kt)("p",null,"We assume any reaction that happens on the surface of grains can also happen\nin the bulk (just more slowly due to binding energy). The user therefore only\nlists surface reactions in their input reaction file and we duplicate here."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.freeze_checks"}),(0,i.kt)("h4",{id:"freeze_checks"},"freeze","_","checks"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def freeze_checks() -> None\n")),(0,i.kt)("p",null,"Check that every species freezes out and alert the user if a\nspecies freezes out via mutiple routes. This isn't necessarily an\nerror so best just print."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.duplicate_checks"}),(0,i.kt)("h4",{id:"duplicate_checks"},"duplicate","_","checks"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def duplicate_checks() -> None\n")),(0,i.kt)("p",null,"Check reaction network to make sure no reaction appears twice unless\nthey have different temperature ranges."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.index_important_reactions"}),(0,i.kt)("h4",{id:"index_important_reactions"},"index","_","important","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def index_important_reactions() -> None\n")),(0,i.kt)("p",null,"We have a whole bunch of important reactions and we want to store\ntheir indices. We find them all here."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.index_important_species"}),(0,i.kt)("h4",{id:"index_important_species"},"index","_","important","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def index_important_species() -> None\n")),(0,i.kt)("p",null,"Obtain the indices for all the important reactions."),(0,i.kt)("a",{id:"uclchem.makerates.network.LoadedNetwork"}),(0,i.kt)("h2",{id:"loadednetwork-objects"},"LoadedNetwork Objects"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"class LoadedNetwork(Network)\n")),(0,i.kt)("p",null,"Network version that skips all steps and just loads two lists. This is another\nhere be dragons version, use this with exceeding caution as no checks are performed for you."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Network")," ",(0,i.kt)("strong",{parentName:"li"},"type")," - ",(0,i.kt)("em",{parentName:"li"},"description"))),(0,i.kt)("a",{id:"uclchem.makerates.network.LoadedNetwork.__init__"}),(0,i.kt)("h4",{id:"__init__-2"},"_","_","init","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __init__(species: list[Species], reactions: list[Reaction]) -> None\n")),(0,i.kt)("p",null,"A loader of networks without any checks."),(0,i.kt)("p",null,"Here be dragons."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of species objects"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - A list of reaction objects.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions"}),(0,i.kt)("h1",{id:"uclchemmakeratesio_functions"},"uclchem.makerates.io","_","functions"),(0,i.kt)("p",null,"Functions to read in the species and reaction files and write output files"),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.read_species_file"}),(0,i.kt)("h4",{id:"read_species_file"},"read","_","species","_","file"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def read_species_file(file_name: Path) -> list[Species]\n")),(0,i.kt)("p",null,"Reads in a Makerates species file"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to file containing the species list")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list")," - List of Species objects")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.read_reaction_file"}),(0,i.kt)("h4",{id:"read_reaction_file"},"read","_","reaction","_","file"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def read_reaction_file(file_name: Path, species_list: list[Species],\n ftype: str) -> tuple[list[Reaction], list[Reaction]]\n")),(0,i.kt)("p",null,"Reads in a reaction file of any kind (user, UMIST, KIDA)\nproduces a list of reactions for the network, filtered by species_list"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - A file name for the reaction file to read."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of chemical species to be used in the reading."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ftype")," ",(0,i.kt)("em",{parentName:"li"},"str")," - 'UMIST','UCL', or 'KIDA' to describe format of file_name")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list,list")," - Lists of kept and dropped reactions.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.check_reaction"}),(0,i.kt)("h4",{id:"check_reaction"},"check","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_reaction(reaction_row, keep_list) -> bool\n")),(0,i.kt)("p",null,"Checks a row parsed from a reaction file and checks it only contains acceptable things.\nIt checks if all species in the reaction are present, and adds the temperature range is none is specified."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_row")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List parsed from a reaction file and formatted to be able to called Reaction(reaction_row)"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"keep_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - list of elements that are acceptable in the reactant or product bits of row")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - Whether the row contains acceptable entries.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.kida_parser"}),(0,i.kt)("h4",{id:"kida_parser"},"kida","_","parser"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def kida_parser(kida_file)\n")),(0,i.kt)("p",null,"KIDA used a fixed format file so we read each line in the chunks they specify\nand use python built in classes to convert to the necessary types.\nNOTE KIDA defines some of the same reaction types to UMIST but with different names\nand coefficients. We fix that by converting them here."),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.output_drops"}),(0,i.kt)("h4",{id:"output_drops"},"output","_","drops"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def output_drops(dropped_reactions: list[Reaction],\n output_dir: str,\n write_files=True)\n")),(0,i.kt)("p",null,"Writes the reactions that are dropped to disk/logs"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"dropped_reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - The reactions that were dropped"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"output_dir")," ",(0,i.kt)("em",{parentName:"li"},"str")," - The directory that dropped_reactions.csv will be written to."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"write_files")," ",(0,i.kt)("em",{parentName:"li"},"bool, optional")," - Whether or not to write the file. Defaults to True.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_outputs"}),(0,i.kt)("h4",{id:"write_outputs"},"write","_","outputs"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_outputs(network: Network, output_dir: str = None) -> None\n")),(0,i.kt)("p",null,"Write the ODE and Network fortran source files to the fortran source."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"network")," ",(0,i.kt)("em",{parentName:"li"},"network")," - The makerates Network class"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"output_dir")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - The directory to write to.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_species"}),(0,i.kt)("h4",{id:"write_species"},"write","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_species(file_name: Path, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Write the human readable species file. Note UCLCHEM doesn't use this file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to output file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species objects for network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_reactions"}),(0,i.kt)("h4",{id:"write_reactions"},"write","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_reactions(fileName, reaction_list) -> None\n")),(0,i.kt)("p",null,"Write the human readable reaction file. Note UCLCHEM doesn't use this file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to output file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reaction objects for network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_odes_f90"}),(0,i.kt)("h4",{id:"write_odes_f90"},"write","_","odes","_","f90"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_odes_f90(file_name: Path, species_list: list[Species],\n reaction_list: list[Reaction], three_phase: bool) -> None\n")),(0,i.kt)("p",null,"Write the ODEs in Modern Fortran. This is an actual code file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Path to file where code will be written"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species describing network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reactions describing network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - Flag for whether this is a 3 phase network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_jacobian"}),(0,i.kt)("h4",{id:"write_jacobian"},"write","_","jacobian"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_jacobian(file_name: Path, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Write jacobian in Modern Fortran. This has never improved UCLCHEM's speed\nand so is not used in the code as it stands.\nCurrent only works for three phase model."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Path to jacobian file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"species_list")," - List of species AFTER being processed by build_ode_string")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.build_ode_string"}),(0,i.kt)("h4",{id:"build_ode_string"},"build","_","ode","_","string"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def build_ode_string(species_list: list[Species],\n reaction_list: list[Reaction], three_phase: bool) -> str\n")),(0,i.kt)("p",null,"A long, complex function that does the messy work of creating the actual ODE\ncode to calculate the rate of change of each species. Test any change to this code\nthoroughly because ODE mistakes are very hard to spot."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species in network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reactions in network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - Bool denoting if this is a three phase network")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"str")," - One long string containing the entire ODE fortran code.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.species_ode_string"}),(0,i.kt)("h4",{id:"species_ode_string"},"species","_","ode","_","string"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def species_ode_string(n: int, species: Species) -> str\n")),(0,i.kt)("p",null,"Build the string of Fortran code for a species once it's loss and gains\nstrings have been produced."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"n")," ",(0,i.kt)("em",{parentName:"li"},"int")," - Index of species in python format"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - species object")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"str")," - the fortran code for the rate of change of the species")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_evap_lists"}),(0,i.kt)("h4",{id:"write_evap_lists"},"write","_","evap","_","lists"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_evap_lists(network_file, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Two phase networks mimic episodic thermal desorption seen in lab (see Viti et al. 2004)\nby desorbing fixed fractions of material at specific temperatures. Three phase networks just\nuse binding energy and that fact we set binding energies in bulk to water by default.\nThis function writes all necessary arrays to the network file so these processes work."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"network_file")," ",(0,i.kt)("em",{parentName:"li"},"file")," - Open file object to which the network code is being written"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - List of species in network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.truncate_line"}),(0,i.kt)("h4",{id:"truncate_line"},"truncate","_","line"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def truncate_line(input_string: str, lineLength: int = 72) -> str\n")),(0,i.kt)("p",null,"Take a string and adds line endings at regular intervals\nkeeps us from overshooting fortran's line limits and, frankly,\nmakes for nicer ode.f90 even if human readability isn't very important"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"input_string")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Line of code to be truncated"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"lineLength")," ",(0,i.kt)("em",{parentName:"li"},"int, optional")," - rough line length. 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For example, in the inner parts of a molecular cloud where Av ",(0,r.kt)("span",{parentName:"p",className:"math math-inline"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("mo",{parentName:"mrow"},"\u2273")),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"\\gtrsim")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.95916em",verticalAlign:"-0.22958em"}}),(0,r.kt)("span",{parentName:"span",className:"mrel amsrm"},"\u2273")))))," 10 there are very few depth dependent processes. 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You can find a complete list of modifiable parameters and their default values in ",(0,r.kt)("a",{parentName:"p",href:"/docs/parameters"},"our parameter docs"),"."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'# set a parameter dictionary for phase 1 collapse model\n\nout_species = ["SO","CO"]\nparam_dict = {\n "endAtFinalDensity": False,#stop at finalTime\n "freefall": False,#don\'t increase density in freefall\n "initialDens": 1e4, #starting density\n "initialTemp": 10.0,#temperature of gas\n "finalTime": 1.0e6, #final time\n "rout":0.1, #radius of cloud in pc\n "baseAv":1.0, #visual extinction at cloud edge.\n "outputFile": "../examples/test-output/static-full.dat",#full UCLCHEM output\n "abundSaveFile": "../examples/test-output/startstatic.dat",#save final abundances to file\n}\nresult = uclchem.model.cloud(param_dict=param_dict,out_species=out_species)\nprint(result)\n\n')),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"[1, 3.331065659699488e-11, 3.576305642378658e-05]\n")),(0,r.kt)("h2",{id:"checking-the-output"},"Checking the output"),(0,r.kt)("p",null,"At the end of the previous cell, we printed ",(0,r.kt)("inlineCode",{parentName:"p"},"result")," which is a list returned by every UCLCHEM model function. The first element is always an integer which will be positive if the code completed and negative otherwise. You can send negative values to ",(0,r.kt)("inlineCode",{parentName:"p"},"uclchem.utils.check_error()")," to get a more detailed error message."),(0,r.kt)("p",null,"The subsequent elements are the final abundances of any species listed in ",(0,r.kt)("inlineCode",{parentName:"p"},"out_species"),", in this case we have the abundance of SO and CO. This is useful when we want to use UCLCHEM as part of something like an MCMC procedure, obtaining abundances for given parameters. However, we also write the final abundances of all species to ",(0,r.kt)("inlineCode",{parentName:"p"},"abundSaveFile")," and the abundances of all species at every time step in ",(0,r.kt)("inlineCode",{parentName:"p"},"outputFile")," so it is not necessary to acquire abundances in this way."),(0,r.kt)("p",null,"The output file is just a simple csv with some header rows, UCLCHEM has a utility function to read that file into a pandas dataframe. Let's load it up and look at it."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'result_df=uclchem.analysis.read_output_file("../examples/test-output/static-full.dat")\nresult_df.head()\n')),(0,r.kt)("div",null,(0,r.kt)("table",{border:"1",class:"dataframe"},(0,r.kt)("thead",null,(0,r.kt)("tr",null,(0,r.kt)("th",null),(0,r.kt)("th",null,"Time"),(0,r.kt)("th",null,"Density"),(0,r.kt)("th",null,"gasTemp"),(0,r.kt)("th",null,"av"),(0,r.kt)("th",null,"zeta"),(0,r.kt)("th",null,"point"),(0,r.kt)("th",null,"H"),(0,r.kt)("th",null,"#H"),(0,r.kt)("th",null,"H+"),(0,r.kt)("th",null,"@H"),(0,r.kt)("th",null,"..."),(0,r.kt)("th",null,"HS2+"),(0,r.kt)("th",null,"HSO2+"),(0,r.kt)("th",null,"H2S2+"),(0,r.kt)("th",null,"H2S2"),(0,r.kt)("th",null,"#H2S2"),(0,r.kt)("th",null,"@H2S2"),(0,r.kt)("th",null,"E-"),(0,r.kt)("th",null,"BULK"),(0,r.kt)("th",null,"SURFACE"),(0,r.kt)("th",null,"radfield"))),(0,r.kt)("tbody",null,(0,r.kt)("tr",null,(0,r.kt)("th",null,"0"),(0,r.kt)("td",null,"0.000000e+00"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"1"),(0,r.kt)("td",null,"1.000000e-07"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.680300e-13"),(0,r.kt)("td",null,"1.789040e-17"),(0,r.kt)("td",null,"4.269620e-20"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.629010e-20"),(0,r.kt)("td",null,"7.488850e-13"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"2"),(0,r.kt)("td",null,"1.000000e-06"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.646510e-12"),(0,r.kt)("td",null,"1.789080e-16"),(0,r.kt)("td",null,"4.219000e-18"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.631720e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000020e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.562330e-18"),(0,r.kt)("td",null,"7.444370e-12"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"3"),(0,r.kt)("td",null,"1.000000e-05"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.641430e-11"),(0,r.kt)("td",null,"1.789520e-15"),(0,r.kt)("td",null,"4.212520e-16"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"7.762720e-29"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000050e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000010e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.554260e-16"),(0,r.kt)("td",null,"7.438940e-11"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"4"),(0,r.kt)("td",null,"1.000000e-04"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.480630e-10"),(0,r.kt)("td",null,"1.793810e-14"),(0,r.kt)("td",null,"4.079690e-14"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"7.864380e-27"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000070e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000150e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.425070e-14"),(0,r.kt)("td",null,"7.351600e-10"),(0,r.kt)("td",null,"1.0")))),(0,r.kt)("p",null,"5 rows \xd7 321 columns")),(0,r.kt)("p",null,"We can also test whether the model run went well by checking for element conservation. We do this because integrator errors often show up as a failure to conserve elemental abundances. "),(0,r.kt)("p",null,"We can use ",(0,r.kt)("inlineCode",{parentName:"p"},"check_element_conservation()")," to test whether we conserve elements in this run. This function returns a dictionary where each entry gives the change in the total abundance of an element as a percentage of the original abundance. In an ideal case, these values are 0\\% indicating the total abundance at the end of the model is exactly the same as the total at the start."),(0,r.kt)("p",null,"Changes of less than 1\\% are fine for many cases but if they are too high, you could consider changing the ",(0,r.kt)("inlineCode",{parentName:"p"},"reltol")," and ",(0,r.kt)("inlineCode",{parentName:"p"},"abstol")," parameters that control the integrator accuracy. They are error tolerance so smaller values lead to smaller errors and (usually) longer integration times. The default values were chosen by running a large grid of models and choosing the tolerances with the lowest average run time from those that conserved elements well and rarely failed. Despite this, there are no one-size-fits-all perfect tolerances and you may run into issues with different networks or models."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'conservation=uclchem.analysis.check_element_conservation(result_df,element_list=["H","N","C","O","S"])\nprint("Percentage change in total abundances:")\nprint(conservation)\n')),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"Percentage change in total abundances:\n{'H': '0.001%', 'N': '0.000%', 'C': '0.000%', 'O': '0.000%', 'S': '0.000%'}\n")),(0,r.kt)("h2",{id:"plotting-results"},"Plotting Results"),(0,r.kt)("p",null,"Finally, you will want to plot your results. This can be done with any plotting library but UCLCHEM does provide a few functions to make quick plots. Note the use of $ symbols in the species list below, this gets the total ice abundance of a species. For two phase models, this is just the surface abudance but for three phase it is the sum of surface and bulk."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'species=["H","H2","$H","$H2","H2O","$H2O","CO","$CO","$CH3OH","CH3OH"]\nfig,ax=uclchem.analysis.create_abundance_plot(result_df,species,figsize=(10,7))\nax=ax.set(xscale="log",ylim=(1e-15,1),xlim=(1e3,1e6))\n')),(0,r.kt)("p",null,(0,r.kt)("img",{alt:"png",src:n(8899).Z,width:"712",height:"496"})),(0,r.kt)("p",null,"and that's it! You've run your first UCLCHEM model, checked that the element conservation is correct, and plotted the abundances."))}k.isMDXComponent=!0},8899:(e,t,n)=>{n.d(t,{Z:()=>l});const l=n.p+"assets/images/first_model_9_0-fff8b0e800895dbb0e755cc2b9459720.png"}}]); \ No newline at end of file diff --git a/assets/js/1c8e445f.ddb57b80.js b/assets/js/1c8e445f.ddb57b80.js new file mode 100644 index 00000000..3ccbf1d1 --- /dev/null +++ b/assets/js/1c8e445f.ddb57b80.js @@ -0,0 +1 @@ +"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[5591],{3905:(e,t,a)=>{a.d(t,{Zo:()=>c,kt:()=>h});var s=a(7294);function n(e,t,a){return t in e?Object.defineProperty(e,t,{value:a,enumerable:!0,configurable:!0,writable:!0}):e[t]=a,e}function r(e,t){var a=Object.keys(e);if(Object.getOwnPropertySymbols){var s=Object.getOwnPropertySymbols(e);t&&(s=s.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),a.push.apply(a,s)}return a}function i(e){for(var t=1;t=0||(n[a]=e[a]);return n}(e,t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);for(s=0;s=0||Object.prototype.propertyIsEnumerable.call(e,a)&&(n[a]=e[a])}return n}var l=s.createContext({}),p=function(e){var t=s.useContext(l),a=t;return e&&(a="function"==typeof e?e(t):i(i({},t),e)),a},c=function(e){var t=p(e.components);return s.createElement(l.Provider,{value:t},e.children)},m={inlineCode:"code",wrapper:function(e){var t=e.children;return s.createElement(s.Fragment,{},t)}},u=s.forwardRef((function(e,t){var a=e.components,n=e.mdxType,r=e.originalType,l=e.parentName,c=o(e,["components","mdxType","originalType","parentName"]),u=p(a),h=n,d=u["".concat(l,".").concat(h)]||u[h]||m[h]||r;return a?s.createElement(d,i(i({ref:t},c),{},{components:a})):s.createElement(d,i({ref:t},c))}));function h(e,t){var a=arguments,n=t&&t.mdxType;if("string"==typeof e||n){var r=a.length,i=new Array(r);i[0]=u;var o={};for(var l in t)hasOwnProperty.call(t,l)&&(o[l]=t[l]);o.originalType=e,o.mdxType="string"==typeof e?e:n,i[1]=o;for(var p=2;p{a.r(t),a.d(t,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>o,metadata:()=>p,toc:()=>m});var s=a(7462),n=a(3366),r=(a(7294),a(3905)),i=["components"],o={id:"network",title:"Creating a Network"},l=void 0,p={unversionedId:"network",id:"version-v3.3.1/network",title:"Creating a Network",description:"MakeRates",source:"@site/versioned_docs/version-v3.3.1/start-network.md",sourceDirName:".",slug:"/network",permalink:"/docs/network",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{id:"network",title:"Creating a Network"},sidebar:"docs",previous:{title:"Installation",permalink:"/docs/"},next:{title:"Model Parameters",permalink:"/docs/parameters"}},c={},m=[{value:"MakeRates",id:"makerates",level:2},{value:"Input",id:"input",level:2},{value:"Default Network",id:"default-network",level:2},{value:"Outputs",id:"outputs",level:2},{value:"What MakeRates Does",id:"what-makerates-does",level:2},{value:"Creating your own Network",id:"creating-your-own-network",level:2},{value:"Species list",id:"species-list",level:4},{value:"Reaction list",id:"reaction-list",level:4},{value:"Three Phase Chemistry",id:"three-phase-chemistry",level:2}],u={toc:m};function h(e){var t=e.components,a=(0,n.Z)(e,i);return(0,r.kt)("wrapper",(0,s.Z)({},u,a,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h2",{id:"makerates"},"MakeRates"),(0,r.kt)("p",null,"In order to make a chemical model flexible, the ability to solve a user supplied chemical network is a must. UCLCHEM uses a preprocessing python script to turn csv lists of species and reactions into fortran files for use in the main code. This script is called MakeRates and can be found in the Makerates subdirectory of the repository. It combines a gas phase reaction database with user supplied lists of species and additional reactions into the necessary Fortran code to run UCLCHEM. It also supplies a number of human readable outputs."),(0,r.kt)("p",null,"In the sections below, we discuss how to build your network and set the inputs for MakeRates but once that is done, you can run MakeRates with the following commands:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"cd MakeRates\npython MakeRates.py\ncd ..\npip install -e . \n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"Note the pip install at the end of the process. Any output from MakeRates requires that the code be recompiled because MakeRates produces new source code for UCLCHEM!")),(0,r.kt)("h2",{id:"input"},"Input"),(0,r.kt)("p",null,"Makerates is controlled using a yaml file ",(0,r.kt)("inlineCode",{parentName:"p"},"Makerates/user_settings.yaml"),". By changing the values in this file, you can create different networks. The default values of this file are copied below."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-yaml"},"#Your list of all species\nspecies_file : inputFiles/default_species.csv\n\n#core reactions from gas phase database\ndatabase_reaction_file : inputFiles/umist12-ucledit.csv\ndatabase_reaction_type : UMIST\n\n#set of additional reactions: eg grain network\ncustom_reaction_file : inputFiles/default_grain_network.csv\ncustom_reaction_type : UCL\n\n#whether to automatically expand to three phase network\nthree_phase : True\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"species_file")," is a csv list of species and their properties. We provide a default list and detailed instructions below."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"database_reaction_file")," is your first reaction file, we expect most users to use UMIST12 or KIDA2014 for this but you could create your own file from an alternative database. Makerates can read files formatted in the same manner as the UMIST or KIDA databases as well as our own simple csv format, the ",(0,r.kt)("inlineCode",{parentName:"p"},"database_reaction_type")," setting lets MakeRates know which and should be set to 'UMIST', 'KIDA', or 'UCL'."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"custom_reaction_file")," is an additional reaction file. In the example file, we include all of our grain surface reactions which is the intended use of this file. "),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"three_phase")," is a toggle that tells MakeRates whether to automatically expand your network into a three phase model."),(0,r.kt)("h2",{id:"default-network"},"Default Network"),(0,r.kt)("p",null,"A basic version of each of the required file is supplied in the repository. The network that MakeRates produces from those files is also include in the source code so that a new user who simply installs UCLCHEM without running MakeRates will be using our default network. These default files serve largely as examples of how the files should be formatted and we also describe each one below so that the user can produce their own network."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"We do not endorse the default network"),", we have simply produced a grain surface network that was relatively up to date in 2018. It produces reasonable ice mantle abundances for major species and ignores larger COMs. We strongly suggest any published work be based on a network in which the user has confidence. However, where the user is not greatly concerned with grain surface chemistry, the default network is a good starting point."),(0,r.kt)("h2",{id:"outputs"},"Outputs"),(0,r.kt)("p",null,"Outputs from MakeRates are automatically moved to the ",(0,r.kt)("inlineCode",{parentName:"p"},"src/")," directory so the user can ",(0,r.kt)("inlineCode",{parentName:"p"},"pip install .")," and update their installation of UCLCHEM to use their new network. However, by adding the parameter ",(0,r.kt)("inlineCode",{parentName:"p"},"output_directory")," to the yaml file, you can have all the files moved to a directory instead without copying them to your UCLCHEM src folder. If you do, the following files will be produced:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"network.f90 - Fortran arrays containing lists of species names and properties (mass, binding energy etc) as well as reaction reactants, products and rate coefficients."),(0,r.kt)("li",{parentName:"ul"},"odes.f90 - Code to calculate the rate of change of each species' abundance for the numerical solver"),(0,r.kt)("li",{parentName:"ul"},"species.csv - A list of all species in the network and their properties. Made for humans not UCLCHEM."),(0,r.kt)("li",{parentName:"ul"},"reactions.csv - A list of all reactions including reactants, products and coefficients. Made for humans not UCLCHEM.")),(0,r.kt)("h2",{id:"what-makerates-does"},"What MakeRates Does"),(0,r.kt)("p",null,"MakeRates does the following:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"Combines the two input reaction lists"),(0,r.kt)("li",{parentName:"ul"},"Filters to remove any reactions containing species not in the input species list"),(0,r.kt)("li",{parentName:"ul"},"Adds freeze out and desorption reactions for all species"),(0,r.kt)("li",{parentName:"ul"},"Creates branching reactions for Langmuir-Hinshelwood and Eley-Rideal reactions where products chemically desorb"),(0,r.kt)("li",{parentName:"ul"},"Optionally: creates additional reactions and species needed for a three phase network"),(0,r.kt)("li",{parentName:"ul"},"Does basic network consistency checks and alerts user of problems"),(0,r.kt)("li",{parentName:"ul"},"Writes fortran files for UCLCHEM"),(0,r.kt)("li",{parentName:"ul"},"Writes other output files")),(0,r.kt)("h2",{id:"creating-your-own-network"},"Creating your own Network"),(0,r.kt)("p",null,"To create your own network you need to produce a species list and a reaction list."),(0,r.kt)("h4",{id:"species-list"},"Species list"),(0,r.kt)("p",null,"The species list should simply be a list with one row per species in the network. Each row should contain the species name, mass, binding energy and enthalpy of formation. The latter two are only used for surface species so can be set to zero for the gas phase species. MakeRates will check the mass is correct for each species and alert you of discrepancies."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"C,12,0,0,0,0,0\n#CH4,16,960,0,0.7,0.667,-15.9\n")),(0,r.kt)("p",null,"In the above example, C is a gas phase species so we have set the mass but ignored the other variables. #CH4 is methane in the ice so we have additionally set a binding energy of 960 K and enthalpy of formation of -15.9 kcal/mol. The other three values (0, 0.7, 0.667) are desorption fractions that three phase chemistry networks ignore. For two phase networks, we mimic the multiple desorption events seen in TPD experiments by setting these fractions. See ",(0,r.kt)("a",{parentName:"p",href:"https://ui.adsabs.harvard.edu/abs/2004MNRAS.354.1141V/abstract"},"Viti et al. 2004")," for more information."),(0,r.kt)("p",null,"The enthalpy of formation for essentially any species can be found in chemical databases such as the ",(0,r.kt)("a",{parentName:"p",href:"https://webbook.nist.gov/"},"NIST web book"),". They're usually in kj/mol but the conversion to kcal/mol is easy enough and NIST has an option to switch values to kcal. A fantastic resource for binding energies is ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1016/j.molap.2017.01.002"},"Wakelam et al. 2017")," but these are harder to find in general. In the absolute worse case, you can sum up the binding energies of sub-groups in your molecule but this is pretty inaccurate."),(0,r.kt)("h4",{id:"reaction-list"},"Reaction list"),(0,r.kt)("p",null,"The second reaction list is intended to contain your surface network but can also be used to augment the gas phase databases by including additional gas phase reactions. The reaction list should be a list with one row per reaction and each row should be a comma separated list of 3 reactants, 4 products, three coefficients (alpha,beta,gamma) and a minimum and maximum temperature. Any missing values such as a third reactant can be left blank. In particular, the temperatures are optional but can be useful when you include multiple versions of the same reaction. In that case, UCLCHEM will only use each one within its specified temperature range."),(0,r.kt)("p",null,"The third reactant can be used as a keyword to tell MakeRates what kind of reaction is occuring. In the absence of a keyword, MakeRates and UCLCHEM will treat any reaction as a gas-phase two body reaction. Two keywords the user may wish to use are ER and LH for Eley-Rideal and Langmuir-Hinshelwood reactions respectively (see ",(0,r.kt)("a",{parentName:"p",href:"grain/"},"Grain Chemisty"),"). If a keyword is not added, UCLCHEM will assume a reaction between two surface reactions follows a Kooji-Arrhenius equation."),(0,r.kt)("p",null,"Two other useful reactions types to include are FREEZE and DESORB. Makerates adds freeze out and desorption reactions for every species, assuming they remain unchanged by the process. For example, CO in the gas becomes #CO on the grain. If you would instead like to specify the products, you can include a reaction:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"H3O+,FREEZE,,#H2O,H,,,1,0,0,,,\n#HPN,DESORB,,HPN+,,,,1,0,0,,,\n")),(0,r.kt)("p",null,"which will override the desorption or freeze out products of a species. "),(0,r.kt)("h2",{id:"three-phase-chemistry"},"Three Phase Chemistry"),(0,r.kt)("p",null,"The input ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," controls whether the ices are treated as a single phase or the surface is treated separated to the bulk. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to true, the chemical network will have gas, grain surface, and bulk ice chemistry. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to false, the chemical network will have gas and grain surface chemistry."),(0,r.kt)("p",null,"When true, MakeRates will create the bulk ice chemistry by duplicating the surface species and reactions in your input files. The difference will be that, unless you specifically override the bulk binding energy, every species in the bulk has a binding energy equal to the H2O binding energy. It will also add terms to the ODEs to allow transfer between the bulk and the surface. See the chemistry sections for more information."),(0,r.kt)("p",null,'You can override the binding energy of material in the bulk by explicitly including the bulk species in your species file rather than allowing MakeRates to automatically add it. Bulk species are designated with an "@". 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This tutorial demonstrates how to use some of the functionality of the UCLCHEM library to analyse model outputs and discover these explanations."),(0,m.kt)("p",null,"We do recommend caution when following the approach laid out in this tutorial. There are many pitfalls which we will try to point out as we go. Ultimately, a comprehensive view of how important a reaction is to the outcome of your model requires detailed statistical calculations such as the use of ",(0,m.kt)("a",{parentName:"p",href:"https://github.com/slundberg/shap"},"SHAP values")," to assign meaningful scores to how much various reactions in a network contribute to a species' abundance. 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Furthermore, since H3O+ was increased in abundance by increasing CRIR and SO was destroyed, their ratio was extremely sensitive to the rate. "),(0,m.kt)("p",null,"In the work, we present the plot below which shows how the equilibrium abundance of each species changes with the CRIR as well as the ratio. We plot this for a range of temperatures to show that this behaviour is not particularly sensitive to the gas temperature."),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"crir_h3o_so_example",src:t(3292).Z,width:"1600",height:"1067"})),(0,m.kt)("p",null,"In a sense, this is all the information we need. A complex array of reactions all compete and contribute to produce the outcome of the model. Whatever they are, we see the abundance of these species are very sensitive to the CR over a wide range of temperature and density. 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Hopefully, we'll see the same reactions are most important to the abundance of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," and SO at all densities and tempertures. If we don't find that that's the case, then the chemistry is these species is fairly complex and perhaps trying to present a simple cause for the CRIR dependence is not a good idea."),(0,m.kt)("p",null,"So, let's analyse the outputs!"),(0,m.kt)("h4",{id:"21-h_3o"},"2.1 ",(0,m.kt)("span",{parentName:"h4",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))),(0,m.kt)("p",null,(0,m.kt)("inlineCode",{parentName:"p"},"analysis()")," takes three arguments: the species, the output file to analyse, and a file to store the analsis output. Let's run it for every model in our little grid so we can inspect the outputs."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'outputs=glob("../output/[0-9]*.csv") #all files that start with a number\nfor output in outputs:\n \n analysis_output="../output/H3O-analysis-"+output[10:]\n uclchem.analysis.analysis("H3O+",output,analysis_output)\n')),(0,m.kt)("p",null,"This will produce one file per model output with lists of the most important reactions at each time step. Analysis will only print a time step when the most important reactions change from the previous one so we often see many fewer steps than in the full output. Let's look at the low temperature, low density, low zeta case:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 7.90e+05 years\nFormation = 1.92e-18 from:\nH2 + H2O+ -> H3O+ + H : 78.49%\nH2O + HCO+ -> CO + H3O+ : 17.68%\nH3+ + H2O -> H3O+ + H2 : 3.40%\n\nDestruction = -1.92e-18 from:\nH3O+ + E- -> OH + H + H : 65.43%\nH3O+ + E- -> H2O + H : 15.21%\nH3O+ + E- -> OH + H2 : 11.52%\nH3O+ + H2S -> H3S+ + H2O : 5.17%\nH3O+ + E- -> O + H2 + H : 1.20%\nH3O+ + HCN -> HCNH+ + H2O : 0.33%\nH3O+ + SIO -> SIOH+ + H2O : 0.33%\n")),(0,m.kt)("p",null,"What this shows is the reactions that cause 99.9% of the formation and 99.9% of the destruction of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," at a time step. The total rate of formation and destruction in units of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"s"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"1")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"s^{-1}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"s"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"1")))))))))))))," is given as well the percentage of the total that each reaction contributes. "),(0,m.kt)("p",null,"What we need to find is a pattern in these reactions which holds across time and across different densities and temperatures. It actually turns out that the reactions printed above are the dominate formation and destruction routes of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," for all parameters for all times. For example, at high temperature, high density and high zeta, we get:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.00e+04 years\nFormation = 2.03e-14 from:\nH2 + H2O+ -> H3O+ + H : 95.47%\nH3+ + H2O -> H3O+ + H2 : 3.14%\nH2O + HCO+ -> CO + H3O+ : 1.05%\n\nDestruction = -2.03e-14 from:\nH3O+ + E- -> OH + H + H : 69.82%\nH3O+ + E- -> H2O + H : 16.23%\nH3O+ + E- -> OH + H2 : 12.29%\nH3O+ + E- -> O + H2 + H : 1.28%\n")),(0,m.kt)("p",null,"The sole difference being that the formation rate is much higher. Since equilibrium is reached, the destruction rate is also higher and so we need to use the fact we know the ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord 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with CRIR to infer that the destruction rate is only faster because there is more ",(0,m.kt)("span",{parentName:"p",className:"math 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destroy."),(0,m.kt)("p",null,"However, there are some problems here! Why does ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"}))))))))))," + ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," become so efficient at high CRIR? We know the rate of a two body reaction does not depend on CRIR (",(0,m.kt)("a",{parentName:"p",href:"/docs/gas"},"see the chemistry docs"),") so it must be that ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is increasing in abundance. We can run analysis on ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"2")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_2O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," to see what is driving that. In fact, as we report in the paper, following this thread we find that a chain of hydrogenations starting from ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mi",{parentName:"mrow"},"O"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"H"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"OH^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is the overall route of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," formation and that this chain starts with small ions that are primarly formed through cosmic ray reactions. ",(0,m.kt)("em",{parentName:"p"},"It will very often be the case that analysing one species requires you to run analysis on another.")),(0,m.kt)("h4",{id:"22-so"},"2.2 SO"),(0,m.kt)("p",null,"With a strong explanation for ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+")))))))))))),", we can now look at SO. We start by running analysis again and then by looking at the reactions as before."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'outputs=glob("../output/[0-9]*.csv") #won\'t pick up H3O+ analysis because it\'s not a number\nfor output in outputs:\n \n analysis_output="../output/SO-analysis-"+output[10:]\n uclchem.analysis.analysis("SO",output,analysis_output)\n')),(0,m.kt)("p",null,"Again, let's start by looking at the low temperature, high density, low zeta case:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.31e+04 years\nFormation = 3.67e-22 from:\n#SO + THERM -> SO : 68.11%\nHSO+ + E- -> SO + H : 21.04%\n#SO + DEUVCR -> SO : 9.87%\n\nDestruction = -3.78e-22 from:\nSO + FREEZE -> #SO : 78.04%\nHCO+ + SO -> HSO+ + CO : 20.97%\n")),(0,m.kt)("p",null,"An interesting point here is that equilbrium is reached at around ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1.31"),(0,m.kt)("mo",{parentName:"mrow"},"\xd7"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mn",{parentName:"msup"},"4"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"1.31 \\times 10^4")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.72777em",verticalAlign:"-0.08333em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},"."),(0,m.kt)("span",{parentName:"span",className:"mord"},"3"),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2222222222222222em"}}),(0,m.kt)("span",{parentName:"span",className:"mbin"},"\xd7"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2222222222222222em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4"))))))))))))," yr in this model. Since ",(0,m.kt)("inlineCode",{parentName:"p"},"analysis()")," only prints a time step when the most important reactions are different to the last one, this time step is the last output from the analysis. We can see that we broadly reach an equilibrium between thermal desorption and freeze out of SO, with some formation and destruction via ions. "),(0,m.kt)("p",null,"This doesn't hold up at lower densities or higher temperatures, looking at the high temperature, low density, low zeta case, we see a second pattern of reactions:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 9.50e+05 years\nFormation = 1.05e-20 from:\nO2 + S -> SO + O : 98.10%\nO + NS -> SO + N : 1.48%\n\nDestruction = -1.02e-20 from:\nC + SO -> CS + O : 39.10%\nC + SO -> S + CO : 39.10%\nC+ + SO -> SO+ + C : 4.33%\nC+ + SO -> CS+ + O : 4.33%\nC+ + SO -> S+ + CO : 4.33%\nC+ + SO -> S + CO+ : 4.33%\nN + SO -> S + NO : 3.46%\nH+ + SO -> SO+ + H : 0.28%\n")),(0,m.kt)("p",null,"However, it's not so complex. All the low zeta outputs show one of these two sets of reactions. Essentially, higher temperatures are opening up gas phase reaction routes which form and destroy SO. These new routes are not particularly quick with a total rate of change of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"20"))),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"s"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"1")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"10^{-20} s^{-1}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"0"))))))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"s"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"1"))))))))))))),". Note that quite a lot of these are due to reactions with ions."),(0,m.kt)("p",null,"Finally, we look at the high zeta cases and find that no matter the temperature or density, we see the same reactions:"),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"New Important Reactions At: 1.81e+04 years\nFormation = 5.64e-17 from:\nO2 + S -> SO + O : 85.30%\nHSO+ + E- -> SO + H : 13.19%\nO + NS -> SO + N : 1.19%\n\nDestruction = -5.64e-17 from:\nH+ + SO -> SO+ + H : 13.16%\nC+ + SO -> SO+ + C : 10.52%\nC+ + SO -> CS+ + O : 10.52%\nC+ + SO -> S+ + CO : 10.52%\nC+ + SO -> S + CO+ : 10.52%\nH3+ + SO -> HSO+ + H2 : 9.86%\nC + SO -> CS + O : 8.90%\nC + SO -> S + CO : 8.90%\nSO + CRPHOT -> S + O : 4.11%\nSO + CRPHOT -> SO+ + E- : 4.11%\nHCO+ + SO -> HSO+ + CO : 3.20%\nHE+ + SO -> S+ + O + HE : 1.93%\nHE+ + SO -> S + O+ + HE : 1.93%\nN + SO -> S + NO : 0.87%\n")),(0,m.kt)("p",null,"Ions take over the destruction of SO when the CRIR is high and these reactions are proceeding about 1000 times faster than the low zeta rates. This makes sense as increasing the CRIR will greatly increase the abundances of these simple ionic species."),(0,m.kt)("p",null,"All in all, we can conclude that a range of gas phase reactions control the abundance of SO at low zeta but once the CRIR is high, destruction via ions dominates the SO chemistry leading to the decreasing abundance that we see."),(0,m.kt)("h2",{id:"summary-notes"},"Summary Notes"),(0,m.kt)("p",null,"In this notebook, we've run some representative models to look at why the SO and ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," abundances seem to so heavily depend on the CRIR. We find that a chain of very efficient reactions starting with simple ions comprise the primary formation route of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," so that the total production of this species depends entirely on the abundance of those ions. With high CRIR, those ions become very abundant and we get a lot of ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"H"),(0,m.kt)("mn",{parentName:"msub"},"3")),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"O"),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"H_3O^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.921331em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.08125em"}},"H"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.08125em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.02778em"}},"O"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," formation."),(0,m.kt)("p",null,"SO is complex at first glance since the formation routes vary by parameter. However, looking at the destruction routes we can see that it's simply that SO can be easily destroyed by simple ions and, again, these are very abundant in gas exposed to a high CRIR."),(0,m.kt)("p",null,"An interesting note about SO is that we could potentially say that destruction via C",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," is the dominant destruction route. However, we would caution users to be careful with that kind of statement. Reactions with H",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+")))))))))))),", HE",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," and other also destroy SO. It could be that if we turned off the C",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mo",{parentName:"msup"},"+"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^+")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.771331em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.771331em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mbin mtight"},"+"))))))))))))," reactions, the SO chemistry would be unchanged as other ions take up the slack. 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However, over the course of a time step, abundances change and reactions rise and fall in importance. More importantly, complex interplay between reactions can contribute to an outcome. 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",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msub"},"C"),(0,m.kt)("mrow",{parentName:"msub"},(0,m.kt)("mi",{parentName:"mrow"},"i"),(0,m.kt)("mi",{parentName:"mrow"},"o"),(0,m.kt)("mi",{parentName:"mrow"},"n")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"C_{ion}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.07153em"}},"C"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.31166399999999994em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.07153em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"i"),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"o"),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"n"))))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"}))))))))))," is a factor that increases the freeze out rate of ions due to electrostatic forces."),(0,m.kt)("p",null,"The branching ratio is an artefact of older versions of UCLCHEM which allows the user to include some grain processing of species without surface reactions. For a given species (eg C) we can determine several species that will rapidly form on the grain (CH,CH4) and freeze some portion of the original species (C) out to these products. This allows fast processes like hydrogenation to be treated without a network of surface reactions. ",(0,m.kt)("em",{parentName:"p"},"However, users should default to using a branching ratio of 1 and allowing surface reactions to take place"),"."),(0,m.kt)("p",null,"For efficiency, freeze out is turned off when the desorption rate is so high that ignoring freeze out would produce an error of around 10",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"20")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^{-20}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"0")))))))))))))," on the abundances of the gas phase species. We also turn off freeze out when the temperature exceeds the binding energy of H",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msub",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msub"}),(0,m.kt)("mn",{parentName:"msub"},"2"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"_2")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.45110799999999995em",verticalAlign:"-0.15em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.30110799999999993em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"2")))),(0,m.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,m.kt)("span",{parentName:"span"})))))))))),"O."),(0,m.kt)("h2",{id:"thermal-desorption"},"Thermal Desorption"),(0,m.kt)("p",null,"We include thermal desorption of material from the grains based on the binding energy of each species to the ices. 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However, for two phases, we multiply by the fraction of the total ice particle which are a given species and by the number of surface sites per volume. This accounts for the fact a majority of the ice material cannot thermally desorb as it not on the surface."),(0,m.kt)("p",null,"Thermal desorption is most relevant to hot core models. As the temperature increases, sublimation can occur. However, TPD experiments (Collings et al. 2004) show that this happens in bursts rather than as a continuous process. These bursts happen naturally in the three phase model as the surface is removed and then the bulk. However, for a two phase network, such bursts need to be simulated. For this reason, the hot core model handles these bursts in the two phase case and the user should turn off thermal desorption."),(0,m.kt)("h2",{id:"non-thermal-desorption-methods"},"Non-thermal Desorption Methods"),(0,m.kt)("h5",{id:"h2-formation"},"H2 Formation"),(0,m.kt)("p",null,"H2 molecules form when H atoms meet briefly on grain surfaces. The reaction is sufficiently exothermic that not only is the product is released into the gas phase but the surrounding grain material is also heated. "),(0,m.kt)("h5",{id:"cosmic-rays"},"Cosmic Rays"),(0,m.kt)("p",null,"Cosmic rays which impact the grains can free molecules from the surface."),(0,m.kt)("h5",{id:"uv-photons"},"UV photons"),(0,m.kt)("p",null,"Surface molecules which absorb a UV photon may gain sufficient energy to escape the surface. We consider secondary photons created by cosmic rays as well as the interstellar radiation field."),(0,m.kt)("h5",{id:"chemical-desorption"},"Chemical Desorption"),(0,m.kt)("p",null,"Other than H2 formation, the desorption of species due to exothermic reactions happening nearby on the grain is not treated. However, as described in the grain surface reaction section, any exothermic grain surface reaction has a probability of releasing the products into the gas phase and this is accounted for."))}h.isMDXComponent=!0}}]); \ No newline at end of file diff --git a/assets/js/6aaec6ca.bcc2e4c8.js b/assets/js/6aaec6ca.bcc2e4c8.js deleted file mode 100644 index 5987fc19..00000000 --- a/assets/js/6aaec6ca.bcc2e4c8.js +++ /dev/null @@ -1 +0,0 @@ -"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[1138],{3905:(e,t,a)=>{a.d(t,{Zo:()=>c,kt:()=>h});var s=a(7294);function n(e,t,a){return t in e?Object.defineProperty(e,t,{value:a,enumerable:!0,configurable:!0,writable:!0}):e[t]=a,e}function r(e,t){var a=Object.keys(e);if(Object.getOwnPropertySymbols){var s=Object.getOwnPropertySymbols(e);t&&(s=s.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),a.push.apply(a,s)}return a}function i(e){for(var t=1;t=0||(n[a]=e[a]);return n}(e,t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);for(s=0;s=0||Object.prototype.propertyIsEnumerable.call(e,a)&&(n[a]=e[a])}return n}var l=s.createContext({}),p=function(e){var t=s.useContext(l),a=t;return e&&(a="function"==typeof e?e(t):i(i({},t),e)),a},c=function(e){var t=p(e.components);return s.createElement(l.Provider,{value:t},e.children)},m={inlineCode:"code",wrapper:function(e){var t=e.children;return s.createElement(s.Fragment,{},t)}},u=s.forwardRef((function(e,t){var a=e.components,n=e.mdxType,r=e.originalType,l=e.parentName,c=o(e,["components","mdxType","originalType","parentName"]),u=p(a),h=n,d=u["".concat(l,".").concat(h)]||u[h]||m[h]||r;return a?s.createElement(d,i(i({ref:t},c),{},{components:a})):s.createElement(d,i({ref:t},c))}));function h(e,t){var a=arguments,n=t&&t.mdxType;if("string"==typeof e||n){var r=a.length,i=new Array(r);i[0]=u;var o={};for(var l in t)hasOwnProperty.call(t,l)&&(o[l]=t[l]);o.originalType=e,o.mdxType="string"==typeof e?e:n,i[1]=o;for(var p=2;p{a.r(t),a.d(t,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>o,metadata:()=>p,toc:()=>m});var s=a(7462),n=a(3366),r=(a(7294),a(3905)),i=["components"],o={id:"network",title:"Creating a Network"},l=void 0,p={unversionedId:"network",id:"version-v3.3.0/network",title:"Creating a Network",description:"MakeRates",source:"@site/versioned_docs/version-v3.3.0/start-network.md",sourceDirName:".",slug:"/network",permalink:"/docs/network",draft:!1,tags:[],version:"v3.3.0",frontMatter:{id:"network",title:"Creating a Network"},sidebar:"docs",previous:{title:"Installation",permalink:"/docs/"},next:{title:"Model Parameters",permalink:"/docs/parameters"}},c={},m=[{value:"MakeRates",id:"makerates",level:2},{value:"Input",id:"input",level:2},{value:"Default Network",id:"default-network",level:2},{value:"Outputs",id:"outputs",level:2},{value:"What MakeRates Does",id:"what-makerates-does",level:2},{value:"Creating your own Network",id:"creating-your-own-network",level:2},{value:"Species list",id:"species-list",level:4},{value:"Reaction list",id:"reaction-list",level:4},{value:"Three Phase Chemistry",id:"three-phase-chemistry",level:2}],u={toc:m};function h(e){var t=e.components,a=(0,n.Z)(e,i);return(0,r.kt)("wrapper",(0,s.Z)({},u,a,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h2",{id:"makerates"},"MakeRates"),(0,r.kt)("p",null,"In order to make a chemical model flexible, the ability to solve a user supplied chemical network is a must. UCLCHEM uses a preprocessing python script to turn csv lists of species and reactions into fortran files for use in the main code. This script is called MakeRates and can be found in the Makerates subdirectory of the repository. It combines a gas phase reaction database with user supplied lists of species and additional reactions into the necessary Fortran code to run UCLCHEM. It also supplies a number of human readable outputs."),(0,r.kt)("p",null,"In the sections below, we discuss how to build your network and set the inputs for MakeRates but once that is done, you can run MakeRates with the following commands:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"cd MakeRates\npython MakeRates.py\ncd ..\npip install .\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"Note the pip install at the end of the process. Any output from MakeRates requires that the code be recompiled because MakeRates produces new source code for UCLCHEM!")),(0,r.kt)("h2",{id:"input"},"Input"),(0,r.kt)("p",null,"Makerates is controlled using a yaml file ",(0,r.kt)("inlineCode",{parentName:"p"},"Makerates/user_settings.yaml"),". By changing the values in this file, you can create different networks. The default values of this file are copied below."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-yaml"},"#Your list of all species\nspecies_file : inputFiles/default_species.csv\n\n#core reactions from gas phase database\ndatabase_reaction_file : inputFiles/umist12-ucledit.csv\ndatabase_reaction_type : UMIST\n\n#set of additional reactions: eg grain network\ncustom_reaction_file : inputFiles/default_grain_network.csv\ncustom_reaction_type : UCL\n\n#whether to automatically expand to three phase network\nthree_phase : True\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"species_file")," is a csv list of species and their properties. We provide a default list and detailed instructions below."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"database_reaction_file")," is your first reaction file, we expect most users to use UMIST12 or KIDA2014 for this but you could create your own file from an alternative database. Makerates can read files formatted in the same manner as the UMIST or KIDA databases as well as our own simple csv format, the ",(0,r.kt)("inlineCode",{parentName:"p"},"database_reaction_type")," setting lets MakeRates know which and should be set to 'UMIST', 'KIDA', or 'UCL'."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"custom_reaction_file")," is an additional reaction file. In the example file, we include all of our grain surface reactions which is the intended use of this file. "),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"three_phase")," is a toggle that tells MakeRates whether to automatically expand your network into a three phase model."),(0,r.kt)("h2",{id:"default-network"},"Default Network"),(0,r.kt)("p",null,"A basic version of each of the required file is supplied in the repository. The network that MakeRates produces from those files is also include in the source code so that a new user who simply installs UCLCHEM without running MakeRates will be using our default network. These default files serve largely as examples of how the files should be formatted and we also describe each one below so that the user can produce their own network."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"We do not endorse the default network"),", we have simply produced a grain surface network that was relatively up to date in 2018. It produces reasonable ice mantle abundances for major species and ignores larger COMs. We strongly suggest any published work be based on a network in which the user has confidence. However, where the user is not greatly concerned with grain surface chemistry, the default network is a good starting point."),(0,r.kt)("h2",{id:"outputs"},"Outputs"),(0,r.kt)("p",null,"Outputs from MakeRates are automatically moved to the ",(0,r.kt)("inlineCode",{parentName:"p"},"src/")," directory so the user can ",(0,r.kt)("inlineCode",{parentName:"p"},"pip install .")," and update their installation of UCLCHEM to use their new network. However, by adding the parameter ",(0,r.kt)("inlineCode",{parentName:"p"},"output_directory")," to the yaml file, you can have all the files moved to a directory instead without copying them to your UCLCHEM src folder. If you do, the following files will be produced:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"network.f90 - Fortran arrays containing lists of species names and properties (mass, binding energy etc) as well as reaction reactants, products and rate coefficients."),(0,r.kt)("li",{parentName:"ul"},"odes.f90 - Code to calculate the rate of change of each species' abundance for the numerical solver"),(0,r.kt)("li",{parentName:"ul"},"species.csv - A list of all species in the network and their properties. Made for humans not UCLCHEM."),(0,r.kt)("li",{parentName:"ul"},"reactions.csv - A list of all reactions including reactants, products and coefficients. Made for humans not UCLCHEM.")),(0,r.kt)("h2",{id:"what-makerates-does"},"What MakeRates Does"),(0,r.kt)("p",null,"MakeRates does the following:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"Combines the two input reaction lists"),(0,r.kt)("li",{parentName:"ul"},"Filters to remove any reactions containing species not in the input species list"),(0,r.kt)("li",{parentName:"ul"},"Adds freeze out and desorption reactions for all species"),(0,r.kt)("li",{parentName:"ul"},"Creates branching reactions for Langmuir-Hinshelwood and Eley-Rideal reactions where products chemically desorb"),(0,r.kt)("li",{parentName:"ul"},"Optionally: creates additional reactions and species needed for a three phase network"),(0,r.kt)("li",{parentName:"ul"},"Does basic network consistency checks and alerts user of problems"),(0,r.kt)("li",{parentName:"ul"},"Writes fortran files for UCLCHEM"),(0,r.kt)("li",{parentName:"ul"},"Writes other output files")),(0,r.kt)("h2",{id:"creating-your-own-network"},"Creating your own Network"),(0,r.kt)("p",null,"To create your own network you need to produce a species list and a reaction list."),(0,r.kt)("h4",{id:"species-list"},"Species list"),(0,r.kt)("p",null,"The species list should simply be a list with one row per species in the network. Each row should contain the species name, mass, binding energy and enthalpy of formation. The latter two are only used for surface species so can be set to zero for the gas phase species. MakeRates will check the mass is correct for each species and alert you of discrepancies."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"C,12,0,0,0,0,0\n#CH4,16,960,0,0.7,0.667,-15.9\n")),(0,r.kt)("p",null,"In the above example, C is a gas phase species so we have set the mass but ignored the other variables. #CH4 is methane in the ice so we have additionally set a binding energy of 960 K and enthalpy of formation of -15.9 kcal/mol. The other three values (0, 0.7, 0.667) are desorption fractions that three phase chemistry networks ignore. For two phase networks, we mimic the multiple desorption events seen in TPD experiments by setting these fractions. See ",(0,r.kt)("a",{parentName:"p",href:"https://ui.adsabs.harvard.edu/abs/2004MNRAS.354.1141V/abstract"},"Viti et al. 2004")," for more information."),(0,r.kt)("p",null,"The enthalpy of formation for essentially any species can be found in chemical databases such as the ",(0,r.kt)("a",{parentName:"p",href:"https://webbook.nist.gov/"},"NIST web book"),". They're usually in kj/mol but the conversion to kcal/mol is easy enough and NIST has an option to switch values to kcal. A fantastic resource for binding energies is ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1016/j.molap.2017.01.002"},"Wakelam et al. 2017")," but these are harder to find in general. In the absolute worse case, you can sum up the binding energies of sub-groups in your molecule but this is pretty inaccurate."),(0,r.kt)("h4",{id:"reaction-list"},"Reaction list"),(0,r.kt)("p",null,"The second reaction list is intended to contain your surface network but can also be used to augment the gas phase databases by including additional gas phase reactions. The reaction list should be a list with one row per reaction and each row should be a comma separated list of 3 reactants, 4 products, three coefficients (alpha,beta,gamma) and a minimum and maximum temperature. Any missing values such as a third reactant can be left blank. In particular, the temperatures are optional but can be useful when you include multiple versions of the same reaction. In that case, UCLCHEM will only use each one within its specified temperature range."),(0,r.kt)("p",null,"The third reactant can be used as a keyword to tell MakeRates what kind of reaction is occuring. In the absence of a keyword, MakeRates and UCLCHEM will treat any reaction as a gas-phase two body reaction. Two keywords the user may wish to use are ER and LH for Eley-Rideal and Langmuir-Hinshelwood reactions respectively (see ",(0,r.kt)("a",{parentName:"p",href:"grain/"},"Grain Chemisty"),"). If a keyword is not added, UCLCHEM will assume a reaction between two surface reactions follows a Kooji-Arrhenius equation."),(0,r.kt)("p",null,"Two other useful reactions types to include are FREEZE and DESORB. Makerates adds freeze out and desorption reactions for every species, assuming they remain unchanged by the process. For example, CO in the gas becomes #CO on the grain. If you would instead like to specify the products, you can include a reaction:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"H3O+,FREEZE,,#H2O,H,,,1,0,0,,,\n#HPN,DESORB,,HPN+,,,,1,0,0,,,\n")),(0,r.kt)("p",null,"which will override the desorption or freeze out products of a species. "),(0,r.kt)("h2",{id:"three-phase-chemistry"},"Three Phase Chemistry"),(0,r.kt)("p",null,"The input ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," controls whether the ices are treated as a single phase or the surface is treated separated to the bulk. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to true, the chemical network will have gas, grain surface, and bulk ice chemistry. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to false, the chemical network will have gas and grain surface chemistry."),(0,r.kt)("p",null,"When true, MakeRates will create the bulk ice chemistry by duplicating the surface species and reactions in your input files. The difference will be that, unless you specifically override the bulk binding energy, every species in the bulk has a binding energy equal to the H2O binding energy. It will also add terms to the ODEs to allow transfer between the bulk and the surface. See the chemistry sections for more information."),(0,r.kt)("p",null,'You can override the binding energy of material in the bulk by explicitly including the bulk species in your species file rather than allowing MakeRates to automatically add it. Bulk species are designated with an "@". 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If you set the binding energy to "Inf", the species will not leave the grains during thermal desorption. 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This notebook sets up a simple approach to doing so for regular grids.",source:"@site/versioned_docs/version-v3.3.1/running_a_grid.md",sourceDirName:".",slug:"/running_a_grid",permalink:"/docs/running_a_grid",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{},sidebar:"docs",previous:{title:"Advanced Physical Modelling",permalink:"/docs/modelling_objects"},next:{title:"Chemical Analysis",permalink:"/docs/chemical_analysis"}},d={},c=[{value:"A Simple Grid",id:"a-simple-grid",level:2},{value:"Define Parameter Space",id:"define-parameter-space",level:3},{value:"Set up the model",id:"set-up-the-model",level:3},{value:"Run Grid",id:"run-grid",level:3},{value:"The Simple Way",id:"the-simple-way",level:4},{value:"The Fast Way",id:"the-fast-way",level:4},{value:"Checking Your Grid",id:"checking-your-grid",level:2},{value:"Complex Grid",id:"complex-grid",level:2},{value:"Summary",id:"summary",level:2}],p={toc:c};function m(e){var t=e.components,l=(0,r.Z)(e,o);return(0,a.kt)("wrapper",(0,n.Z)({},p,l,{components:t,mdxType:"MDXLayout"}),(0,a.kt)("h1",{id:"running-a-grid"},"Running a Grid"),(0,a.kt)("p",null,"A common task is to run UCLCHEM over a grid of parameter combinations. This notebook sets up a simple approach to doing so for regular grids."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"import uclchem\nimport numpy as np\nimport pandas as pd\nfrom multiprocessing import Pool\nimport os\n")),(0,a.kt)("h2",{id:"a-simple-grid"},"A Simple Grid"),(0,a.kt)("h3",{id:"define-parameter-space"},"Define Parameter Space"),(0,a.kt)("p",null,"First, we define our parameter space. We do this by using numpy and pandas to produce a table of all possible combinations of some parameters of interest."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'# This part can be substituted with any choice of grid\n#here we just vary the density, temperature and zeta \ntemperatures = np.linspace(10, 50, 3)\ndensities = np.logspace(4,6,3)\nzetas = np.logspace(1, 3, 3)\n\n#meshgrid will give all combinations, then we shape into columns and put into a table\nparameterSpace = np.asarray(np.meshgrid(temperatures,densities,zetas)).reshape(3, -1)\nmodel_table=pd.DataFrame(parameterSpace.T, columns=[\'temperature\',\'density\',\'zeta\'])\n\n#keep track of where each model output will be saved and make sure that folder exists\nmodel_table["outputFile"]=model_table.apply(lambda row: f"../grid_folder/{row.temperature}_{row.density}_{row.zeta}.csv", axis=1)\nprint(f"{model_table.shape[0]} models to run")\nif not os.path.exists("../grid_folder"):\n os.makedirs("../grid_folder")\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre"},"27 models to run\n")),(0,a.kt)("h3",{id:"set-up-the-model"},"Set up the model"),(0,a.kt)("p",null,"Next, we need a function that will run our model. We write a quick function that takes a row from our dataframe and uses it to populate a parameter dictionary for UCLCHEM and then run a cloud model. We can then map our dataframe to that function."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'def run_model(row):\n #basic set of parameters we\'ll use for this grid. \n ParameterDictionary = {"endatfinaldensity":False,\n "freefall": False,\n "initialDens": row.density,\n "initialTemp": row.temperature,\n "zeta": row.zeta,\n "outputFile": row.outputFile,\n "finalTime":1.0e6,\n "baseAv":10}\n result = uclchem.model.cloud(param_dict=ParameterDictionary)\n return result[0]#just the integer error code\n')),(0,a.kt)("h3",{id:"run-grid"},"Run Grid"),(0,a.kt)("h4",{id:"the-simple-way"},"The Simple Way"),(0,a.kt)("p",null,"We can use pandas apply to simply pass each row to our helper function in turn. This will take some time since we're running the models one by one. I'll use the ",(0,a.kt)("inlineCode",{parentName:"p"},"head")," function just to run five rows as an example here."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"result=model_table.head().apply(run_model, axis=1)\n")),(0,a.kt)("h4",{id:"the-fast-way"},"The Fast Way"),(0,a.kt)("p",null,"Alternatively, we can use multiprocessing to run the models in parallel. That will allow us to run many models simulataneously and make use of all the cores available on our machine."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"def pool_func(x):\n i,row=x\n return run_model(row)\n\nwith Pool(processes=6) as pool:\n results = pool.map(pool_func, model_table.iterrows())\n")),(0,a.kt)("h2",{id:"checking-your-grid"},"Checking Your Grid"),(0,a.kt)("p",null,"After running, we should do two things. First, let's add ",(0,a.kt)("inlineCode",{parentName:"p"},"results")," to our dataframe as a new column. Positive results mean a successful UCLCHEM run and negative ones are unsuccessful. Then we can run each model through ",(0,a.kt)("inlineCode",{parentName:"p"},"check_element_conservation")," to check the integration was successful. We'll use both these things to flag models that failed in some way."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"def element_check(output_file):\n df=uclchem.analysis.read_output_file(output_file)\n #get conservation values\n conserves=uclchem.analysis.check_element_conservation(df)\n #check if any error is greater than 1%\n return all([float(x[:-1])<1 for x in conserves.values()])\n")),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'model_table["run_result"]=results\nmodel_table["elements_conserved"]=model_table["outputFile"].map(element_check)\n#check both conditions are met\nmodel_table["Successful"]=(model_table.run_result>=0) & (model_table.elements_conserved)\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"model_table.head()\n")),(0,a.kt)("div",null,(0,a.kt)("table",{border:"1",class:"dataframe"},(0,a.kt)("thead",null,(0,a.kt)("tr",null,(0,a.kt)("th",null),(0,a.kt)("th",null,"temperature"),(0,a.kt)("th",null,"density"),(0,a.kt)("th",null,"zeta"),(0,a.kt)("th",null,"outputFile"),(0,a.kt)("th",null,"run_result"),(0,a.kt)("th",null,"elements_conserved"),(0,a.kt)("th",null,"Successful"))),(0,a.kt)("tbody",null,(0,a.kt)("tr",null,(0,a.kt)("th",null,"0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_10.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"1"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"100.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_100.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"2"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"1000.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_1000.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"3"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"../grid_folder/30.0_10000.0_10.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"4"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"100.0"),(0,a.kt)("td",null,"../grid_folder/30.0_10000.0_100.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True"))))),(0,a.kt)("h2",{id:"complex-grid"},"Complex Grid"),(0,a.kt)("p",null,"The above was straightforward enough but what about a modelling a grid of shocks? Not only do we want to loop over relevant parameters, we also need to run a few preliminary models to give ourselves starting abundances. We'll start by defining two helper functions, one to run our preliminary cloud and one to run the shock."),(0,a.kt)("p",null,"Let's further imagine that we want to obtain the abundances of several species at the end of the model. We can use the ",(0,a.kt)("inlineCode",{parentName:"p"},"out_species")," parameter to specify which species we want to track and return them to our dataframe."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'out_species=["CO","H2O","CH3OH"]\n\ndef run_prelim(density):\n #basic set of parameters we\'ll use for this grid. \n ParameterDictionary = {"endatfinaldensity":True,\n "freefall": True,\n "initialDens":1e2,\n "finalDens": density,\n "initialTemp": 10.0,\n "abundSaveFile": f"../grid_folder/starts/{density:.0f}.csv",\n "baseAv":1}\n result = uclchem.model.cloud(param_dict=ParameterDictionary)\n return result\n\ndef run_model(row):\n i,row=row # we know we\'re receiving the iterrows() tuple\n #basic set of parameters we\'ll use for this grid. \n ParameterDictionary = {"endatfinaldensity":False,\n "freefall": False,\n "initialDens": row.density,\n "initialTemp": 10.0,\n "outputFile": row.outputFile,\n "abundLoadFile": f"../grid_folder/starts/{row.density:.0f}.csv",\n "finalTime":1.0e5,\n "abstol_factor":1e-18,\n "reltol":1e-12,\n "baseAv":1}\n result = uclchem.model.cshock(row.shock_velocity,param_dict=ParameterDictionary,out_species=out_species)\n #First check UCLCHEM\'s result flag to seeif it\'s positive, if it is return the abundances\n if result[0]>0:\n return result[:]\n #if not, return NaNs because model failed\n else:\n return([np.nan]*len(out_species))\n')),(0,a.kt)("p",null,"Then we define our parameter space again. We'll create two folders, one to store a set of initial abundances for each starting density in our model and another to store our shock outputs."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'# This part can be substituted with any choice of grid\n# here we just combine various initial and final densities into an easily iterable array\nshock_velocities = np.linspace(10, 50, 3)\ndensities = np.logspace(4,6,3)\n\nparameterSpace = np.asarray(np.meshgrid(shock_velocities,densities)).reshape(2, -1)\nmodel_table=pd.DataFrame(parameterSpace.T, columns=[\'shock_velocity\',\'density\'])\nmodel_table["outputFile"]=model_table.apply(lambda row: f"../grid_folder/shocks/{row.shock_velocity}_{row.density}.csv", axis=1)\nprint(f"{model_table.shape[0]} models to run")\n\nfor folder in ["starts","shocks"]:\n if not os.path.exists(f"../grid_folder/{folder}"):\n os.makedirs(f"../grid_folder/{folder}")\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre"},"9 models to run\n")),(0,a.kt)("p",null,"We can then run our preliminary models followed by our science models. The science models will return the abundances at the final time step of each run so we can unpack those directly to our dataframe."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"with Pool(processes=3) as pool:\n results = pool.map(run_prelim, densities)\n")),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'with Pool(processes=6) as pool:\n results = pool.map(run_model, model_table.iterrows())\nmodel_table[["Result","Dissipation Time"]+out_species]=results\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"model_table\n")),(0,a.kt)("div",null,(0,a.kt)("table",{border:"1",class:"dataframe"},(0,a.kt)("thead",null,(0,a.kt)("tr",null,(0,a.kt)("th",null),(0,a.kt)("th",null,"shock_velocity"),(0,a.kt)("th",null,"density"),(0,a.kt)("th",null,"outputFile"),(0,a.kt)("th",null,"Result"),(0,a.kt)("th",null,"Dissipation Time"),(0,a.kt)("th",null,"CO"),(0,a.kt)("th",null,"H2O"),(0,a.kt)("th",null,"CH3OH"))),(0,a.kt)("tbody",null,(0,a.kt)("tr",null,(0,a.kt)("th",null,"0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"7.316441e-05"),(0,a.kt)("td",null,"4.355495e-06"),(0,a.kt)("td",null,"4.624479e-07")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"1"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"2.591790e-05"),(0,a.kt)("td",null,"2.113885e-05"),(0,a.kt)("td",null,"1.196330e-07")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"2"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"1.320822e-05"),(0,a.kt)("td",null,"8.126066e-06"),(0,a.kt)("td",null,"1.989081e-08")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"3"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"1.082083e-07"),(0,a.kt)("td",null,"1.158740e-09"),(0,a.kt)("td",null,"3.697607e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"4"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"1.121259e-10"),(0,a.kt)("td",null,"3.789106e-10"),(0,a.kt)("td",null,"4.907284e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"5"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"2.454392e-10"),(0,a.kt)("td",null,"3.443643e-10"),(0,a.kt)("td",null,"6.454671e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"6"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"1.084005e-10"),(0,a.kt)("td",null,"3.565914e-11"),(0,a.kt)("td",null,"4.816630e-11")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"7"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"1.897782e-10"),(0,a.kt)("td",null,"6.498499e-11"),(0,a.kt)("td",null,"7.847277e-12")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"8"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"2.167651e-10"),(0,a.kt)("td",null,"6.600196e-12"),(0,a.kt)("td",null,"3.412340e-12"))))),(0,a.kt)("h2",{id:"summary"},"Summary"),(0,a.kt)("p",null,"There are many ways to run grids of models and users will naturally develop their own methods. This notebook is just a simple example of how to run UCLCHEM for many parameter combinations whilst producing a useful output (the model_table) to keep track of all the combinations that were run. In a real script, we'd save the model file to csv at the end."),(0,a.kt)("p",null,"For much larger grids, it's recommended that you find a way to make your script robust to failure. Over a huge range of parameters, it is quite likely UCLCHEM will hit integration trouble for at least a few parameter combinations. Very occasionally, UCLCHEM will get caught in a loop where it fails to integrate and cannot adjust its strategy to manage it. This isn't a problem for small grids as the model can be stopped and the tolerances adjusted. However, for very large grids, you may end up locking all threads as they each get stuck on a different model. 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Since at least fortran version 12 is needed for Ventura.")),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"conda create -n uclchem_osx\nconda activate uclchem_osx\nconda config --env --set subdir osx-arm64\nconda install python=3.10\nconda install gfortran\n")),(0,r.kt)("p",null,"After this, one can continue with the installation instructions above and install. In order to use\nUCLCHEM in a new terminal session one has to use the command ",(0,r.kt)("inlineCode",{parentName:"p"},"conda activate uclchem_osx"),"."),(0,r.kt)("h3",{id:"apple-intel"},"Apple Intel"),(0,r.kt)("p",null,"Similar instructions as for M1, but now with the x86_64 instruction set. 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These provide the physical properties of a gas through time as it is subjected to a shock. Whilst the most accurate MHD shock models solve the chemistry, MHD and radiative transfer problems simulataneously, few of these models include chemistry as detailed as UCLCHEM. We assume that the MHD models on which our parameterizations were validated used detailed enough chemistry that the shock profiles could be accurately calculated. This means that more detailed chemistry can be safely post-processed using UCLCHEM, a parameterization simply means the user can select parameters freely rather than from a preset selection of profiles from another code such as ",(0,r.kt)("a",{parentName:"p",href:"http://cdsads.u-strasbg.fr/abs/2015A&A...578A..63F"},"MHDvode"),"."),(0,r.kt)("h3",{id:"c-shocks"},"C-Shocks"),(0,r.kt)("p",null,"The C-shock is based on the parameterization by ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361:20078054"},"Jimenez-Serra et al. 2008"),". 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The C-shock function will return the dissipation time (see ",(0,r.kt)("a",{parentName:"p",href:"/docs/physics-shocks#dimensions"},"below"),") and will also uses shorter timesteps for a number of years equal to twice the dissipation time in order to fully resolve the shock. The number of these time steps is controlled by an optional parameter."),(0,r.kt)("h3",{id:"j-shocks"},"J-shocks"),(0,r.kt)("p",null,"jshock is a similar parameterization for j-shocks from ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201936536"},"James et al.")," validated against more recent results from MHDvode (",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201525740"},"Flower et al. 2015"),"). See the ",(0,r.kt)("a",{parentName:"p",href:"/docs/pythonapi#uclchem.model.jshock"},"j-shock function docs")," for details."),(0,r.kt)("h2",{id:"dimensions"},"Dimensions"),(0,r.kt)("p",null,"Both shock models are intended to be run as single point models only and the code will return an error for ",(0,r.kt)("inlineCode",{parentName:"p"},"points > 1"),". However, you can look at the 1D profile of a shock by converting between time and distance. If we assume the shock is stationary, that is that it's structure is unchanged as it moves through a cloud of gas, then the points that are far away in time are the same as those far away in space."),(0,r.kt)("img",{src:"/img/shock.png",width:"600","margin-left":"40%"}),(0,r.kt)("p",null,"As an illustration, as a shock front moves through a cloud and first hits a parcel of gas, this is t=0 in our shock model output. 5000 years later, the shock front has moved on, thus the output of UCLCHEM at t=5000 years is the state of a parcel of gas that was first hit 5000 years ago and is now far behind the shock front."),(0,r.kt)("p",null,"By using the shock velocity, you can translate 5000 years to the distance between the parcel that was shocked 5000 years ago and the parcel that is just being reached by the shock front,"),(0,r.kt)("div",{className:"math math-display"},(0,r.kt)("span",{parentName:"div",className:"katex-display"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML",display:"block"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("mi",{parentName:"mrow"},"z"),(0,r.kt)("mo",{parentName:"mrow"},"="),(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"v"),(0,r.kt)("mi",{parentName:"msub"},"s")),(0,r.kt)("mi",{parentName:"mrow"},"t")),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"z= v_s t")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.43056em",verticalAlign:"0em"}}),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.04398em"}},"z"),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}}),(0,r.kt)("span",{parentName:"span",className:"mrel"},"="),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.76508em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.03588em"}},"v"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.03588em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"})))))),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal"},"t")))))),(0,r.kt)("p",null,"Thus the history of a single point in a shocked cloud that is output by UCLCHEM can also be translated to a snapshot of a cloud that covers distance z."),(0,r.kt)("h2",{id:"sputtering"},"Sputtering"),(0,r.kt)("p",null,"The C-shock model uses the sputtering process described by ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361:20078054"},"Jimenez-Serra et al. 2008"),". Briefly, we calculate the average energy imparted on the grains from a collision between the shocked gas and the grains. We then combine this with the collision rate and average yield for a given energy to calculate the sputtering rate which we integrate through time. 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This is the time at which the silicon abundance stops increasing in more detailed models, used as a proxy for when the ices are fully sputtered. Thus it is likely that you will see a step change in the ice abundances where sputtering has not occurred yet in one time step and is complete in the second unless your timestep is very small."),(0,r.kt)("p",null,"The J-shock would begin with ",(0,r.kt)("span",{parentName:"p",className:"math math-inline"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"V"),(0,r.kt)("mi",{parentName:"msub"},"s"))),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"V_s")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.22222em"}},"V"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.22222em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"}))))))))))," as the initial drift velocity of the sputtering routine described above and would instantaneously sputter at t = 0 yr. Furthermore, temperatures typically reach a minimum of 1000 K meaning the thermal sublimation is almost complete. 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species due to gas phase reactions is then just the sum of these terms for all reactions where it is a product minus the sum of all reactions where it is a reactant."),(0,n.kt)("p",null,"As a rule, any part of a reaction ODE which does not depend on abundance (eg the rate itself) is calculated between timesteps by the subroutine ",(0,n.kt)("inlineCode",{parentName:"p"},"calculateReactionRates")," in ",(0,n.kt)("inlineCode",{parentName:"p"},"rates.f90"),". 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Defaults to 0.99.")),(0,i.kt)("a",{id:"uclchem.analysis.total_element_abundance"}),(0,i.kt)("h4",{id:"total_element_abundance"},"total","_","element","_","abundance"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def total_element_abundance(element, df)\n")),(0,i.kt)("p",null,"Calculates that the total elemental abundance of a species as a function of time. Allows you to check conservation."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"element")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Name of element"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"df")," ",(0,i.kt)("em",{parentName:"li"},"pandas.DataFrame")," - DataFrame from ",(0,i.kt)("inlineCode",{parentName:"li"},"read_output_file()"))),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"pandas.Series")," - Total abundance of element for all time steps in df.")),(0,i.kt)("a",{id:"uclchem.analysis.check_element_conservation"}),(0,i.kt)("h4",{id:"check_element_conservation"},"check","_","element","_","conservation"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},'def check_element_conservation(df,\n element_list=["H", "N", "C", "O"],\n percent=True)\n')),(0,i.kt)("p",null,"Check the conservation of major element by comparing total abundance at start and end of model"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"df")," ",(0,i.kt)("em",{parentName:"li"},"pandas.DataFrame")," - UCLCHEM output in format from ",(0,i.kt)("inlineCode",{parentName:"li"},"read_output_file")),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"element_list")," ",(0,i.kt)("em",{parentName:"li"},"list, optional")," - List of elements to check. 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Then calculate mass and alert user if it doesn't match\ninput mass."),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.get_n_atoms"}),(0,i.kt)("h4",{id:"get_n_atoms"},"get","_","n","_","atoms"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_n_atoms() -> int\n")),(0,i.kt)("p",null,"Obtain the number of atoms in the molecule"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"int")," - The number of atoms")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.set_n_atoms"}),(0,i.kt)("h4",{id:"set_n_atoms"},"set","_","n","_","atoms"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_n_atoms(new_n_atoms: int) -> None\n")),(0,i.kt)("p",null,"Set the number of atoms"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_n_atoms")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The new number of atoms")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__eq__"}),(0,i.kt)("h4",{id:"__eq__"},"_","_","eq","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __eq__(other)\n")),(0,i.kt)("p",null,"Check for equality based on either a string or another Species instance."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"str, Species")," - Another species")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"NotImplementedError")," - We can only compare between species or strings of species.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if two species are identical.")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__lt__"}),(0,i.kt)("h4",{id:"__lt__"},"_","_","lt","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __lt__(other) -> bool\n")),(0,i.kt)("p",null,"Compare the mass of the species"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - Another species instance")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if less than the other species")),(0,i.kt)("a",{id:"uclchem.makerates.species.Species.__gt__"}),(0,i.kt)("h4",{id:"__gt__"},"_","_","gt","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __gt__(other) -> bool\n")),(0,i.kt)("p",null,"Compare the mass of the species"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"other")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - Another species instance")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - True if larger than than the other species")),(0,i.kt)("a",{id:"uclchem.makerates"}),(0,i.kt)("h1",{id:"uclchemmakerates"},"uclchem.makerates"),(0,i.kt)("a",{id:"uclchem.makerates.makerates"}),(0,i.kt)("h1",{id:"uclchemmakeratesmakerates"},"uclchem.makerates.makerates"),(0,i.kt)("a",{id:"uclchem.makerates.makerates.run_makerates"}),(0,i.kt)("h4",{id:"run_makerates"},"run","_","makerates"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},'def run_makerates(configuration_file: str = "user_settings.yaml",\n write_files: bool = True) -> Network\n')),(0,i.kt)("p",null,"The main run wrapper for makerates, it loads a configuration, parses it in Network\nand then returns the Network. 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Defaults to None."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"path_to_reaction_file")," ",(0,i.kt)("em",{parentName:"li"},"Union","[str, bytes, os.PathLike]",", optional")," - Path to a reactions.csv in/from the src directory. Defaults to None."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"verbosity")," ",(0,i.kt)("em",{parentName:"li"},"LEVEL, optional")," - The verbosity level as specified in logging. Defaults to None.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - You cannot specify both an input configuration and species+reaction.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Network")," - A chemical reaction network.")),(0,i.kt)("a",{id:"uclchem.makerates.network"}),(0,i.kt)("h1",{id:"uclchemmakeratesnetwork"},"uclchem.makerates.network"),(0,i.kt)("p",null,"This python file contains all functions for de-duplicating species and reaction lists,\nchecking for common errors, and automatic addition of reactions such as freeze out,\ndesorption and bulk reactions for three phase models."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network"}),(0,i.kt)("h2",{id:"network-objects"},"Network Objects"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"class Network()\n")),(0,i.kt)("p",null,"The network class stores all the information about reaction network."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.__init__"}),(0,i.kt)("h4",{id:"__init__-1"},"_","_","init","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __init__(species: list[Species],\n reactions: list[Reaction],\n three_phase: bool = False,\n user_defined_bulk: list = [])\n")),(0,i.kt)("p",null,"A class to store network information such as indices of important reactions."),(0,i.kt)("p",null,"The class fully utilizes getters and setters, which can be used to add/remove\nreactions and the species involved. Important is that you do not directly edit\nthe internal dictionaries that store the species and reactions, unless you\nknow what you are doing. The network by default checks for duplicates in species\nand identical reactions that overlap in temperature ranges, potentially causing\nproblems."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of chemical species that are added to the network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - A list of chemical reactions that are added to the network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool, optional")," - Whether to use a three phase model (gas, surface, bulk). Defaults to False."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"user_defined_bulk")," ",(0,i.kt)("em",{parentName:"li"},"list, optional")," - List of user defined bulk. Defaults to [].")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.find_similar_reactions"}),(0,i.kt)("h4",{id:"find_similar_reactions"},"find","_","similar","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def find_similar_reactions(reaction: Reaction) -> dict[int, Reaction]\n")),(0,i.kt)("p",null,"Reactions are similar if the reaction has the same reactants and products,\nfind all reactions that are similar, returning their index and the reaction itself."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - Reaction with possible identical (but for temperature range) reactions in the network")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[int, Reaction]",": A dict with the identical reactions."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_reaction_by_index"}),(0,i.kt)("h4",{id:"remove_reaction_by_index"},"remove","_","reaction","_","by","_","index"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_reaction_by_index(reaction_idx: int) -> None\n")),(0,i.kt)("p",null,"Remove a reaction by its index in the internal _reactions_dict, this is the only way\nto remove reactions that are defined piecewise across temperature ranges."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - Index of the reaction to remove")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_reaction"}),(0,i.kt)("h4",{id:"remove_reaction"},"remove","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_reaction(reaction: Reaction) -> None\n")),(0,i.kt)("p",null,"Remove the reaction by giving the object itself, this only works if the reaction is\nnot piecewise defined across the temperature ranges."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - The reaction you wish to delete.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction"}),(0,i.kt)("h4",{id:"get_reaction"},"get","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction(reaction_idx: int) -> Reaction\n")),(0,i.kt)("p",null,"Obtain a reaction from the reaction set given an index of the internal _reactions_dict."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The reaction index")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Reaction")," - the desired reaction")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_reaction"}),(0,i.kt)("h4",{id:"set_reaction"},"set","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_reaction(reaction_idx: int, reaction: Reaction) -> None\n")),(0,i.kt)("p",null,"This setter explicitely sets the reaction for a certain index."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_idx")," ",(0,i.kt)("em",{parentName:"li"},"int")," - The index to be written to"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction")," ",(0,i.kt)("em",{parentName:"li"},"Reaction")," - The reaction to be added to the index.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction_dict"}),(0,i.kt)("h4",{id:"get_reaction_dict"},"get","_","reaction","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction_dict() -> dict[int, Reaction]\n")),(0,i.kt)("p",null,"Returns the whole internal reaction dictionary."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[int, Reaction]",": A copy of the internal reactions dictionary."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_reaction_dict"}),(0,i.kt)("h4",{id:"set_reaction_dict"},"set","_","reaction","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_reaction_dict(new_dict: dict[int, Reaction]) -> None\n")),(0,i.kt)("p",null,"Override the reactions dictionary with a new dictionar."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_dict")," ",(0,i.kt)("em",{parentName:"li"},"dict","[int, Reaction]")," - The new reactions_dictionary.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_reaction_list"}),(0,i.kt)("h4",{id:"get_reaction_list"},"get","_","reaction","_","list"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_reaction_list() -> list[Reaction]\n")),(0,i.kt)("p",null,"Obtain all the reactions in the Network."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list[Reaction]")," - A list with all the reaction objects")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.sort_reactions"}),(0,i.kt)("h4",{id:"sort_reactions"},"sort","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def sort_reactions() -> None\n")),(0,i.kt)("p",null,"Sort the reaction dictionary by reaction type first and by the first reactant second."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_species"}),(0,i.kt)("h4",{id:"add_species"},"add","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_species(species: Union[Union[Species, str], list[Union[Species,\n str]]])\n")),(0,i.kt)("p",null,"Add species to the network, given a (list of) species. If it is a list of strings,\nit tries to instantiate a species class with it. It also checks for duplicate entries and\nfilters out attempts to add reaction types to the species."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Union[Union","[Species, str]",", list[Union","[Species, str]","]]")," - A (list of) species or strings.")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Raises"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - If we cannot parse the (list of) reactions"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ValueError")," - If an ice specie with binding energy of zero is added.")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.remove_species"}),(0,i.kt)("h4",{id:"remove_species"},"remove","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def remove_species(specie_name: str) -> None\n")),(0,i.kt)("p",null,"Remove a specie from the network"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"specie_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Species to remove")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_species_list"}),(0,i.kt)("h4",{id:"get_species_list"},"get","_","species","_","list"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_species_list() -> list[Species]\n")),(0,i.kt)("p",null,"Obtain a list with all the species in the network"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list[Species]")," - A list of all the species in the reaction network")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_species_dict"}),(0,i.kt)("h4",{id:"get_species_dict"},"get","_","species","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_species_dict() -> dict[str, Species]\n")),(0,i.kt)("p",null,"Get the internal dictionary that stores all the species, it consists\nof all species' names as key, with the species object as value."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("p",null," dict","[str, Species]",": A dictionary with the species"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.get_specie"}),(0,i.kt)("h4",{id:"get_specie"},"get","_","specie"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def get_specie(specie_name: str) -> Species\n")),(0,i.kt)("p",null,"Get the species of the reaction network (from the internal dictionary)"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"specie_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - the name of the species as a string")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Species")," - The species object")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_specie"}),(0,i.kt)("h4",{id:"set_specie"},"set","_","specie"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_specie(species_name: str, species: Species) -> None\n")),(0,i.kt)("p",null,"Set the species of the reaction network in the internal dictionary"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - The name of the species as string"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - The Species object to set")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.set_species_dict"}),(0,i.kt)("h4",{id:"set_species_dict"},"set","_","species","_","dict"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def set_species_dict(new_species_dict: dict[str, Species]) -> None\n")),(0,i.kt)("p",null,"Set the internal species dict"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"new_species_dict")," ",(0,i.kt)("em",{parentName:"li"},"dict","[str, Species]")," - The new dictionary to set")),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.sort_species"}),(0,i.kt)("h4",{id:"sort_species"},"sort","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def sort_species() -> None\n")),(0,i.kt)("p",null,"Sort the species based on their mass in ascending order. We always make sure the Electron is last."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_network"}),(0,i.kt)("h4",{id:"check_network"},"check","_","network"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_network() -> None\n")),(0,i.kt)("p",null,"Run through the list of reactions and check for obvious errors such\nas duplicate reactions, multiple freeze out routes (to warn, not necessarily\nan error), etc."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_and_filter_species"}),(0,i.kt)("h4",{id:"check_and_filter_species"},"check","_","and","_","filter","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_and_filter_species() -> None\n")),(0,i.kt)("p",null,"Check every speces in network appears in at least one reaction.\nRemove any that do not and alert user."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_bulk_species"}),(0,i.kt)("h4",{id:"add_bulk_species"},"add","_","bulk","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_bulk_species() -> None\n")),(0,i.kt)("p",null,"For three phase models, MakeRates will produce the version of the species in the bulk\nso that the user doesn't have to endlessly relist the same species"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_freeze_and_desorbs"}),(0,i.kt)("h4",{id:"check_freeze_and_desorbs"},"check","_","freeze","_","and","_","desorbs"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_freeze_and_desorbs() -> None\n")),(0,i.kt)("p",null,(0,i.kt)("inlineCode",{parentName:"p"},"add_freeze_reactions()")," and ",(0,i.kt)("inlineCode",{parentName:"p"},"add_desorb_reactions()")," automatically generate\nall desorption and freeze out reactions. However, user may want to change a species on freeze out\neg C+ becomes ",(0,i.kt)("inlineCode",{parentName:"p"},"C")," rather than ",(0,i.kt)("inlineCode",{parentName:"p"},"C"),"+. This function checks for that and updates species so they'll\nfreeze or desorb correctly when reactions are generated."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_freeze_reactions"}),(0,i.kt)("h4",{id:"add_freeze_reactions"},"add","_","freeze","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_freeze_reactions() -> None\n")),(0,i.kt)("p",null,"Save the user effort by automatically generating freeze out reactions"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_desorb_reactions"}),(0,i.kt)("h4",{id:"add_desorb_reactions"},"add","_","desorb","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_desorb_reactions() -> None\n")),(0,i.kt)("p",null,"Save the user effort by automatically generating desorption reactions"),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_chemdes_reactions"}),(0,i.kt)("h4",{id:"add_chemdes_reactions"},"add","_","chemdes","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_chemdes_reactions() -> None\n")),(0,i.kt)("p",null,"We have the user list all Langmuir-Hinshelwood and Eley-Rideal\nreactions once. Then we duplicate so that the reaction branches\nwith products on grain and products desorbing."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.check_for_excited_species"}),(0,i.kt)("h4",{id:"check_for_excited_species"},"check","_","for","_","excited","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_for_excited_species() -> bool\n")),(0,i.kt)("p",null,"Check if there are any exicted species in the network, true if there are any."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_excited_surface_reactions"}),(0,i.kt)("h4",{id:"add_excited_surface_reactions"},"add","_","excited","_","surface","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_excited_surface_reactions() -> None\n")),(0,i.kt)("p",null,"All excited species will relax to the ground state if they do not react\nthe vibrational frequency of the species is used as a pseudo approximation of the rate coefficient\nWe assume all grain reactions have an excited variant. For example:\n",(0,i.kt)("inlineCode",{parentName:"p"},"A"),", ",(0,i.kt)("inlineCode",{parentName:"p"},"B")," LH ",(0,i.kt)("inlineCode",{parentName:"p"},"C")," will have the variants:\n",(0,i.kt)("inlineCode",{parentName:"p"},"A"),(0,i.kt)("em",{parentName:"p"},", ",(0,i.kt)("inlineCode",{parentName:"em"},"B")," EXSOLID ",(0,i.kt)("inlineCode",{parentName:"em"},"C")," and ",(0,i.kt)("inlineCode",{parentName:"em"},"A"),", ",(0,i.kt)("inlineCode",{parentName:"em"},"B"))," EXSOLID ",(0,i.kt)("inlineCode",{parentName:"p"},"C"),"\nIf only one of the reactants in the base reaction has an excited counterpart then\nonly one excited version of that reaction is created."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.add_bulk_reactions"}),(0,i.kt)("h4",{id:"add_bulk_reactions"},"add","_","bulk","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def add_bulk_reactions() -> None\n")),(0,i.kt)("p",null,"We assume any reaction that happens on the surface of grains can also happen\nin the bulk (just more slowly due to binding energy). The user therefore only\nlists surface reactions in their input reaction file and we duplicate here."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.freeze_checks"}),(0,i.kt)("h4",{id:"freeze_checks"},"freeze","_","checks"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def freeze_checks() -> None\n")),(0,i.kt)("p",null,"Check that every species freezes out and alert the user if a\nspecies freezes out via mutiple routes. This isn't necessarily an\nerror so best just print."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.duplicate_checks"}),(0,i.kt)("h4",{id:"duplicate_checks"},"duplicate","_","checks"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def duplicate_checks() -> None\n")),(0,i.kt)("p",null,"Check reaction network to make sure no reaction appears twice unless\nthey have different temperature ranges."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.index_important_reactions"}),(0,i.kt)("h4",{id:"index_important_reactions"},"index","_","important","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def index_important_reactions() -> None\n")),(0,i.kt)("p",null,"We have a whole bunch of important reactions and we want to store\ntheir indices. We find them all here."),(0,i.kt)("a",{id:"uclchem.makerates.network.Network.index_important_species"}),(0,i.kt)("h4",{id:"index_important_species"},"index","_","important","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def index_important_species() -> None\n")),(0,i.kt)("p",null,"Obtain the indices for all the important reactions."),(0,i.kt)("a",{id:"uclchem.makerates.network.LoadedNetwork"}),(0,i.kt)("h2",{id:"loadednetwork-objects"},"LoadedNetwork Objects"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"class LoadedNetwork(Network)\n")),(0,i.kt)("p",null,"Network version that skips all steps and just loads two lists. This is another\nhere be dragons version, use this with exceeding caution as no checks are performed for you."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"Network")," ",(0,i.kt)("strong",{parentName:"li"},"type")," - ",(0,i.kt)("em",{parentName:"li"},"description"))),(0,i.kt)("a",{id:"uclchem.makerates.network.LoadedNetwork.__init__"}),(0,i.kt)("h4",{id:"__init__-2"},"_","_","init","_","_"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def __init__(species: list[Species], reactions: list[Reaction]) -> None\n")),(0,i.kt)("p",null,"A loader of networks without any checks."),(0,i.kt)("p",null,"Here be dragons."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of species objects"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - A list of reaction objects.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions"}),(0,i.kt)("h1",{id:"uclchemmakeratesio_functions"},"uclchem.makerates.io","_","functions"),(0,i.kt)("p",null,"Functions to read in the species and reaction files and write output files"),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.read_species_file"}),(0,i.kt)("h4",{id:"read_species_file"},"read","_","species","_","file"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def read_species_file(file_name: Path) -> list[Species]\n")),(0,i.kt)("p",null,"Reads in a Makerates species file"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to file containing the species list")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list")," - List of Species objects")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.read_reaction_file"}),(0,i.kt)("h4",{id:"read_reaction_file"},"read","_","reaction","_","file"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def read_reaction_file(file_name: Path, species_list: list[Species],\n ftype: str) -> tuple[list[Reaction], list[Reaction]]\n")),(0,i.kt)("p",null,"Reads in a reaction file of any kind (user, UMIST, KIDA)\nproduces a list of reactions for the network, filtered by species_list"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - A file name for the reaction file to read."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - A list of chemical species to be used in the reading."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"ftype")," ",(0,i.kt)("em",{parentName:"li"},"str")," - 'UMIST','UCL', or 'KIDA' to describe format of file_name")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"list,list")," - Lists of kept and dropped reactions.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.check_reaction"}),(0,i.kt)("h4",{id:"check_reaction"},"check","_","reaction"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def check_reaction(reaction_row, keep_list) -> bool\n")),(0,i.kt)("p",null,"Checks a row parsed from a reaction file and checks it only contains acceptable things.\nIt checks if all species in the reaction are present, and adds the temperature range is none is specified."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_row")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List parsed from a reaction file and formatted to be able to called Reaction(reaction_row)"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"keep_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - list of elements that are acceptable in the reactant or product bits of row")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"bool")," - Whether the row contains acceptable entries.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.kida_parser"}),(0,i.kt)("h4",{id:"kida_parser"},"kida","_","parser"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def kida_parser(kida_file)\n")),(0,i.kt)("p",null,"KIDA used a fixed format file so we read each line in the chunks they specify\nand use python built in classes to convert to the necessary types.\nNOTE KIDA defines some of the same reaction types to UMIST but with different names\nand coefficients. We fix that by converting them here."),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.output_drops"}),(0,i.kt)("h4",{id:"output_drops"},"output","_","drops"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def output_drops(dropped_reactions: list[Reaction],\n output_dir: str,\n write_files=True)\n")),(0,i.kt)("p",null,"Writes the reactions that are dropped to disk/logs"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"dropped_reactions")," ",(0,i.kt)("em",{parentName:"li"},"list","[Reaction]")," - The reactions that were dropped"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"output_dir")," ",(0,i.kt)("em",{parentName:"li"},"str")," - The directory that dropped_reactions.csv will be written to."),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"write_files")," ",(0,i.kt)("em",{parentName:"li"},"bool, optional")," - Whether or not to write the file. Defaults to True.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_outputs"}),(0,i.kt)("h4",{id:"write_outputs"},"write","_","outputs"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_outputs(network: Network, output_dir: str = None) -> None\n")),(0,i.kt)("p",null,"Write the ODE and Network fortran source files to the fortran source."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"network")," ",(0,i.kt)("em",{parentName:"li"},"network")," - The makerates Network class"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"output_dir")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - The directory to write to.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_species"}),(0,i.kt)("h4",{id:"write_species"},"write","_","species"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_species(file_name: Path, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Write the human readable species file. Note UCLCHEM doesn't use this file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to output file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species objects for network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_reactions"}),(0,i.kt)("h4",{id:"write_reactions"},"write","_","reactions"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_reactions(fileName, reaction_list) -> None\n")),(0,i.kt)("p",null,"Write the human readable reaction file. Note UCLCHEM doesn't use this file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"fileName")," ",(0,i.kt)("em",{parentName:"li"},"str")," - path to output file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reaction objects for network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_odes_f90"}),(0,i.kt)("h4",{id:"write_odes_f90"},"write","_","odes","_","f90"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_odes_f90(file_name: Path, species_list: list[Species],\n reaction_list: list[Reaction], three_phase: bool) -> None\n")),(0,i.kt)("p",null,"Write the ODEs in Modern Fortran. This is an actual code file."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Path to file where code will be written"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species describing network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reactions describing network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - Flag for whether this is a 3 phase network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_jacobian"}),(0,i.kt)("h4",{id:"write_jacobian"},"write","_","jacobian"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_jacobian(file_name: Path, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Write jacobian in Modern Fortran. This has never improved UCLCHEM's speed\nand so is not used in the code as it stands.\nCurrent only works for three phase model."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"file_name")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Path to jacobian file"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"species_list")," - List of species AFTER being processed by build_ode_string")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.build_ode_string"}),(0,i.kt)("h4",{id:"build_ode_string"},"build","_","ode","_","string"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def build_ode_string(species_list: list[Species],\n reaction_list: list[Reaction], three_phase: bool) -> str\n")),(0,i.kt)("p",null,"A long, complex function that does the messy work of creating the actual ODE\ncode to calculate the rate of change of each species. Test any change to this code\nthoroughly because ODE mistakes are very hard to spot."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of species in network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"reaction_list")," ",(0,i.kt)("em",{parentName:"li"},"list")," - List of reactions in network"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"three_phase")," ",(0,i.kt)("em",{parentName:"li"},"bool")," - Bool denoting if this is a three phase network")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"str")," - One long string containing the entire ODE fortran code.")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.species_ode_string"}),(0,i.kt)("h4",{id:"species_ode_string"},"species","_","ode","_","string"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def species_ode_string(n: int, species: Species) -> str\n")),(0,i.kt)("p",null,"Build the string of Fortran code for a species once it's loss and gains\nstrings have been produced."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"n")," ",(0,i.kt)("em",{parentName:"li"},"int")," - Index of species in python format"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species")," ",(0,i.kt)("em",{parentName:"li"},"Species")," - species object")),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Returns"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"str")," - the fortran code for the rate of change of the species")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.write_evap_lists"}),(0,i.kt)("h4",{id:"write_evap_lists"},"write","_","evap","_","lists"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def write_evap_lists(network_file, species_list: list[Species]) -> None\n")),(0,i.kt)("p",null,"Two phase networks mimic episodic thermal desorption seen in lab (see Viti et al. 2004)\nby desorbing fixed fractions of material at specific temperatures. Three phase networks just\nuse binding energy and that fact we set binding energies in bulk to water by default.\nThis function writes all necessary arrays to the network file so these processes work."),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"network_file")," ",(0,i.kt)("em",{parentName:"li"},"file")," - Open file object to which the network code is being written"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"species_list")," ",(0,i.kt)("em",{parentName:"li"},"list","[Species]")," - List of species in network")),(0,i.kt)("a",{id:"uclchem.makerates.io_functions.truncate_line"}),(0,i.kt)("h4",{id:"truncate_line"},"truncate","_","line"),(0,i.kt)("pre",null,(0,i.kt)("code",{parentName:"pre",className:"language-python"},"def truncate_line(input_string: str, lineLength: int = 72) -> str\n")),(0,i.kt)("p",null,"Take a string and adds line endings at regular intervals\nkeeps us from overshooting fortran's line limits and, frankly,\nmakes for nicer ode.f90 even if human readability isn't very important"),(0,i.kt)("p",null,(0,i.kt)("strong",{parentName:"p"},"Arguments"),":"),(0,i.kt)("ul",null,(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"input_string")," ",(0,i.kt)("em",{parentName:"li"},"str")," - Line of code to be truncated"),(0,i.kt)("li",{parentName:"ul"},(0,i.kt)("inlineCode",{parentName:"li"},"lineLength")," ",(0,i.kt)("em",{parentName:"li"},"int, optional")," - rough line length. 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The first element is always an integer which will be positive if the code completed and negative otherwise. You can send negative values to ",(0,r.kt)("inlineCode",{parentName:"p"},"uclchem.utils.check_error()")," to get a more detailed error message."),(0,r.kt)("p",null,"The subsequent elements are the final abundances of any species listed in ",(0,r.kt)("inlineCode",{parentName:"p"},"out_species"),", in this case we have the abundance of SO and CO. This is useful when we want to use UCLCHEM as part of something like an MCMC procedure, obtaining abundances for given parameters. However, we also write the final abundances of all species to ",(0,r.kt)("inlineCode",{parentName:"p"},"abundSaveFile")," and the abundances of all species at every time step in ",(0,r.kt)("inlineCode",{parentName:"p"},"outputFile")," so it is not necessary to acquire abundances in this way."),(0,r.kt)("p",null,"The output file is just a simple csv with some header rows, UCLCHEM has a utility function to read that file into a pandas dataframe. Let's load it up and look at it."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'result_df=uclchem.analysis.read_output_file("../examples/test-output/static-full.dat")\nresult_df.head()\n')),(0,r.kt)("div",null,(0,r.kt)("table",{border:"1",class:"dataframe"},(0,r.kt)("thead",null,(0,r.kt)("tr",null,(0,r.kt)("th",null),(0,r.kt)("th",null,"Time"),(0,r.kt)("th",null,"Density"),(0,r.kt)("th",null,"gasTemp"),(0,r.kt)("th",null,"av"),(0,r.kt)("th",null,"zeta"),(0,r.kt)("th",null,"point"),(0,r.kt)("th",null,"H"),(0,r.kt)("th",null,"#H"),(0,r.kt)("th",null,"H+"),(0,r.kt)("th",null,"@H"),(0,r.kt)("th",null,"..."),(0,r.kt)("th",null,"HS2+"),(0,r.kt)("th",null,"HSO2+"),(0,r.kt)("th",null,"H2S2+"),(0,r.kt)("th",null,"H2S2"),(0,r.kt)("th",null,"#H2S2"),(0,r.kt)("th",null,"@H2S2"),(0,r.kt)("th",null,"E-"),(0,r.kt)("th",null,"BULK"),(0,r.kt)("th",null,"SURFACE"),(0,r.kt)("th",null,"radfield"))),(0,r.kt)("tbody",null,(0,r.kt)("tr",null,(0,r.kt)("th",null,"0"),(0,r.kt)("td",null,"0.000000e+00"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"1"),(0,r.kt)("td",null,"1.000000e-07"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.680300e-13"),(0,r.kt)("td",null,"1.789040e-17"),(0,r.kt)("td",null,"4.269620e-20"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.629010e-20"),(0,r.kt)("td",null,"7.488850e-13"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"2"),(0,r.kt)("td",null,"1.000000e-06"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.646510e-12"),(0,r.kt)("td",null,"1.789080e-16"),(0,r.kt)("td",null,"4.219000e-18"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"1.631720e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000020e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.562330e-18"),(0,r.kt)("td",null,"7.444370e-12"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"3"),(0,r.kt)("td",null,"1.000000e-05"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.641430e-11"),(0,r.kt)("td",null,"1.789520e-15"),(0,r.kt)("td",null,"4.212520e-16"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"7.762720e-29"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000050e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000010e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.554260e-16"),(0,r.kt)("td",null,"7.438940e-11"),(0,r.kt)("td",null,"1.0")),(0,r.kt)("tr",null,(0,r.kt)("th",null,"4"),(0,r.kt)("td",null,"1.000000e-04"),(0,r.kt)("td",null,"10000.0"),(0,r.kt)("td",null,"10.0"),(0,r.kt)("td",null,"2.9287"),(0,r.kt)("td",null,"1.0"),(0,r.kt)("td",null,"1"),(0,r.kt)("td",null,"0.5"),(0,r.kt)("td",null,"5.480630e-10"),(0,r.kt)("td",null,"1.793810e-14"),(0,r.kt)("td",null,"4.079690e-14"),(0,r.kt)("td",null,"..."),(0,r.kt)("td",null,"7.864380e-27"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000070e-30"),(0,r.kt)("td",null,"1.000000e-30"),(0,r.kt)("td",null,"1.000150e-30"),(0,r.kt)("td",null,"0.000182"),(0,r.kt)("td",null,"5.425070e-14"),(0,r.kt)("td",null,"7.351600e-10"),(0,r.kt)("td",null,"1.0")))),(0,r.kt)("p",null,"5 rows \xd7 321 columns")),(0,r.kt)("p",null,"We can also test whether the model run went well by checking for element conservation. We do this because integrator errors often show up as a failure to conserve elemental abundances. "),(0,r.kt)("p",null,"We can use ",(0,r.kt)("inlineCode",{parentName:"p"},"check_element_conservation()")," to test whether we conserve elements in this run. This function returns a dictionary where each entry gives the change in the total abundance of an element as a percentage of the original abundance. In an ideal case, these values are 0\\% indicating the total abundance at the end of the model is exactly the same as the total at the start."),(0,r.kt)("p",null,"Changes of less than 1\\% are fine for many cases but if they are too high, you could consider changing the ",(0,r.kt)("inlineCode",{parentName:"p"},"reltol")," and ",(0,r.kt)("inlineCode",{parentName:"p"},"abstol")," parameters that control the integrator accuracy. They are error tolerance so smaller values lead to smaller errors and (usually) longer integration times. The default values were chosen by running a large grid of models and choosing the tolerances with the lowest average run time from those that conserved elements well and rarely failed. Despite this, there are no one-size-fits-all perfect tolerances and you may run into issues with different networks or models."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'conservation=uclchem.analysis.check_element_conservation(result_df,element_list=["H","N","C","O","S"])\nprint("Percentage change in total abundances:")\nprint(conservation)\n')),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"Percentage change in total abundances:\n{'H': '0.001%', 'N': '0.000%', 'C': '0.000%', 'O': '0.000%', 'S': '0.000%'}\n")),(0,r.kt)("h2",{id:"plotting-results"},"Plotting Results"),(0,r.kt)("p",null,"Finally, you will want to plot your results. This can be done with any plotting library but UCLCHEM does provide a few functions to make quick plots. Note the use of $ symbols in the species list below, this gets the total ice abundance of a species. For two phase models, this is just the surface abudance but for three phase it is the sum of surface and bulk."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-python"},'species=["H","H2","$H","$H2","H2O","$H2O","CO","$CO","$CH3OH","CH3OH"]\nfig,ax=uclchem.analysis.create_abundance_plot(result_df,species,figsize=(10,7))\nax=ax.set(xscale="log",ylim=(1e-15,1),xlim=(1e3,1e6))\n')),(0,r.kt)("p",null,(0,r.kt)("img",{alt:"png",src:n(1671).Z,width:"712",height:"496"})),(0,r.kt)("p",null,"and that's it! You've run your first UCLCHEM model, checked that the element conservation is correct, and plotted the abundances."))}k.isMDXComponent=!0},1671:(e,t,n)=>{n.d(t,{Z:()=>l});const l=n.p+"assets/images/first_model_9_0-fff8b0e800895dbb0e755cc2b9459720.png"}}]); \ No newline at end of file diff --git a/assets/js/ade0c702.1d88833a.js b/assets/js/ade0c702.1d88833a.js new file mode 100644 index 00000000..fe1da8d5 --- /dev/null +++ b/assets/js/ade0c702.1d88833a.js @@ -0,0 +1 @@ +"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[3796],{3905:(a,e,s)=>{s.d(e,{Zo:()=>i,kt:()=>o});var t=s(7294);function m(a,e,s){return e in a?Object.defineProperty(a,e,{value:s,enumerable:!0,configurable:!0,writable:!0}):a[e]=s,a}function n(a,e){var s=Object.keys(a);if(Object.getOwnPropertySymbols){var t=Object.getOwnPropertySymbols(a);e&&(t=t.filter((function(e){return Object.getOwnPropertyDescriptor(a,e).enumerable}))),s.push.apply(s,t)}return s}function p(a){for(var e=1;e=0||(m[s]=a[s]);return m}(a,e);if(Object.getOwnPropertySymbols){var n=Object.getOwnPropertySymbols(a);for(t=0;t=0||Object.prototype.propertyIsEnumerable.call(a,s)&&(m[s]=a[s])}return m}var N=t.createContext({}),l=function(a){var e=t.useContext(N),s=e;return a&&(s="function"==typeof a?a(e):p(p({},e),a)),s},i=function(a){var e=l(a.components);return t.createElement(N.Provider,{value:e},a.children)},k={inlineCode:"code",wrapper:function(a){var e=a.children;return t.createElement(t.Fragment,{},e)}},c=t.forwardRef((function(a,e){var s=a.components,m=a.mdxType,n=a.originalType,N=a.parentName,i=r(a,["components","mdxType","originalType","parentName"]),c=l(s),o=m,h=c["".concat(N,".").concat(o)]||c[o]||k[o]||n;return s?t.createElement(h,p(p({ref:e},i),{},{components:s})):t.createElement(h,p({ref:e},i))}));function o(a,e){var s=arguments,m=e&&e.mdxType;if("string"==typeof a||m){var n=s.length,p=new Array(n);p[0]=c;var r={};for(var N in e)hasOwnProperty.call(e,N)&&(r[N]=e[N]);r.originalType=a,r.mdxType="string"==typeof a?a:m,p[1]=r;for(var l=2;l{s.r(e),s.d(e,{assets:()=>i,contentTitle:()=>N,default:()=>o,frontMatter:()=>r,metadata:()=>l,toc:()=>k});var t=s(7462),m=s(3366),n=(s(7294),s(3905)),p=["components"],r={id:"grain",title:"Grain Surface Reactions"},N=void 0,l={unversionedId:"grain",id:"version-v3.3.1/grain",title:"Grain Surface Reactions",description:"Whilst the basic treatment of gas phase chemistry is well established, grain surface chemistry is more complex. There are three possible ways to treat grain surface chemistry in UCLCHEM. In general we assume that:",source:"@site/versioned_docs/version-v3.3.1/chem-grain.md",sourceDirName:".",slug:"/grain",permalink:"/docs/grain",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{id:"grain",title:"Grain Surface Reactions"},sidebar:"docs",previous:{title:"Gas Phase Reactions",permalink:"/docs/gas"},next:{title:"Adsorption & Desorption Reactions",permalink:"/docs/desorb"}},i={},k=[{value:"Langmuir-Hinshelwood Mechanism",id:"langmuir-hinshelwood-mechanism",level:3},{value:"Eley-Rideal Mechanism",id:"eley-rideal-mechanism",level:3}],c={toc:k};function o(a){var e=a.components,s=(0,m.Z)(a,p);return(0,n.kt)("wrapper",(0,t.Z)({},c,s,{components:e,mdxType:"MDXLayout"}),(0,n.kt)("p",null,"Whilst the basic treatment of gas phase chemistry is well established, grain surface chemistry is more complex. There are three possible ways to treat grain surface chemistry in UCLCHEM. In general we assume that:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},"All dust grains are well covered by the species in question so we can take a rate equation approach based on fractional abundance rather than tracking if molecule A is on the same dust grain as molecule B."),(0,n.kt)("li",{parentName:"ul"},"Grains are spherical objects of a uniform size."),(0,n.kt)("li",{parentName:"ul"},"All species are thermalized on the grains.")),(0,n.kt)("p",null,"This allows a fairly straight forward treatment of the grain chemistry. Below we list several processes that are important in UCLCHEM's treatment of the grain chemistry."),(0,n.kt)("h3",{id:"langmuir-hinshelwood-mechanism"},"Langmuir-Hinshelwood Mechanism"),(0,n.kt)("p",null,"Reactions via diffusion of reactants across the grain surface was added to UCLCHEM by ",(0,n.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1093/mnras/stx2960"},"Quenard et al. 2018"),", drawing their formalism from ",(0,n.kt)("a",{parentName:"p",href:"http://adsabs.harvard.edu/doi/10.1086/191713"},"Hasegawa et al. 1992"),", ",(0,n.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1088/0004-637X/735/1/15"},"Garrod & Pauly 2011"),", and ",(0,n.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1093/mnras/stw887"},"Ruaud et al. 2016"),". These reactions can be included in your grain file in the form,"),(0,n.kt)("pre",null,(0,n.kt)("code",{parentName:"pre"},"#H,#CO,LH,#HCO,,,,alpha,0.0,gamma,,,\n")),(0,n.kt)("p",null,"where alpha is a branching ratio if you include multiple versions of the same reaction and gamma is the energy barrier to the reaction. Including this reaction in your MakeRates input will result in two reactions being created in the actual network: one with gas phase products and one with grain surface products. This is to account for the desorption of products of exothermic reactions and the branching ratio is determined within UCLCHEM using the binding energy of the products and energy released by the reaction following ",(0,n.kt)("a",{parentName:"p",href:"https://www.aanda.org/10.1051/0004-6361/201525981"},"Minissale et al. 2016"),". 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Grid",i={unversionedId:"running_a_grid",id:"version-v3.3.0/running_a_grid",title:"Running a Grid",description:"A common task is to run UCLCHEM over a grid of parameter combinations. This notebook sets up a simple approach to doing so for regular grids.",source:"@site/versioned_docs/version-v3.3.0/running_a_grid.md",sourceDirName:".",slug:"/running_a_grid",permalink:"/docs/running_a_grid",draft:!1,tags:[],version:"v3.3.0",frontMatter:{},sidebar:"docs",previous:{title:"Advanced Physical Modelling",permalink:"/docs/modelling_objects"},next:{title:"Chemical Analysis",permalink:"/docs/chemical_analysis"}},d={},c=[{value:"A Simple Grid",id:"a-simple-grid",level:2},{value:"Define Parameter Space",id:"define-parameter-space",level:3},{value:"Set up the model",id:"set-up-the-model",level:3},{value:"Run Grid",id:"run-grid",level:3},{value:"The Simple Way",id:"the-simple-way",level:4},{value:"The Fast Way",id:"the-fast-way",level:4},{value:"Checking Your Grid",id:"checking-your-grid",level:2},{value:"Complex Grid",id:"complex-grid",level:2},{value:"Summary",id:"summary",level:2}],p={toc:c};function m(e){var t=e.components,l=(0,r.Z)(e,o);return(0,a.kt)("wrapper",(0,n.Z)({},p,l,{components:t,mdxType:"MDXLayout"}),(0,a.kt)("h1",{id:"running-a-grid"},"Running a Grid"),(0,a.kt)("p",null,"A common task is to run UCLCHEM over a grid of parameter combinations. This notebook sets up a simple approach to doing so for regular grids."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"import uclchem\nimport numpy as np\nimport pandas as pd\nfrom multiprocessing import Pool\nimport os\n")),(0,a.kt)("h2",{id:"a-simple-grid"},"A Simple Grid"),(0,a.kt)("h3",{id:"define-parameter-space"},"Define Parameter Space"),(0,a.kt)("p",null,"First, we define our parameter space. We do this by using numpy and pandas to produce a table of all possible combinations of some parameters of interest."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'# This part can be substituted with any choice of grid\n#here we just vary the density, temperature and zeta \ntemperatures = np.linspace(10, 50, 3)\ndensities = np.logspace(4,6,3)\nzetas = np.logspace(1, 3, 3)\n\n#meshgrid will give all combinations, then we shape into columns and put into a table\nparameterSpace = np.asarray(np.meshgrid(temperatures,densities,zetas)).reshape(3, -1)\nmodel_table=pd.DataFrame(parameterSpace.T, columns=[\'temperature\',\'density\',\'zeta\'])\n\n#keep track of where each model output will be saved and make sure that folder exists\nmodel_table["outputFile"]=model_table.apply(lambda row: f"../grid_folder/{row.temperature}_{row.density}_{row.zeta}.csv", axis=1)\nprint(f"{model_table.shape[0]} models to run")\nif not os.path.exists("../grid_folder"):\n os.makedirs("../grid_folder")\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre"},"27 models to run\n")),(0,a.kt)("h3",{id:"set-up-the-model"},"Set up the model"),(0,a.kt)("p",null,"Next, we need a function that will run our model. 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I'll use the ",(0,a.kt)("inlineCode",{parentName:"p"},"head")," function just to run five rows as an example here."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"result=model_table.head().apply(run_model, axis=1)\n")),(0,a.kt)("h4",{id:"the-fast-way"},"The Fast Way"),(0,a.kt)("p",null,"Alternatively, we can use multiprocessing to run the models in parallel. That will allow us to run many models simulataneously and make use of all the cores available on our machine."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"def pool_func(x):\n i,row=x\n return run_model(row)\n\nwith Pool(processes=6) as pool:\n results = pool.map(pool_func, model_table.iterrows())\n")),(0,a.kt)("h2",{id:"checking-your-grid"},"Checking Your Grid"),(0,a.kt)("p",null,"After running, we should do two things. First, let's add ",(0,a.kt)("inlineCode",{parentName:"p"},"results")," to our dataframe as a new column. Positive results mean a successful UCLCHEM run and negative ones are unsuccessful. Then we can run each model through ",(0,a.kt)("inlineCode",{parentName:"p"},"check_element_conservation")," to check the integration was successful. We'll use both these things to flag models that failed in some way."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"def element_check(output_file):\n df=uclchem.analysis.read_output_file(output_file)\n #get conservation values\n conserves=uclchem.analysis.check_element_conservation(df)\n #check if any error is greater than 1%\n return all([float(x[:-1])<1 for x in conserves.values()])\n")),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'model_table["run_result"]=results\nmodel_table["elements_conserved"]=model_table["outputFile"].map(element_check)\n#check both conditions are met\nmodel_table["Successful"]=(model_table.run_result>=0) & (model_table.elements_conserved)\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"model_table.head()\n")),(0,a.kt)("div",null,(0,a.kt)("table",{border:"1",class:"dataframe"},(0,a.kt)("thead",null,(0,a.kt)("tr",null,(0,a.kt)("th",null),(0,a.kt)("th",null,"temperature"),(0,a.kt)("th",null,"density"),(0,a.kt)("th",null,"zeta"),(0,a.kt)("th",null,"outputFile"),(0,a.kt)("th",null,"run_result"),(0,a.kt)("th",null,"elements_conserved"),(0,a.kt)("th",null,"Successful"))),(0,a.kt)("tbody",null,(0,a.kt)("tr",null,(0,a.kt)("th",null,"0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_10.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"1"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"100.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_100.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"2"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"1000.0"),(0,a.kt)("td",null,"../grid_folder/10.0_10000.0_1000.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"3"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"../grid_folder/30.0_10000.0_10.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"4"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"100.0"),(0,a.kt)("td",null,"../grid_folder/30.0_10000.0_100.0.csv"),(0,a.kt)("td",null,"1"),(0,a.kt)("td",null,"True"),(0,a.kt)("td",null,"True"))))),(0,a.kt)("h2",{id:"complex-grid"},"Complex Grid"),(0,a.kt)("p",null,"The above was straightforward enough but what about a modelling a grid of shocks? Not only do we want to loop over relevant parameters, we also need to run a few preliminary models to give ourselves starting abundances. We'll start by defining two helper functions, one to run our preliminary cloud and one to run the shock."),(0,a.kt)("p",null,"Let's further imagine that we want to obtain the abundances of several species at the end of the model. We can use the ",(0,a.kt)("inlineCode",{parentName:"p"},"out_species")," parameter to specify which species we want to track and return them to our dataframe."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'out_species=["CO","H2O","CH3OH"]\n\ndef run_prelim(density):\n #basic set of parameters we\'ll use for this grid. \n ParameterDictionary = {"endatfinaldensity":True,\n "freefall": True,\n "initialDens":1e2,\n "finalDens": density,\n "initialTemp": 10.0,\n "abundSaveFile": f"../grid_folder/starts/{density:.0f}.csv",\n "baseAv":1}\n result = uclchem.model.cloud(param_dict=ParameterDictionary)\n return result\n\ndef run_model(row):\n i,row=row # we know we\'re receiving the iterrows() tuple\n #basic set of parameters we\'ll use for this grid. \n ParameterDictionary = {"endatfinaldensity":False,\n "freefall": False,\n "initialDens": row.density,\n "initialTemp": 10.0,\n "outputFile": row.outputFile,\n "abundLoadFile": f"../grid_folder/starts/{row.density:.0f}.csv",\n "finalTime":1.0e5,\n "abstol_factor":1e-18,\n "reltol":1e-12,\n "baseAv":1}\n result = uclchem.model.cshock(row.shock_velocity,param_dict=ParameterDictionary,out_species=out_species)\n #First check UCLCHEM\'s result flag to seeif it\'s positive, if it is return the abundances\n if result[0]>0:\n return result[:]\n #if not, return NaNs because model failed\n else:\n return([np.nan]*len(out_species))\n')),(0,a.kt)("p",null,"Then we define our parameter space again. We'll create two folders, one to store a set of initial abundances for each starting density in our model and another to store our shock outputs."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'# This part can be substituted with any choice of grid\n# here we just combine various initial and final densities into an easily iterable array\nshock_velocities = np.linspace(10, 50, 3)\ndensities = np.logspace(4,6,3)\n\nparameterSpace = np.asarray(np.meshgrid(shock_velocities,densities)).reshape(2, -1)\nmodel_table=pd.DataFrame(parameterSpace.T, columns=[\'shock_velocity\',\'density\'])\nmodel_table["outputFile"]=model_table.apply(lambda row: f"../grid_folder/shocks/{row.shock_velocity}_{row.density}.csv", axis=1)\nprint(f"{model_table.shape[0]} models to run")\n\nfor folder in ["starts","shocks"]:\n if not os.path.exists(f"../grid_folder/{folder}"):\n os.makedirs(f"../grid_folder/{folder}")\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre"},"9 models to run\n")),(0,a.kt)("p",null,"We can then run our preliminary models followed by our science models. The science models will return the abundances at the final time step of each run so we can unpack those directly to our dataframe."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"with Pool(processes=3) as pool:\n results = pool.map(run_prelim, densities)\n")),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'with Pool(processes=6) as pool:\n results = pool.map(run_model, model_table.iterrows())\nmodel_table[["Result","Dissipation Time"]+out_species]=results\n')),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},"model_table\n")),(0,a.kt)("div",null,(0,a.kt)("table",{border:"1",class:"dataframe"},(0,a.kt)("thead",null,(0,a.kt)("tr",null,(0,a.kt)("th",null),(0,a.kt)("th",null,"shock_velocity"),(0,a.kt)("th",null,"density"),(0,a.kt)("th",null,"outputFile"),(0,a.kt)("th",null,"Result"),(0,a.kt)("th",null,"Dissipation Time"),(0,a.kt)("th",null,"CO"),(0,a.kt)("th",null,"H2O"),(0,a.kt)("th",null,"CH3OH"))),(0,a.kt)("tbody",null,(0,a.kt)("tr",null,(0,a.kt)("th",null,"0"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"7.316441e-05"),(0,a.kt)("td",null,"4.355495e-06"),(0,a.kt)("td",null,"4.624479e-07")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"1"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"2.591790e-05"),(0,a.kt)("td",null,"2.113885e-05"),(0,a.kt)("td",null,"1.196330e-07")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"2"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"10000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_10000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"1171.898734"),(0,a.kt)("td",null,"1.320822e-05"),(0,a.kt)("td",null,"8.126066e-06"),(0,a.kt)("td",null,"1.989081e-08")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"3"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"1.082083e-07"),(0,a.kt)("td",null,"1.158740e-09"),(0,a.kt)("td",null,"3.697607e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"4"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"1.121259e-10"),(0,a.kt)("td",null,"3.789106e-10"),(0,a.kt)("td",null,"4.907284e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"5"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"100000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_100000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"117.189873"),(0,a.kt)("td",null,"2.454392e-10"),(0,a.kt)("td",null,"3.443643e-10"),(0,a.kt)("td",null,"6.454671e-10")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"6"),(0,a.kt)("td",null,"10.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/10.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"1.084005e-10"),(0,a.kt)("td",null,"3.565914e-11"),(0,a.kt)("td",null,"4.816630e-11")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"7"),(0,a.kt)("td",null,"30.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/30.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"1.897782e-10"),(0,a.kt)("td",null,"6.498499e-11"),(0,a.kt)("td",null,"7.847277e-12")),(0,a.kt)("tr",null,(0,a.kt)("th",null,"8"),(0,a.kt)("td",null,"50.0"),(0,a.kt)("td",null,"1000000.0"),(0,a.kt)("td",null,"../grid_folder/shocks/50.0_1000000.0.csv"),(0,a.kt)("td",null,"1.0"),(0,a.kt)("td",null,"11.718987"),(0,a.kt)("td",null,"2.167651e-10"),(0,a.kt)("td",null,"6.600196e-12"),(0,a.kt)("td",null,"3.412340e-12"))))),(0,a.kt)("h2",{id:"summary"},"Summary"),(0,a.kt)("p",null,"There are many ways to run grids of models and users will naturally develop their own methods. This notebook is just a simple example of how to run UCLCHEM for many parameter combinations whilst producing a useful output (the model_table) to keep track of all the combinations that were run. In a real script, we'd save the model file to csv at the end."),(0,a.kt)("p",null,"For much larger grids, it's recommended that you find a way to make your script robust to failure. Over a huge range of parameters, it is quite likely UCLCHEM will hit integration trouble for at least a few parameter combinations. Very occasionally, UCLCHEM will get caught in a loop where it fails to integrate and cannot adjust its strategy to manage it. This isn't a problem for small grids as the model can be stopped and the tolerances adjusted. However, for very large grids, you may end up locking all threads as they each get stuck on a different model. The best solution we've found for this case is to add a check so that models in your dataframe are skipped if their file already exists, this allows you to stop and restart the grid script as needed."))}m.isMDXComponent=!0}}]); \ No newline at end of file diff --git a/assets/js/b0746780.49d05f02.js b/assets/js/b0746780.49d05f02.js new file mode 100644 index 00000000..0c783e14 --- /dev/null +++ b/assets/js/b0746780.49d05f02.js @@ -0,0 +1 @@ +"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[3601],{3905:(e,t,r)=>{r.d(t,{Zo:()=>p,kt:()=>f});var n=r(7294);function o(e,t,r){return t in e?Object.defineProperty(e,t,{value:r,enumerable:!0,configurable:!0,writable:!0}):e[t]=r,e}function a(e,t){var r=Object.keys(e);if(Object.getOwnPropertySymbols){var n=Object.getOwnPropertySymbols(e);t&&(n=n.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),r.push.apply(r,n)}return r}function l(e){for(var t=1;t=0||(o[r]=e[r]);return o}(e,t);if(Object.getOwnPropertySymbols){var a=Object.getOwnPropertySymbols(e);for(n=0;n=0||Object.prototype.propertyIsEnumerable.call(e,r)&&(o[r]=e[r])}return o}var s=n.createContext({}),c=function(e){var t=n.useContext(s),r=t;return e&&(r="function"==typeof e?e(t):l(l({},t),e)),r},p=function(e){var t=c(e.components);return n.createElement(s.Provider,{value:t},e.children)},u={inlineCode:"code",wrapper:function(e){var t=e.children;return n.createElement(n.Fragment,{},t)}},d=n.forwardRef((function(e,t){var r=e.components,o=e.mdxType,a=e.originalType,s=e.parentName,p=i(e,["components","mdxType","originalType","parentName"]),d=c(r),f=o,m=d["".concat(s,".").concat(f)]||d[f]||u[f]||a;return r?n.createElement(m,l(l({ref:t},p),{},{components:r})):n.createElement(m,l({ref:t},p))}));function f(e,t){var r=arguments,o=t&&t.mdxType;if("string"==typeof e||o){var a=r.length,l=new Array(a);l[0]=d;var i={};for(var s in t)hasOwnProperty.call(t,s)&&(i[s]=t[s]);i.originalType=e,i.mdxType="string"==typeof e?e:o,l[1]=i;for(var c=2;c{r.r(t),r.d(t,{assets:()=>p,contentTitle:()=>s,default:()=>f,frontMatter:()=>i,metadata:()=>c,toc:()=>u});var n=r(7462),o=r(3366),a=(r(7294),r(3905)),l=["components"],i={id:"physics-collapse",title:"Collapse Models"},s=void 0,c={unversionedId:"physics-collapse",id:"version-v3.3.1/physics-collapse",title:"Collapse Models",description:"Main Contributors: Felix Priestley",source:"@site/versioned_docs/version-v3.3.1/physics-collapse.md",sourceDirName:".",slug:"/physics-collapse",permalink:"/docs/physics-collapse",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{id:"physics-collapse",title:"Collapse Models"},sidebar:"docs",previous:{title:"Shock Models",permalink:"/docs/physics-shocks"},next:{title:"Chemistry",permalink:"/docs/category/chemistry"}},p={},u=[],d={toc:u};function f(e){var t=e.components,r=(0,o.Z)(e,l);return(0,a.kt)("wrapper",(0,n.Z)({},d,r,{components:t,mdxType:"MDXLayout"}),(0,a.kt)("p",null,(0,a.kt)("strong",{parentName:"p"},"Main Contributors"),": Felix Priestley"),(0,a.kt)("p",null,"The freefall collapse function used to control the density in most UCLCHEM models is fairly simplistic. ",(0,a.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.3847/1538-3881/aac957"},"Priestley et al. 2018")," created the collapse model which parameterizes the density profile of a collapsing core as a function of time and radius. 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We've collected here some of the most common problems and hope they resolve most issues.",source:"@site/versioned_docs/version-v3.3.1/trouble-compile.md",sourceDirName:".",slug:"/trouble-compile",permalink:"/docs/trouble-compile",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{id:"trouble-compile",title:"Compilation Issues"},sidebar:"docs",previous:{title:"Chemical Analysis",permalink:"/docs/chemical_analysis"},next:{title:"Integration",permalink:"/docs/trouble-integration"}},u={},p=[{value:"Pip fails",id:"pip-fails",level:2},{value:"Windows Trouble",id:"windows-trouble",level:2},{value:"Mac Trouble",id:"mac-trouble",level:2},{value:"x86 Macs",id:"x86-macs",level:3},{value:"gfortran",id:"gfortran",level:4},{value:"conda-Xcode compatibility",id:"conda-xcode-compatibility",level:4},{value:"Apple silicon Macs",id:"apple-silicon-macs",level:3},{value:"Architectures",id:"architectures",level:2}],d={toc:p};function h(e){var t=e.components,o=(0,a.Z)(e,i);return(0,r.kt)("wrapper",(0,n.Z)({},d,o,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("p",null,"Given that UCLCHEM is supplied as source code, used across many machine types, and is a fairly complex model, things will occasionally go wrong. We've collected here some of the most common problems and hope they resolve most issues."),(0,r.kt)("h2",{id:"pip-fails"},"Pip fails"),(0,r.kt)("p",null,"Pip is a package manager for Python. It is used to install and manage Python packages but we're hijacking its set up process to ask it to compile UCLCHEM. If the compilation goes wrong, the error message is often a bit useless. Please go to ",(0,r.kt)("inlineCode",{parentName:"p"},"src/fortran_src")," in your terminal and type ",(0,r.kt)("inlineCode",{parentName:"p"},"make python"),". You will get a more useful error which you can then try to debug or send to the team."),(0,r.kt)("p",null,"Installing via pip may fail if your environment is not set up. Whilst pip will check that you have the necessary python libraries installed, it will not check that you have the necessary compilers. In order to compile you need gfortran which is packaged with the ",(0,r.kt)("a",{parentName:"p",href:"https://gcc.gnu.org/"},"gnu compiler")," suite. You also need make which is part of the GNU toolset. You can likely install these things through your operating system's package manager rather than from their websites."),(0,r.kt)("p",null,"Advanced users who do not wish to change compiler may want to check the Makefile. It can be found in ",(0,r.kt)("inlineCode",{parentName:"p"},"src/fortran_src/Makefile"),". There are variables to control the choice of compiler, compilation flags and the F2PY flags which tell numpy.f2py which fortran compiler was used. These can all be altered if you do not wish to use gfortran."),(0,r.kt)("h2",{id:"windows-trouble"},"Windows Trouble"),(0,r.kt)("p",null,"UCLCHEM was written on a GNU/Linux machine and therefore makes a lot of assumptions about how your environment is set up. Whilst these assumptions hold for basically all Linux (and most Mac) distributions, Windows users often run into trouble. You can attempt to install a GNU toolset through packages like MinGW but the most straightforward way we've found for Windows users is to use the Windows Subsystem for linux."),(0,r.kt)("p",null,"Open a powershell as an administrator and type ",(0,r.kt)("inlineCode",{parentName:"p"},"wsl --install")," to install the Windows Subsystem for Linux. It will then ask you to reboot. Once you've done this, you'll find Ubuntu in your Windows App Store. Installing this Ubuntu app will give you access to a terminal that is indistinguishable from one running on a Linux system but it will have access to all your Windows files. You can set up your linux environment with all necessary tools:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"sudo apt update\nsudo apt install make\nsudo apt install python3-pip\nsudo apt install gfortran\n")),(0,r.kt)("p",null,"and then you'll find your files in ",(0,r.kt)("inlineCode",{parentName:"p"},"/mnt"),". For example, your C: drive can be accessed via ",(0,r.kt)("inlineCode",{parentName:"p"},"cd /mnt/c"),". With the above tools installed, you'll be able to follow our basic install instructions and run UCLCHEM via your Ubuntu installation."),(0,r.kt)("h2",{id:"mac-trouble"},"Mac Trouble"),(0,r.kt)("p",null,"The troubleshooting for macbooks is divided into troubleshooting for macbooks using x86 architectures (Intel) and apple silicon ARM (M1/M2). You can see which type of chip you have via About This Mac."),(0,r.kt)("h3",{id:"x86-macs"},"x86 Macs"),(0,r.kt)("h4",{id:"gfortran"},"gfortran"),(0,r.kt)("p",null,"A problem Mac users commonly come across is that fortran codes compile but do not run because the gfortran libraries are not in the expected location. If you get an error like:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"Exception has occurred: ImportErrordlopen(/usr/local/lib/python3.9/site-packages/uclchemwrap.cpython-39-darwin.so, 2): Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib Referenced from: /usr/local/lib/python3.9/site-packages/uclchemwrap.cpython-39-darwin.so Reason: image not found\n")),(0,r.kt)("p",null,"then this is likely what has happened to you. You can fix it by following the instructions in ",(0,r.kt)("a",{parentName:"p",href:"https://stackoverflow.com/questions/57207357/dyld-library-not-loaded-usr-local-gfortran-lib-libgfortran-3-dylib-reason-im"},"this Stackoverflow post"),". "),(0,r.kt)("p",null,"However, the underlying problem is that Apple would prefer you do not use GNU compilers. As Mac OS updates come in, the exact issue may change. You will usually find many stackoverflow posts about your problem if you search for people having similar errors with gfortran on Mac. Many members of the UCLCHEM group also use Mac so do get in touch if you cannot find a solution.xit"),(0,r.kt)("h4",{id:"conda-xcode-compatibility"},"conda-Xcode compatibility"),(0,r.kt)("p",null,"Sometimes the version of the Xcode SDK is not compatible with the conda packages that are generated with\nan older version. 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This includes physical parameter values and all abundances at every time step.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"columnFile"),(0,l.kt)("td",{parentName:"tr",align:null},'"output/column.dat"'),(0,l.kt)("td",{parentName:"tr",align:null},"File to write specific species abundances, see outSpecies.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"writeStep"),(0,l.kt)("td",{parentName:"tr",align:null},"1"),(0,l.kt)("td",{parentName:"tr",align:null},"Writing to columnFile only happens every writeStep timesteps.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abundSaveFile"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"File to store final abundances at the end of the model so future models can use them as the initial abundances. If not provided, no file will be produced.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abundLoadFile"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"File from which to load initial abundances for the model, created through ",(0,l.kt)("inlineCode",{parentName:"td"},"abundSaveFile"),". If not provided, the model starts from elemental gas.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"outSpecies"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"A space separated list of species to output to columnFile. Supplied as a separate list argument to most python functions, see python API docs.")))),(0,l.kt)("h2",{id:"initial-abundances"},"Initial Abundances"),(0,l.kt)("p",null,(0,l.kt)("em",{parentName:"p"},"Unless otherwise specified, we take all abundances from Jenkins et al. 2009, using the heavily depleted case from Table 4.")),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"metallicity"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Scale the abundances of all elements heavier than He by this factor.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ion"),(0,l.kt)("td",{parentName:"tr",align:null},"2"),(0,l.kt)("td",{parentName:"tr",align:null},"Sets how much elemental C is initially atomic (0")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fh"),(0,l.kt)("td",{parentName:"tr",align:null},"0.5"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of H is always 1 by definition because abundances are relative to number of H nuclei. Use fh to set how much to initially put in atomic H, the rest goes to H2.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fhe"),(0,l.kt)("td",{parentName:"tr",align:null},"0.1"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of He.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fc"),(0,l.kt)("td",{parentName:"tr",align:null},"1.77d-04"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of C.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fo"),(0,l.kt)("td",{parentName:"tr",align:null},"3.34d-04"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of O.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fn"),(0,l.kt)("td",{parentName:"tr",align:null},"6.18d-05"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of N.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fs"),(0,l.kt)("td",{parentName:"tr",align:null},"3.51d-6"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of S.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fmg"),(0,l.kt)("td",{parentName:"tr",align:null},"2.256d-06"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Mg.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fsi"),(0,l.kt)("td",{parentName:"tr",align:null},"1.78d-06"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Si.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fcl"),(0,l.kt)("td",{parentName:"tr",align:null},"3.39d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Cl.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fp"),(0,l.kt)("td",{parentName:"tr",align:null},"7.78d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of P.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ffe"),(0,l.kt)("td",{parentName:"tr",align:null},"2.01d-7"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Fe.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ff"),(0,l.kt)("td",{parentName:"tr",align:null},"3.6d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"fp depleted 1/100 of solar from Asplund 2009.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fd"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"The following elements are not typically used. We do not recommend any particular value.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fli"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Li.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fna"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Na.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fpah"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of PAHs.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f15n"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 15N.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f13c"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 13C.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f18O"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 18O.")))),(0,l.kt)("h2",{id:"integration-controls"},"Integration Controls"),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"reltol"),(0,l.kt)("td",{parentName:"tr",align:null},"1d-8"),(0,l.kt)("td",{parentName:"tr",align:null},"Relative tolerance for integration, see ",(0,l.kt)("a",{parentName:"td",href:"/docs/trouble-integration"},"integration docs")," for advice.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abstol_factor"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-14"),(0,l.kt)("td",{parentName:"tr",align:null},"Absolute tolerance for integration is calculated by multiplying species abundance by this factor.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abstol_min"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-25"),(0,l.kt)("td",{parentName:"tr",align:null},"Minimum value absolute tolerances can take.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"MXSTEP"),(0,l.kt)("td",{parentName:"tr",align:null},"10000"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum steps allowed in integration before warning is thrown.")))),(0,l.kt)("h2",{id:"here-be-dragons"},"Here be Dragons"),(0,l.kt)("p",null,(0,l.kt)("em",{parentName:"p"},"These are not recommended to be changed unless you know what you are doing")),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxh2"),(0,l.kt)("td",{parentName:"tr",align:null},"1.21d3"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by H2 formation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxcr"),(0,l.kt)("td",{parentName:"tr",align:null},"1.21d3"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by cosmic ray ionisation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxuvcr"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d4"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by UV photons.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"epsilon"),(0,l.kt)("td",{parentName:"tr",align:null},"0.01"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per H2 formation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"uv_yield"),(0,l.kt)("td",{parentName:"tr",align:null},"0.1"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per UV photon.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"phi"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d5"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per cosmic ray ionisation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"uvcreff"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-3"),(0,l.kt)("td",{parentName:"tr",align:null},"Ratio of CR induced UV photons to ISRF UV photons.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"omega"),(0,l.kt)("td",{parentName:"tr",align:null},"0.5"),(0,l.kt)("td",{parentName:"tr",align:null},"Dust grain albedo.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"alpha"),(0,l.kt)("td",{parentName:"tr",align:null},"{1:0.0,2:0.0}"),(0,l.kt)("td",{parentName:"tr",align:null},"Set alpha coeffecients of reactions using a python dictionary where keys are reaction numbers and values are the 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You also need make which is part of the GNU toolset. You can likely install these things through your operating system's package manager rather than from their websites."),(0,r.kt)("p",null,"Advanced users who do not wish to change compiler may want to check the Makefile. It can be found in ",(0,r.kt)("inlineCode",{parentName:"p"},"src/fortran_src/Makefile"),". There are variables to control the choice of compiler, compilation flags and the F2PY flags which tell numpy.f2py which fortran compiler was used. These can all be altered if you do not wish to use gfortran."),(0,r.kt)("h2",{id:"windows-trouble"},"Windows Trouble"),(0,r.kt)("p",null,"UCLCHEM was written on a GNU/Linux machine and therefore makes a lot of assumptions about how your environment is set up. Whilst these assumptions hold for basically all Linux (and most Mac) distributions, Windows users often run into trouble. 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For example, your C: drive can be accessed via ",(0,r.kt)("inlineCode",{parentName:"p"},"cd /mnt/c"),". With the above tools installed, you'll be able to follow our basic install instructions and run UCLCHEM via your Ubuntu installation."),(0,r.kt)("h2",{id:"mac-trouble"},"Mac Trouble"),(0,r.kt)("p",null,"The troubleshooting for macbooks is divided into troubleshooting for macbooks using x86 architectures (Intel) and apple silicon ARM (M1/M2). You can see which type of chip you have via About This Mac."),(0,r.kt)("h3",{id:"x86-macs"},"x86 Macs"),(0,r.kt)("h4",{id:"gfortran"},"gfortran"),(0,r.kt)("p",null,"A problem Mac users commonly come across is that fortran codes compile but do not run because the gfortran libraries are not in the expected location. If you get an error like:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"Exception has occurred: ImportErrordlopen(/usr/local/lib/python3.9/site-packages/uclchemwrap.cpython-39-darwin.so, 2): Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib Referenced from: /usr/local/lib/python3.9/site-packages/uclchemwrap.cpython-39-darwin.so Reason: image not found\n")),(0,r.kt)("p",null,"then this is likely what has happened to you. You can fix it by following the instructions in ",(0,r.kt)("a",{parentName:"p",href:"https://stackoverflow.com/questions/57207357/dyld-library-not-loaded-usr-local-gfortran-lib-libgfortran-3-dylib-reason-im"},"this Stackoverflow post"),". "),(0,r.kt)("p",null,"However, the underlying problem is that Apple would prefer you do not use GNU compilers. As Mac OS updates come in, the exact issue may change. You will usually find many stackoverflow posts about your problem if you search for people having similar errors with gfortran on Mac. Many members of the UCLCHEM group also use Mac so do get in touch if you cannot find a solution.xit"),(0,r.kt)("h4",{id:"conda-xcode-compatibility"},"conda-Xcode compatibility"),(0,r.kt)("p",null,"Sometimes the version of the Xcode SDK is not compatible with the conda packages that are generated with\nan older version. This means you will have to downgrade the SDK you are using as seen in ",(0,r.kt)("a",{parentName:"p",href:"https://stackoverflow.com/questions/69236331/conda-macos-big-sur-ld-unsupported-tapi-file-type-tapi-tbd-in-yaml-file"},"this Stackoverflow post")),(0,r.kt)("h3",{id:"apple-silicon-macs"},"Apple silicon Macs"),(0,r.kt)("p",null,"If you by accident install any package that was meant for x86 architectures (brew, pip, conda etc.) you will encounter problems as Rosetta 2 does not seem to work well with the gfortran.\nCurrently we recommend uninstalling all packages/software that might cause interference with uclchcem, such as gfortran installed via brew and reinstalling everything using conda as listed in the ","[docs/start-basicuse]"," document."),(0,r.kt)("h2",{id:"architectures"},"Architectures"),(0,r.kt)("p",null,"F2PY defaults to x86_64 architecture. This is fine for most users, but if you are using a different architecture, you may need to specify this in the Makefile. 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This is unlikely to meet everybody's modelling needs and UCLCHEM is capable of modelling much more complex environments such as hot cores and shocks. In this tutorial, we model both a hot core and a shock to explore how these models work and to demonstrate the workflow that the UCLCHEM team normally follow.",source:"@site/versioned_docs/version-v3.3.1/modelling_objects.md",sourceDirName:".",slug:"/modelling_objects",permalink:"/docs/modelling_objects",draft:!1,tags:[],version:"v3.3.1",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{},sidebar:"docs",previous:{title:"Running Your First Models",permalink:"/docs/first_model"},next:{title:"Running a Grid",permalink:"/docs/running_a_grid"}},o={},c=[{value:"The Hot Core",id:"the-hot-core",level:2},{value:"Initial Conditions (Phase 1)",id:"initial-conditions-phase-1",level:3},{value:"Running the Science Model (Phase 2)",id:"running-the-science-model-phase-2",level:3},{value:"Checking the Result",id:"checking-the-result",level:3},{value:"Shocks",id:"shocks",level:2},{value:"C-shock",id:"c-shock",level:3},{value:"J-shock",id:"j-shock",level:3}],h={toc:c};function N(a){var e=a.components,r=(0,n.Z)(a,p);return(0,m.kt)("wrapper",(0,s.Z)({},h,r,{components:e,mdxType:"MDXLayout"}),(0,m.kt)("h1",{id:"advanced-physical-modelling"},"Advanced Physical Modelling"),(0,m.kt)("p",null,"In the previous tutorial, we simply modelled the chemistry of a static cloud for 1 Myr. This is unlikely to meet everybody's modelling needs and UCLCHEM is capable of modelling much more complex environments such as hot cores and shocks. In this tutorial, we model both a hot core and a shock to explore how these models work and to demonstrate the workflow that the UCLCHEM team normally follow."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},"import uclchem\nimport matplotlib.pyplot as plt\n")),(0,m.kt)("h2",{id:"the-hot-core"},"The Hot Core"),(0,m.kt)("h3",{id:"initial-conditions-phase-1"},"Initial Conditions (Phase 1)"),(0,m.kt)("p",null,"UCLCHEM typically starts with the gas in atomic/ionic form with no molecules. However, this clearly is not appropriate when modelling an object such as a hot core. In these objects, the gas is already evolved and there should be molecules in the gas phase as well as ice mantles on the dust. To allow for this, one must provide some initial abundances to the model. 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During this collapse, chemistry will occur and we can assume the final abundances of this model will be reasonable starting abundances for the hot core. "),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'# set a parameter dictionary for cloud collapse model\nparam_dict = {\n "endAtFinalDensity": False,#stop at finalTime\n "freefall": True,#increase density in freefall\n "initialDens": 1e2, #starting density\n "finalDens":1e6, #final density\n "initialTemp": 10.0,#temperature of gas\n "finalTime": 6.0e6, #final time\n "rout":0.1, #radius of cloud in pc\n "baseAv":1.0, #visual extinction at cloud edge.\n "abundSaveFile": "../examples/test-output/startcollapse.dat",#save final abundances to file\n "outputFile":"../examples/test-output/phase1-full.dat"\n\n}\nresult = uclchem.model.cloud(param_dict=param_dict)\nprint(result)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"[1]\n")),(0,m.kt)("p",null,"With that done, we now have a file containing the final abundances of a cloud of gas after this collapse: ",(0,m.kt)("inlineCode",{parentName:"p"},'param_dict["abundSaveFile"]')," we can pass this to our hot core model to use those abundances as our initial abundances."),(0,m.kt)("h3",{id:"running-the-science-model-phase-2"},"Running the Science Model (Phase 2)"),(0,m.kt)("p",null,"We need to change just a few things in ",(0,m.kt)("inlineCode",{parentName:"p"},"param_dict")," to set up the hot core model. The key one is that UCLCHEM saves final abundances to ",(0,m.kt)("inlineCode",{parentName:"p"},"abundSaveFile")," but loads them from ",(0,m.kt)("inlineCode",{parentName:"p"},"abundLoadFile")," so we need to swap that key over to make the abundances we just produced our initial abundances. "),(0,m.kt)("p",null,"We also want to turn off freefall and change how long the model runs for."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'#change other bits of input to set up phase 2\nparam_dict["initialDens"]=1e6\nparam_dict["finalTime"]=1e6\nparam_dict["freefall"]=False\n\n#freeze out is completely overwhelmed by thermal desorption\n#so turning it off has no effect on abundances but speeds up integrator.\nparam_dict["freezeFactor"]=0.0\n\nparam_dict["abstol_factor"]=1e-18\nparam_dict["reltol"]=1e-12\n\n#pop is dangerous, it removes the original key so you can\'t rerun this cell.\nparam_dict["abundLoadFile"]=param_dict.pop("abundSaveFile") \nparam_dict["outputFile"]="../examples/test-output/phase2-full.dat"\n\nresult=uclchem.model.hot_core(temp_indx=3,max_temperature=300.0,param_dict=param_dict)\n')),(0,m.kt)("p",null,"Note that we've changed made two changes to the parameters here which aren't strictly necessary but can be helpful in certain situations."),(0,m.kt)("p",null,"Since the gas temperature increases throughout a hot core model, freeze out is much slower than thermal desorption for all but the first few time steps. Turning it off doesn't affect the abundances but will speed up the solution."),(0,m.kt)("p",null,"We also change abstol and reltol here, largely to demonstrate their use. They control the integrator accuracy and whilst making them smaller does slow down successful runs, it can make runs complete that stall completely otherwise or give correct solutions where lower tolerances allow issues like element conservation failure to sneak in. If your code does not complete or element conservation fails, you can change them."),(0,m.kt)("h3",{id:"checking-the-result"},"Checking the Result"),(0,m.kt)("p",null,"With a successful run, we can check the output. We first load the file and check the abundance conservation, then we can plot it up."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'phase2_df=uclchem.analysis.read_output_file("../examples/test-output/phase2-full.dat")\nuclchem.analysis.check_element_conservation(phase2_df)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"{'H': '0.002%', 'N': '0.000%', 'C': '0.000%', 'O': '0.000%'}\n")),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'species=["CO","H2O","CH3OH","#CO","#H2O","#CH3OH","@H2O","@CO","@CH3OH"]\n\nfig,[ax,ax2]=plt.subplots(1,2,figsize=(16,9))\nax=uclchem.analysis.plot_species(ax,phase2_df,species)\nsettings=ax.set(yscale="log",xlim=(1e2,1e6),ylim=(1e-10,1e-2),\n xlabel="Time / years", \n ylabel="Fractional Abundance",xscale="log")\n\nax2.plot(phase2_df["Time"],phase2_df["Density"],color="black")\nax2.set(xscale="log")\nax3=ax2.twinx()\nax3.plot(phase2_df["Time"],phase2_df["gasTemp"],color="red")\nax2.set(xlabel="Time / year",ylabel="Density")\nax3.set(ylabel="Temperature",facecolor="red",xlim=(1e2,1e6))\nax3.tick_params(axis=\'y\', colors=\'red\')\n')),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"png",src:t(7384).Z,width:"997",height:"549"})),(0,m.kt)("p",null,"Here, we see the value of running a collapse phase before the science run. Having run a collapse, we start this model with well developed ices and having material in the surface and bulk allows us to properly model the effect of warm up in a hot core. For example, the @CO abundance is ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mo",{parentName:"mrow"},"\u223c"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"4")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"\\sim10^{-4}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.36687em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mrel"},"\u223c"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4")))))))))))))," and #CO is ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mo",{parentName:"mrow"},"\u223c"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"6")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"\\sim10^{-6}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.36687em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mrel"},"\u223c"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"6"))))))))))))),". As the gas warms to around 30K, the #CO abundance drops drastically as CO's binding energy is such that it is efficiently desorbed from the surface at this temperature. However, the rest of the CO is trapped in the bulk, surrounded by more strongly bound H2O molecules. Thus, the @CO abundance stays high until the gas reaches around 130K, when the H2O molecules are released along with the entire bulk."),(0,m.kt)("h2",{id:"shocks"},"Shocks"),(0,m.kt)("p",null,"Essentially the same process should be followed for shocks. Let's run a C-type and J-type shock through a gas of density ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mn",{parentName:"msup"},"4")),(0,m.kt)("mi",{parentName:"mrow"},"c"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"m"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"3")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"10^4 cm^{-3}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4")))))))),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"c"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"m"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3"))))))))))))),". Again, we first run a simple cloud model to obtain some reasonable starting abundances, then we can run the shocks."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'# set a parameter dictionary for phase 1 collapse model\n\nparam_dict = {\n "endAtFinalDensity": False,#stop at finalTime\n "freefall": True,#increase density in freefall\n "initialDens": 1e2, #starting density\n "finalDens":1e4, #final density\n "initialTemp": 10.0,#temperature of gas\n "finalTime": 6.0e6, #final time\n "rout":0.1, #radius of cloud in pc\n "baseAv":1.0, #visual extinction at cloud edge.\n "abundSaveFile": "../examples/test-output/shockstart.dat",\n}\nresult = uclchem.model.cloud(param_dict=param_dict)\n')),(0,m.kt)("h3",{id:"c-shock"},"C-shock"),(0,m.kt)("p",null,"We'll first run a c-shock. We'll run a 40 km s ",(0,m.kt)("span",{parentName:"p",className:"math 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Note that c-shock is the only model which returns an additional output in its result list. Not only is the first element the success flag indicating whether UCLCHEM completed, the second element is the dissipation time of the shock. We'll use that time to make our plots look nicer, cutting to a reasonable time. You can also obtain it from ",(0,m.kt)("inlineCode",{parentName:"p"},"uclchem.utils.cshock_dissipation_time()"),"."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'#change other bits of input to set up phase 2\nparam_dict["initialDens"]=1e4\nparam_dict["finalTime"]=1e6\nif "abundSaveFile" in param_dict:\n param_dict.pop("abundSaveFile")\nparam_dict["abundLoadFile"]="../examples/test-output/shockstart.dat"\nparam_dict["outputFile"]="../examples/test-output/cshock.dat"\n\n\nresult=uclchem.model.cshock(shock_vel=40,param_dict=param_dict)\nresult,dissipation_time=result\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"}," Cannot have freefall on during cshock\n setting freefall=0 and continuing\n")),(0,m.kt)("p",null,"The code completes fine. We do get a couple of warnings though. First, we're informed that ",(0,m.kt)("inlineCode",{parentName:"p"},"freefall")," must be set to False for the C-shock model. Then we get a few integrator warnings. These are not important and can be ignored as long as the element conservation looks ok. However, it is an indication that the integrator did struggle with these ODEs under these conditions."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'phase2_df=uclchem.analysis.read_output_file("../examples/test-output/cshock.dat")\nuclchem.analysis.check_element_conservation(phase2_df)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"{'H': '0.005%', 'N': '1.167%', 'C': '1.394%', 'O': '1.326%'}\n")),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'species=["CO","H2O","CH3OH","NH3","$CO","$H2O","$CH3OH","$NH3"]\n\nfig,[ax,ax2]=plt.subplots(1,2,figsize=(16,9))\nax=uclchem.analysis.plot_species(ax,phase2_df,species)\nsettings=ax.set(yscale="log",xlim=(1,20*dissipation_time),ylim=(1e-10,1e-2),\n xlabel="Time / years", \n ylabel="Fractional Abundance",xscale="log")\n\nax2.plot(phase2_df["Time"],phase2_df["Density"],color="black")\nax2.set(xscale="log")\nax3=ax2.twinx()\nax3.plot(phase2_df["Time"],phase2_df["gasTemp"],color="red")\nax2.set(xlabel="Time / year",ylabel="Density")\nax3.set(ylabel="Temperature",facecolor="red",xlim=(1,20*dissipation_time))\nax3.tick_params(axis=\'y\', colors=\'red\')\n')),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"png",src:t(4490).Z,width:"1003",height:"544"})),(0,m.kt)("h3",{id:"j-shock"},"J-shock"),(0,m.kt)("p",null,"Running a j-shock is a simple case of changing function. 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If a parameter is set to ",(0,l.kt)("inlineCode",{parentName:"em"},"True"),", then it is turned on. If it is set to ",(0,l.kt)("inlineCode",{parentName:"em"},"False"),", then it is turned off.")),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"freezeFactor"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Modify freeze out rate of gas parcels by this factor.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"endAtFinalDensity"),(0,l.kt)("td",{parentName:"tr",align:null},".False."),(0,l.kt)("td",{parentName:"tr",align:null},"Choose to end model at final density, otherwise end at final time.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"freefall"),(0,l.kt)("td",{parentName:"tr",align:null},".False."),(0,l.kt)("td",{parentName:"tr",align:null},"Controls whether models density increaes following freefall equation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"freefallFactor"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Modify freefall rate by factor, usually to slow it.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"desorb"),(0,l.kt)("td",{parentName:"tr",align:null},".True."),(0,l.kt)("td",{parentName:"tr",align:null},"Toggles all non-thermal desoprtion processes on or off.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"h2desorb"),(0,l.kt)("td",{parentName:"tr",align:null},".True."),(0,l.kt)("td",{parentName:"tr",align:null},"Individually toggle non-thermal desorption due to H2 formation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"crdesorb"),(0,l.kt)("td",{parentName:"tr",align:null},".True."),(0,l.kt)("td",{parentName:"tr",align:null},"Individually toggle non-thermal desorption due to cosmic rays.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"uvdesorb"),(0,l.kt)("td",{parentName:"tr",align:null},".True."),(0,l.kt)("td",{parentName:"tr",align:null},"Individually toggle non-thermal desorption due to uv photons.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"thermdesorb"),(0,l.kt)("td",{parentName:"tr",align:null},".True."),(0,l.kt)("td",{parentName:"tr",align:null},"Toggle continuous thermal desorption.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"instantSublimation"),(0,l.kt)("td",{parentName:"tr",align:null},".False."),(0,l.kt)("td",{parentName:"tr",align:null},"Toggle instantaneous sublimation of the ices at t")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"cosmicRayAttenuation"),(0,l.kt)("td",{parentName:"tr",align:null},".False."),(0,l.kt)("td",{parentName:"tr",align:null},"Use column density to attenuate cosmic ray ionisation rate following ",(0,l.kt)("a",{parentName:"td",href:"https://arxiv.org/abs/1803.09348"},"Padovani et al. 2018"),".")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ionModel"),(0,l.kt)("td",{parentName:"tr",align:null},"'L'"),(0,l.kt)("td",{parentName:"tr",align:null},"L/H model for cosmic ray attenuation ",(0,l.kt)("a",{parentName:"td",href:"https://arxiv.org/abs/1803.09348"},"Padovani et al. 2018"),".")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"improvedH2CRPDissociation"),(0,l.kt)("td",{parentName:"tr",align:null},".False."),(0,l.kt)("td",{parentName:"tr",align:null},"Use H2 CRP dissociation rate from ",(0,l.kt)("a",{parentName:"td",href:"https://arxiv.org/abs/1809.04168"},"Padovani et al. 2018b"),".")))),(0,l.kt)("h2",{id:"input-and-output"},"Input and Output"),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"outputFile"),(0,l.kt)("td",{parentName:"tr",align:null},'"output/full.dat"'),(0,l.kt)("td",{parentName:"tr",align:null},"File to write full output of UCLCHEM. This includes physical parameter values and all abundances at every time step.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"columnFile"),(0,l.kt)("td",{parentName:"tr",align:null},'"output/column.dat"'),(0,l.kt)("td",{parentName:"tr",align:null},"File to write specific species abundances, see outSpecies.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"writeStep"),(0,l.kt)("td",{parentName:"tr",align:null},"1"),(0,l.kt)("td",{parentName:"tr",align:null},"Writing to columnFile only happens every writeStep timesteps.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abundSaveFile"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"File to store final abundances at the end of the model so future models can use them as the initial abundances. If not provided, no file will be produced.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abundLoadFile"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"File from which to load initial abundances for the model, created through ",(0,l.kt)("inlineCode",{parentName:"td"},"abundSaveFile"),". If not provided, the model starts from elemental gas.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"outSpecies"),(0,l.kt)("td",{parentName:"tr",align:null},"None"),(0,l.kt)("td",{parentName:"tr",align:null},"A space separated list of species to output to columnFile. Supplied as a separate list argument to most python functions, see python API docs.")))),(0,l.kt)("h2",{id:"initial-abundances"},"Initial Abundances"),(0,l.kt)("p",null,(0,l.kt)("em",{parentName:"p"},"Unless otherwise specified, we take all abundances from Jenkins et al. 2009, using the heavily depleted case from Table 4.")),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"metallicity"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Scale the abundances of all elements heavier than He by this factor.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ion"),(0,l.kt)("td",{parentName:"tr",align:null},"2"),(0,l.kt)("td",{parentName:"tr",align:null},"Sets how much elemental C is initially atomic (0")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fh"),(0,l.kt)("td",{parentName:"tr",align:null},"0.5"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of H is always 1 by definition because abundances are relative to number of H nuclei. Use fh to set how much to initially put in atomic H, the rest goes to H2.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fhe"),(0,l.kt)("td",{parentName:"tr",align:null},"0.1"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of He.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fc"),(0,l.kt)("td",{parentName:"tr",align:null},"1.77d-04"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of C.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fo"),(0,l.kt)("td",{parentName:"tr",align:null},"3.34d-04"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of O.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fn"),(0,l.kt)("td",{parentName:"tr",align:null},"6.18d-05"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of N.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fs"),(0,l.kt)("td",{parentName:"tr",align:null},"3.51d-6"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of S.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fmg"),(0,l.kt)("td",{parentName:"tr",align:null},"2.256d-06"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Mg.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fsi"),(0,l.kt)("td",{parentName:"tr",align:null},"1.78d-06"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Si.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fcl"),(0,l.kt)("td",{parentName:"tr",align:null},"3.39d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Cl.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fp"),(0,l.kt)("td",{parentName:"tr",align:null},"7.78d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of P.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ffe"),(0,l.kt)("td",{parentName:"tr",align:null},"2.01d-7"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Fe.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ff"),(0,l.kt)("td",{parentName:"tr",align:null},"3.6d-08"),(0,l.kt)("td",{parentName:"tr",align:null},"fp depleted 1/100 of solar from Asplund 2009.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fd"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"The following elements are not typically used. We do not recommend any particular value.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fli"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Li.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fna"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total elemental abundance of Na.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"fpah"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of PAHs.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f15n"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 15N.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f13c"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 13C.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"f18O"),(0,l.kt)("td",{parentName:"tr",align:null},"0.0"),(0,l.kt)("td",{parentName:"tr",align:null},"Total initial abundance of 18O.")))),(0,l.kt)("h2",{id:"integration-controls"},"Integration Controls"),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"reltol"),(0,l.kt)("td",{parentName:"tr",align:null},"1d-8"),(0,l.kt)("td",{parentName:"tr",align:null},"Relative tolerance for integration, see ",(0,l.kt)("a",{parentName:"td",href:"/docs/trouble-integration"},"integration docs")," for advice.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abstol_factor"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-14"),(0,l.kt)("td",{parentName:"tr",align:null},"Absolute tolerance for integration is calculated by multiplying species abundance by this factor.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"abstol_min"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-25"),(0,l.kt)("td",{parentName:"tr",align:null},"Minimum value absolute tolerances can take.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"MXSTEP"),(0,l.kt)("td",{parentName:"tr",align:null},"10000"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum steps allowed in integration before warning is thrown.")))),(0,l.kt)("h2",{id:"here-be-dragons"},"Here be Dragons"),(0,l.kt)("p",null,(0,l.kt)("em",{parentName:"p"},"These are not recommended to be changed unless you know what you are doing")),(0,l.kt)("table",null,(0,l.kt)("thead",{parentName:"table"},(0,l.kt)("tr",{parentName:"thead"},(0,l.kt)("th",{parentName:"tr",align:null},"Parameter"),(0,l.kt)("th",{parentName:"tr",align:null},"Default Value"),(0,l.kt)("th",{parentName:"tr",align:null},"Description"))),(0,l.kt)("tbody",{parentName:"table"},(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxh2"),(0,l.kt)("td",{parentName:"tr",align:null},"1.21d3"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by H2 formation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxcr"),(0,l.kt)("td",{parentName:"tr",align:null},"1.21d3"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by cosmic ray ionisation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"ebmaxuvcr"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d4"),(0,l.kt)("td",{parentName:"tr",align:null},"Maximum binding energy of species desorbed by UV photons.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"epsilon"),(0,l.kt)("td",{parentName:"tr",align:null},"0.01"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per H2 formation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"uv_yield"),(0,l.kt)("td",{parentName:"tr",align:null},"0.1"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per UV photon.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"phi"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d5"),(0,l.kt)("td",{parentName:"tr",align:null},"Number of molecules desorbed per cosmic ray ionisation.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"uvcreff"),(0,l.kt)("td",{parentName:"tr",align:null},"1.0d-3"),(0,l.kt)("td",{parentName:"tr",align:null},"Ratio of CR induced UV photons to ISRF UV photons.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"omega"),(0,l.kt)("td",{parentName:"tr",align:null},"0.5"),(0,l.kt)("td",{parentName:"tr",align:null},"Dust grain albedo.")),(0,l.kt)("tr",{parentName:"tbody"},(0,l.kt)("td",{parentName:"tr",align:null},"alpha"),(0,l.kt)("td",{parentName:"tr",align:null},"{1:0.0,2:0.0}"),(0,l.kt)("td",{parentName:"tr",align:null},"Set alpha coeffecients of reactions using a python dictionary where keys are reaction numbers and values are the coefficients. 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During this collapse, chemistry will occur and we can assume the final abundances of this model will be reasonable starting abundances for the hot core. "),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'# set a parameter dictionary for cloud collapse model\nparam_dict = {\n "endAtFinalDensity": False,#stop at finalTime\n "freefall": True,#increase density in freefall\n "initialDens": 1e2, #starting density\n "finalDens":1e6, #final density\n "initialTemp": 10.0,#temperature of gas\n "finalTime": 6.0e6, #final time\n "rout":0.1, #radius of cloud in pc\n "baseAv":1.0, #visual extinction at cloud edge.\n "abundSaveFile": "../examples/test-output/startcollapse.dat",#save final abundances to file\n "outputFile":"../examples/test-output/phase1-full.dat"\n\n}\nresult = uclchem.model.cloud(param_dict=param_dict)\nprint(result)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"[1]\n")),(0,m.kt)("p",null,"With that done, we now have a file containing the final abundances of a cloud of gas after this collapse: ",(0,m.kt)("inlineCode",{parentName:"p"},'param_dict["abundSaveFile"]')," we can pass this to our hot core model to use those abundances as our initial abundances."),(0,m.kt)("h3",{id:"running-the-science-model-phase-2"},"Running the Science Model (Phase 2)"),(0,m.kt)("p",null,"We need to change just a few things in ",(0,m.kt)("inlineCode",{parentName:"p"},"param_dict")," to set up the hot core model. The key one is that UCLCHEM saves final abundances to ",(0,m.kt)("inlineCode",{parentName:"p"},"abundSaveFile")," but loads them from ",(0,m.kt)("inlineCode",{parentName:"p"},"abundLoadFile")," so we need to swap that key over to make the abundances we just produced our initial abundances. "),(0,m.kt)("p",null,"We also want to turn off freefall and change how long the model runs for."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'#change other bits of input to set up phase 2\nparam_dict["initialDens"]=1e6\nparam_dict["finalTime"]=1e6\nparam_dict["freefall"]=False\n\n#freeze out is completely overwhelmed by thermal desorption\n#so turning it off has no effect on abundances but speeds up integrator.\nparam_dict["freezeFactor"]=0.0\n\nparam_dict["abstol_factor"]=1e-18\nparam_dict["reltol"]=1e-12\n\n#pop is dangerous, it removes the original key so you can\'t rerun this cell.\nparam_dict["abundLoadFile"]=param_dict.pop("abundSaveFile") \nparam_dict["outputFile"]="../examples/test-output/phase2-full.dat"\n\nresult=uclchem.model.hot_core(temp_indx=3,max_temperature=300.0,param_dict=param_dict)\n')),(0,m.kt)("p",null,"Note that we've changed made two changes to the parameters here which aren't strictly necessary but can be helpful in certain situations."),(0,m.kt)("p",null,"Since the gas temperature increases throughout a hot core model, freeze out is much slower than thermal desorption for all but the first few time steps. 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We first load the file and check the abundance conservation, then we can plot it up."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'phase2_df=uclchem.analysis.read_output_file("../examples/test-output/phase2-full.dat")\nuclchem.analysis.check_element_conservation(phase2_df)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"{'H': '0.002%', 'N': '0.000%', 'C': '0.000%', 'O': '0.000%'}\n")),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'species=["CO","H2O","CH3OH","#CO","#H2O","#CH3OH","@H2O","@CO","@CH3OH"]\n\nfig,[ax,ax2]=plt.subplots(1,2,figsize=(16,9))\nax=uclchem.analysis.plot_species(ax,phase2_df,species)\nsettings=ax.set(yscale="log",xlim=(1e2,1e6),ylim=(1e-10,1e-2),\n xlabel="Time / years", \n ylabel="Fractional Abundance",xscale="log")\n\nax2.plot(phase2_df["Time"],phase2_df["Density"],color="black")\nax2.set(xscale="log")\nax3=ax2.twinx()\nax3.plot(phase2_df["Time"],phase2_df["gasTemp"],color="red")\nax2.set(xlabel="Time / year",ylabel="Density")\nax3.set(ylabel="Temperature",facecolor="red",xlim=(1e2,1e6))\nax3.tick_params(axis=\'y\', colors=\'red\')\n')),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"png",src:t(921).Z,width:"997",height:"549"})),(0,m.kt)("p",null,"Here, we see the value of running a collapse phase before the science run. Having run a collapse, we start this model with well developed ices and having material in the surface and bulk allows us to properly model the effect of warm up in a hot core. For example, the @CO abundance is ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mo",{parentName:"mrow"},"\u223c"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"4")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"\\sim10^{-4}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.36687em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mrel"},"\u223c"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4")))))))))))))," and #CO is ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mo",{parentName:"mrow"},"\u223c"),(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"6")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"\\sim10^{-6}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.36687em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mrel"},"\u223c"),(0,m.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"6"))))))))))))),". As the gas warms to around 30K, the #CO abundance drops drastically as CO's binding energy is such that it is efficiently desorbed from the surface at this temperature. However, the rest of the CO is trapped in the bulk, surrounded by more strongly bound H2O molecules. Thus, the @CO abundance stays high until the gas reaches around 130K, when the H2O molecules are released along with the entire bulk."),(0,m.kt)("h2",{id:"shocks"},"Shocks"),(0,m.kt)("p",null,"Essentially the same process should be followed for shocks. Let's run a C-type and J-type shock through a gas of density ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mn",{parentName:"msup"},"4")),(0,m.kt)("mi",{parentName:"mrow"},"c"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mi",{parentName:"msup"},"m"),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"3")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"10^4 cm^{-3}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"4")))))))),(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"c"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord mathnormal"},"m"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3"))))))))))))),". Again, we first run a simple cloud model to obtain some reasonable starting abundances, then we can run the shocks."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'# set a parameter dictionary for phase 1 collapse model\n\nparam_dict = {\n "endAtFinalDensity": False,#stop at finalTime\n "freefall": True,#increase density in freefall\n "initialDens": 1e2, #starting density\n "finalDens":1e4, #final density\n "initialTemp": 10.0,#temperature of gas\n "finalTime": 6.0e6, #final time\n "rout":0.1, #radius of cloud in pc\n "baseAv":1.0, #visual extinction at cloud edge.\n "abundSaveFile": "../examples/test-output/shockstart.dat",\n}\nresult = uclchem.model.cloud(param_dict=param_dict)\n')),(0,m.kt)("h3",{id:"c-shock"},"C-shock"),(0,m.kt)("p",null,"We'll first run a c-shock. We'll run a 40 km s ",(0,m.kt)("span",{parentName:"p",className:"math 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Note that c-shock is the only model which returns an additional output in its result list. Not only is the first element the success flag indicating whether UCLCHEM completed, the second element is the dissipation time of the shock. We'll use that time to make our plots look nicer, cutting to a reasonable time. You can also obtain it from ",(0,m.kt)("inlineCode",{parentName:"p"},"uclchem.utils.cshock_dissipation_time()"),"."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'#change other bits of input to set up phase 2\nparam_dict["initialDens"]=1e4\nparam_dict["finalTime"]=1e6\nif "abundSaveFile" in param_dict:\n param_dict.pop("abundSaveFile")\nparam_dict["abundLoadFile"]="../examples/test-output/shockstart.dat"\nparam_dict["outputFile"]="../examples/test-output/cshock.dat"\n\n\nresult=uclchem.model.cshock(shock_vel=40,param_dict=param_dict)\nresult,dissipation_time=result\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"}," Cannot have freefall on during cshock\n setting freefall=0 and continuing\n")),(0,m.kt)("p",null,"The code completes fine. We do get a couple of warnings though. First, we're informed that ",(0,m.kt)("inlineCode",{parentName:"p"},"freefall")," must be set to False for the C-shock model. Then we get a few integrator warnings. These are not important and can be ignored as long as the element conservation looks ok. However, it is an indication that the integrator did struggle with these ODEs under these conditions."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'phase2_df=uclchem.analysis.read_output_file("../examples/test-output/cshock.dat")\nuclchem.analysis.check_element_conservation(phase2_df)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"{'H': '0.005%', 'N': '1.167%', 'C': '1.394%', 'O': '1.326%'}\n")),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'species=["CO","H2O","CH3OH","NH3","$CO","$H2O","$CH3OH","$NH3"]\n\nfig,[ax,ax2]=plt.subplots(1,2,figsize=(16,9))\nax=uclchem.analysis.plot_species(ax,phase2_df,species)\nsettings=ax.set(yscale="log",xlim=(1,20*dissipation_time),ylim=(1e-10,1e-2),\n xlabel="Time / years", \n ylabel="Fractional Abundance",xscale="log")\n\nax2.plot(phase2_df["Time"],phase2_df["Density"],color="black")\nax2.set(xscale="log")\nax3=ax2.twinx()\nax3.plot(phase2_df["Time"],phase2_df["gasTemp"],color="red")\nax2.set(xlabel="Time / year",ylabel="Density")\nax3.set(ylabel="Temperature",facecolor="red",xlim=(1,20*dissipation_time))\nax3.tick_params(axis=\'y\', colors=\'red\')\n')),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"png",src:t(6669).Z,width:"1003",height:"544"})),(0,m.kt)("h3",{id:"j-shock"},"J-shock"),(0,m.kt)("p",null,"Running a j-shock is a simple case of changing function. We'll run a 10 km s ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"1")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^{-1}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"1")))))))))))))," shock through a gas of density ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("mn",{parentName:"mrow"},"1"),(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mn",{parentName:"msup"},"0"),(0,m.kt)("mn",{parentName:"msup"},"3"))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"10^3")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},"1"),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span",className:"mord"},"0"),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3"))))))))))))," cm ",(0,m.kt)("span",{parentName:"p",className:"math math-inline"},(0,m.kt)("span",{parentName:"span",className:"katex"},(0,m.kt)("span",{parentName:"span",className:"katex-mathml"},(0,m.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,m.kt)("semantics",{parentName:"math"},(0,m.kt)("mrow",{parentName:"semantics"},(0,m.kt)("msup",{parentName:"mrow"},(0,m.kt)("mrow",{parentName:"msup"}),(0,m.kt)("mrow",{parentName:"msup"},(0,m.kt)("mo",{parentName:"mrow"},"\u2212"),(0,m.kt)("mn",{parentName:"mrow"},"3")))),(0,m.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"^{-3}")))),(0,m.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,m.kt)("span",{parentName:"span",className:"base"},(0,m.kt)("span",{parentName:"span",className:"strut",style:{height:"0.8141079999999999em",verticalAlign:"0em"}}),(0,m.kt)("span",{parentName:"span",className:"mord"},(0,m.kt)("span",{parentName:"span"}),(0,m.kt)("span",{parentName:"span",className:"msupsub"},(0,m.kt)("span",{parentName:"span",className:"vlist-t"},(0,m.kt)("span",{parentName:"span",className:"vlist-r"},(0,m.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.8141079999999999em"}},(0,m.kt)("span",{parentName:"span",style:{top:"-3.063em",marginRight:"0.05em"}},(0,m.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,m.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"\u2212"),(0,m.kt)("span",{parentName:"span",className:"mord mtight"},"3")))))))))))))," gas this time. Note that nothing stops us using the intial abundances we produced for the c-shock. UCLCHEM will not check that the initial density matches the density of the ",(0,m.kt)("inlineCode",{parentName:"p"},"abundLoadFile"),". It may not always be a good idea to do this but we should remember the intial abundances really are just a rough approximation."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'param_dict["initialDens"]=1e3\nparam_dict["freefall"]=False #lets remember to turn it off this time\nparam_dict["reltol"]=1e-12\n\nshock_vel=10.0\n\nif "abundSaveFile" in param_dict:\n param_dict.pop("abundSaveFile")\nparam_dict["abundLoadFile"]="../examples/test-output/shockstart.dat"\nparam_dict["outputFile"]="../examples/test-output/jshock.dat"\n\n\nresult=uclchem.model.jshock(shock_vel=shock_vel,param_dict=param_dict)\n')),(0,m.kt)("p",null,"This time, we've turned off the freefall option and made reltol a little more stringent. The j-shock ends up running a bit slower but we get no warnings on this run."),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'phase2_df=uclchem.analysis.read_output_file(param_dict["outputFile"])\nuclchem.analysis.check_element_conservation(phase2_df)\n')),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre"},"{'H': '0.003%', 'N': '0.000%', 'C': '0.000%', 'O': '0.000%'}\n")),(0,m.kt)("pre",null,(0,m.kt)("code",{parentName:"pre",className:"language-python"},'species=["CO","H2O","CH3OH","NH3","$CO","$H2O","$CH3OH","$NH3"]\n\nfig,[ax,ax2]=plt.subplots(1,2,figsize=(16,9))\nax=uclchem.analysis.plot_species(ax,phase2_df,species)\nsettings=ax.set(yscale="log",xlim=(1e-7,1e6),ylim=(1e-10,1e-2),\n xlabel="Time / years", \n ylabel="Fractional Abundance",xscale="log")\n\nax2.plot(phase2_df["Time"],phase2_df["Density"],color="black")\nax2.set(xscale="log",yscale="log")\nax3=ax2.twinx()\nax3.plot(phase2_df["Time"],phase2_df["gasTemp"],color="red")\nax2.set(xlabel="Time / year",ylabel="Density")\nax3.set(ylabel="Temperature",facecolor="red",xlim=(1e-7,1e6))\nax3.tick_params(axis=\'y\', colors=\'red\')\n')),(0,m.kt)("p",null,(0,m.kt)("img",{alt:"png",src:t(5786).Z,width:"1003",height:"544"})),(0,m.kt)("p",null,"That's everything! We've run various science models using reasonable starting abundances that we produced by running a simple UCLCHEM model beforehand. One benefit of this method is that the abundances are consistent with the network. If we start with arbitrary, perhaps observationally motivated, abundances, it would be possible to initiate the model in a state our network could never produce. "),(0,m.kt)("p",null,"However, one should be aware of the limitations of this method. A freefall collapse from low density to high is not really how a molecular cloud forms and so the abundances are only approximately similar to values they'd truly have in a real cloud. Testing whether your results are sensitive to things like the time you run the preliminary for or the exact density is a good way to make sure these approximations are not problematic."),(0,m.kt)("p",null,"Bear in mind that you can use ",(0,m.kt)("inlineCode",{parentName:"p"},"abundSaveFile")," and ",(0,m.kt)("inlineCode",{parentName:"p"},"abundLoadFile")," in the same model run. This lets you chain model runs together. 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These provide the physical properties of a gas through time as it is subjected to a shock. Whilst the most accurate MHD shock models solve the chemistry, MHD and radiative transfer problems simulataneously, few of these models include chemistry as detailed as UCLCHEM. We assume that the MHD models on which our parameterizations were validated used detailed enough chemistry that the shock profiles could be accurately calculated. This means that more detailed chemistry can be safely post-processed using UCLCHEM, a parameterization simply means the user can select parameters freely rather than from a preset selection of profiles from another code such as ",(0,r.kt)("a",{parentName:"p",href:"http://cdsads.u-strasbg.fr/abs/2015A&A...578A..63F"},"MHDvode"),"."),(0,r.kt)("h3",{id:"c-shocks"},"C-Shocks"),(0,r.kt)("p",null,"The C-shock is based on the parameterization by ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361:20078054"},"Jimenez-Serra et al. 2008"),". It parameterizes the density, temperature and velocity profiles of c-shocks as a function of shock velocity, initial gas density and magnetic field. These were validated against the results of the detailed shock modelling of ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1046/j.1365-8711.2003.06716.x"},"Flower et al. 2003"),". Details of it's use can be found in ",(0,r.kt)("a",{parentName:"p",href:"/docs/pythonapi#uclchem.model.cshock"},"the c-shock function docs"),"."),(0,r.kt)("p",null,"A key value in this model is the dissipation length, which is the distance over which the velocity of the ions and the neutrals equalizes. In some sense, this is the extent of the C-shock, although post-shock cooling does continue for some distance after. The C-shock function will return the dissipation time (see ",(0,r.kt)("a",{parentName:"p",href:"/docs/physics-shocks#dimensions"},"below"),") and will also uses shorter timesteps for a number of years equal to twice the dissipation time in order to fully resolve the shock. The number of these time steps is controlled by an optional parameter."),(0,r.kt)("h3",{id:"j-shocks"},"J-shocks"),(0,r.kt)("p",null,"jshock is a similar parameterization for j-shocks from ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201936536"},"James et al.")," validated against more recent results from MHDvode (",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201525740"},"Flower et al. 2015"),"). See the ",(0,r.kt)("a",{parentName:"p",href:"/docs/pythonapi#uclchem.model.jshock"},"j-shock function docs")," for details."),(0,r.kt)("h2",{id:"dimensions"},"Dimensions"),(0,r.kt)("p",null,"Both shock models are intended to be run as single point models only and the code will return an error for ",(0,r.kt)("inlineCode",{parentName:"p"},"points > 1"),". However, you can look at the 1D profile of a shock by converting between time and distance. If we assume the shock is stationary, that is that it's structure is unchanged as it moves through a cloud of gas, then the points that are far away in time are the same as those far away in space."),(0,r.kt)("img",{src:"/img/shock.png",width:"600","margin-left":"40%"}),(0,r.kt)("p",null,"As an illustration, as a shock front moves through a cloud and first hits a parcel of gas, this is t=0 in our shock model output. 5000 years later, the shock front has moved on, thus the output of UCLCHEM at t=5000 years is the state of a parcel of gas that was first hit 5000 years ago and is now far behind the shock front."),(0,r.kt)("p",null,"By using the shock velocity, you can translate 5000 years to the distance between the parcel that was shocked 5000 years ago and the parcel that is just being reached by the shock front,"),(0,r.kt)("div",{className:"math math-display"},(0,r.kt)("span",{parentName:"div",className:"katex-display"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML",display:"block"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("mi",{parentName:"mrow"},"z"),(0,r.kt)("mo",{parentName:"mrow"},"="),(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"v"),(0,r.kt)("mi",{parentName:"msub"},"s")),(0,r.kt)("mi",{parentName:"mrow"},"t")),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"z= v_s t")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.43056em",verticalAlign:"0em"}}),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.04398em"}},"z"),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}}),(0,r.kt)("span",{parentName:"span",className:"mrel"},"="),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.76508em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.03588em"}},"v"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.03588em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"})))))),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal"},"t")))))),(0,r.kt)("p",null,"Thus the history of a single point in a shocked cloud that is output by UCLCHEM can also be translated to a snapshot of a cloud that covers distance z."),(0,r.kt)("h2",{id:"sputtering"},"Sputtering"),(0,r.kt)("p",null,"The C-shock model uses the sputtering process described by ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361:20078054"},"Jimenez-Serra et al. 2008"),". Briefly, we calculate the average energy imparted on the grains from a collision between the shocked gas and the grains. We then combine this with the collision rate and average yield for a given energy to calculate the sputtering rate which we integrate through time. 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This is the time at which the silicon abundance stops increasing in more detailed models, used as a proxy for when the ices are fully sputtered. 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Furthermore, temperatures typically reach a minimum of 1000 K meaning the thermal sublimation is almost complete. 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For Mac users with Apple silicon special installations instructions are listed below the regular installation instructions."),(0,r.kt)("h3",{id:"apple-siliconm1"},"Apple silicon/M1"),(0,r.kt)("p",null,"For this use case we recommend the usage of the package manager conda (the installer for the minimal version can be found ",(0,r.kt)("a",{parentName:"p",href:"https://docs.conda.io/en/latest/miniconda.html"},"here"),").\nEnsure that you install the apple silicon/M1 version, together with Xcode."),(0,r.kt)("admonition",{type:"caution"},(0,r.kt)("p",{parentName:"admonition"},"If you are on MacOS Ventura (13.X), you need to use ",(0,r.kt)("inlineCode",{parentName:"p"},"conda install -c conda-forge gfortran=12.2"),". Since at least fortran version 12 is needed for Ventura.")),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"conda create -n uclchem_osx\nconda activate uclchem_osx\nconda config --env --set subdir osx-arm64\nconda install python=3.10\nconda install gfortran\n")),(0,r.kt)("p",null,"After this, one can continue with the installation instructions above and install. In order to use\nUCLCHEM in a new terminal session one has to use the command ",(0,r.kt)("inlineCode",{parentName:"p"},"conda activate uclchem_osx"),"."),(0,r.kt)("h3",{id:"apple-intel"},"Apple Intel"),(0,r.kt)("p",null,"Similar instructions as for M1, but now with the x86_64 instruction set. Again this requires Xcode."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"conda create -n uclchem_osx\nconda activate uclchem_osx\nconda config --env --set subdir osx-64\nconda install python=3.9\nconda install clang\nconda install gfortran\n")),(0,r.kt)("p",null,"After this, one can continue with the installation instructions above and install. In order to use\nUCLCHEM in a new terminal session one has to use the command ",(0,r.kt)("inlineCode",{parentName:"p"},"conda activate uclchem_osx"),"."),(0,r.kt)("p",null,"If you encounter further issues please check ",(0,r.kt)("a",{parentName:"p",href:"/docs/trouble-compile"},"troubleshooting"),"."),(0,r.kt)("h2",{id:"installation"},"Installation"),(0,r.kt)("p",null,"UCLCHEM is designed to be compiled to a python library. Despite this, we cannot distribute it as a python package via pypi or similar because the user needs to be able to recompile their own version in order to change the network. 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The rest of the 'Getting Started' section focuses on creating a network and the various parameters the user can control. "),(0,r.kt)("h2",{id:"checking-your-install"},"Checking Your Install"),(0,r.kt)("p",null,"We provide several ways to get acquainted with the code including a series of ",(0,r.kt)("a",{parentName:"p",href:"/docs/category/tutorials"},"tutorials"),". Alternatively, there are python scripts in ",(0,r.kt)("inlineCode",{parentName:"p"},"scripts/")," that can be used as templates for running your own models and comprehensive documentation on the ",(0,r.kt)("a",{parentName:"p",href:"/docs/pythonapi"},"python API")," and ",(0,r.kt)("a",{parentName:"p",href:"/docs/parameters"},"parameters"),"."),(0,r.kt)("p",null,"However, if you simply want to check whether your new network is working, you can use the ",(0,r.kt)("inlineCode",{parentName:"p"},"scripts/run_uclchem_tests.py")," and ",(0,r.kt)("inlineCode",{parentName:"p"},"scripts/plot_uclchem_tests.py")," scripts. 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This is the time at which the silicon abundance stops increasing in more detailed models, used as a proxy for when the ices are fully sputtered. Thus it is likely that you will see a step change in the ice abundances where sputtering has not occurred yet in one time step and is complete in the second unless your timestep is very small."),(0,r.kt)("p",null,"The J-shock would begin with ",(0,r.kt)("span",{parentName:"p",className:"math math-inline"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"V"),(0,r.kt)("mi",{parentName:"msub"},"s"))),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"V_s")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.22222em"}},"V"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.22222em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"}))))))))))," as the initial drift velocity of the sputtering routine described above and would instantaneously sputter at t = 0 yr. Furthermore, temperatures typically reach a minimum of 1000 K meaning the thermal sublimation is almost complete. 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The C-shock function will return the dissipation time (see ",(0,r.kt)("a",{parentName:"p",href:"/docs/physics-shocks#dimensions"},"below"),") and will also uses shorter timesteps for a number of years equal to twice the dissipation time in order to fully resolve the shock. The number of these time steps is controlled by an optional parameter."),(0,r.kt)("h3",{id:"j-shocks"},"J-shocks"),(0,r.kt)("p",null,"jshock is a similar parameterization for j-shocks from ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201936536"},"James et al.")," validated against more recent results from MHDvode (",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361/201525740"},"Flower et al. 2015"),"). See the ",(0,r.kt)("a",{parentName:"p",href:"/docs/pythonapi#uclchem.model.jshock"},"j-shock function docs")," for details."),(0,r.kt)("h2",{id:"dimensions"},"Dimensions"),(0,r.kt)("p",null,"Both shock models are intended to be run as single point models only and the code will return an error for ",(0,r.kt)("inlineCode",{parentName:"p"},"points > 1"),". However, you can look at the 1D profile of a shock by converting between time and distance. If we assume the shock is stationary, that is that it's structure is unchanged as it moves through a cloud of gas, then the points that are far away in time are the same as those far away in space."),(0,r.kt)("img",{src:"/img/shock.png",width:"600","margin-left":"40%"}),(0,r.kt)("p",null,"As an illustration, as a shock front moves through a cloud and first hits a parcel of gas, this is t=0 in our shock model output. 5000 years later, the shock front has moved on, thus the output of UCLCHEM at t=5000 years is the state of a parcel of gas that was first hit 5000 years ago and is now far behind the shock front."),(0,r.kt)("p",null,"By using the shock velocity, you can translate 5000 years to the distance between the parcel that was shocked 5000 years ago and the parcel that is just being reached by the shock front,"),(0,r.kt)("div",{className:"math math-display"},(0,r.kt)("span",{parentName:"div",className:"katex-display"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML",display:"block"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("mi",{parentName:"mrow"},"z"),(0,r.kt)("mo",{parentName:"mrow"},"="),(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"v"),(0,r.kt)("mi",{parentName:"msub"},"s")),(0,r.kt)("mi",{parentName:"mrow"},"t")),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"z= v_s t")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.43056em",verticalAlign:"0em"}}),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.04398em"}},"z"),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}}),(0,r.kt)("span",{parentName:"span",className:"mrel"},"="),(0,r.kt)("span",{parentName:"span",className:"mspace",style:{marginRight:"0.2777777777777778em"}})),(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.76508em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.03588em"}},"v"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.03588em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"})))))),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal"},"t")))))),(0,r.kt)("p",null,"Thus the history of a single point in a shocked cloud that is output by UCLCHEM can also be translated to a snapshot of a cloud that covers distance z."),(0,r.kt)("h2",{id:"sputtering"},"Sputtering"),(0,r.kt)("p",null,"The C-shock model uses the sputtering process described by ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1051/0004-6361:20078054"},"Jimenez-Serra et al. 2008"),". Briefly, we calculate the average energy imparted on the grains from a collision between the shocked gas and the grains. We then combine this with the collision rate and average yield for a given energy to calculate the sputtering rate which we integrate through time. In practice, this sputtering is so quick that it happens almost instantaneously at ",(0,r.kt)("span",{parentName:"p",className:"math math-inline"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"t"),(0,r.kt)("mrow",{parentName:"msub"},(0,r.kt)("mi",{parentName:"mrow"},"s"),(0,r.kt)("mi",{parentName:"mrow"},"a"),(0,r.kt)("mi",{parentName:"mrow"},"t")))),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"t_{sat}")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.76508em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal"},"t"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.2805559999999999em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"0em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s"),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"a"),(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"t"))))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"})))))))))),", the saturation time. This is the time at which the silicon abundance stops increasing in more detailed models, used as a proxy for when the ices are fully sputtered. Thus it is likely that you will see a step change in the ice abundances where sputtering has not occurred yet in one time step and is complete in the second unless your timestep is very small."),(0,r.kt)("p",null,"The J-shock would begin with ",(0,r.kt)("span",{parentName:"p",className:"math math-inline"},(0,r.kt)("span",{parentName:"span",className:"katex"},(0,r.kt)("span",{parentName:"span",className:"katex-mathml"},(0,r.kt)("math",{parentName:"span",xmlns:"http://www.w3.org/1998/Math/MathML"},(0,r.kt)("semantics",{parentName:"math"},(0,r.kt)("mrow",{parentName:"semantics"},(0,r.kt)("msub",{parentName:"mrow"},(0,r.kt)("mi",{parentName:"msub"},"V"),(0,r.kt)("mi",{parentName:"msub"},"s"))),(0,r.kt)("annotation",{parentName:"semantics",encoding:"application/x-tex"},"V_s")))),(0,r.kt)("span",{parentName:"span",className:"katex-html","aria-hidden":"true"},(0,r.kt)("span",{parentName:"span",className:"base"},(0,r.kt)("span",{parentName:"span",className:"strut",style:{height:"0.83333em",verticalAlign:"-0.15em"}}),(0,r.kt)("span",{parentName:"span",className:"mord"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal",style:{marginRight:"0.22222em"}},"V"),(0,r.kt)("span",{parentName:"span",className:"msupsub"},(0,r.kt)("span",{parentName:"span",className:"vlist-t vlist-t2"},(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.151392em"}},(0,r.kt)("span",{parentName:"span",style:{top:"-2.5500000000000003em",marginLeft:"-0.22222em",marginRight:"0.05em"}},(0,r.kt)("span",{parentName:"span",className:"pstrut",style:{height:"2.7em"}}),(0,r.kt)("span",{parentName:"span",className:"sizing reset-size6 size3 mtight"},(0,r.kt)("span",{parentName:"span",className:"mord mathnormal mtight"},"s")))),(0,r.kt)("span",{parentName:"span",className:"vlist-s"},"\u200b")),(0,r.kt)("span",{parentName:"span",className:"vlist-r"},(0,r.kt)("span",{parentName:"span",className:"vlist",style:{height:"0.15em"}},(0,r.kt)("span",{parentName:"span"}))))))))))," as the initial drift velocity of the sputtering routine described above and would instantaneously sputter at t = 0 yr. Furthermore, temperatures typically reach a minimum of 1000 K meaning the thermal sublimation is almost complete. Thus, we do not need to worry about the sputtering process in the J-shock, we simply remove all grain material and add it to the gas at t = 0 yr."))}d.isMDXComponent=!0}}]); \ No newline at end of file diff --git a/assets/js/d26b1119.a5a3956a.js b/assets/js/d26b1119.a5a3956a.js deleted file mode 100644 index 39c9ba4b..00000000 --- a/assets/js/d26b1119.a5a3956a.js +++ /dev/null @@ -1 +0,0 @@ -"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[3053],{3905:(e,t,a)=>{a.d(t,{Zo:()=>c,kt:()=>h});var s=a(7294);function n(e,t,a){return t in e?Object.defineProperty(e,t,{value:a,enumerable:!0,configurable:!0,writable:!0}):e[t]=a,e}function r(e,t){var a=Object.keys(e);if(Object.getOwnPropertySymbols){var s=Object.getOwnPropertySymbols(e);t&&(s=s.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),a.push.apply(a,s)}return a}function i(e){for(var t=1;t=0||(n[a]=e[a]);return n}(e,t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);for(s=0;s=0||Object.prototype.propertyIsEnumerable.call(e,a)&&(n[a]=e[a])}return n}var l=s.createContext({}),p=function(e){var t=s.useContext(l),a=t;return e&&(a="function"==typeof e?e(t):i(i({},t),e)),a},c=function(e){var t=p(e.components);return s.createElement(l.Provider,{value:t},e.children)},m={inlineCode:"code",wrapper:function(e){var t=e.children;return s.createElement(s.Fragment,{},t)}},u=s.forwardRef((function(e,t){var a=e.components,n=e.mdxType,r=e.originalType,l=e.parentName,c=o(e,["components","mdxType","originalType","parentName"]),u=p(a),h=n,d=u["".concat(l,".").concat(h)]||u[h]||m[h]||r;return a?s.createElement(d,i(i({ref:t},c),{},{components:a})):s.createElement(d,i({ref:t},c))}));function h(e,t){var a=arguments,n=t&&t.mdxType;if("string"==typeof e||n){var r=a.length,i=new Array(r);i[0]=u;var o={};for(var l in t)hasOwnProperty.call(t,l)&&(o[l]=t[l]);o.originalType=e,o.mdxType="string"==typeof e?e:n,i[1]=o;for(var p=2;p{a.r(t),a.d(t,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>o,metadata:()=>p,toc:()=>m});var s=a(7462),n=a(3366),r=(a(7294),a(3905)),i=["components"],o={id:"network",title:"Creating a Network"},l=void 0,p={unversionedId:"network",id:"network",title:"Creating a Network",description:"MakeRates",source:"@site/docs/start-network.md",sourceDirName:".",slug:"/network",permalink:"/docs/next/network",draft:!1,tags:[],version:"current",lastUpdatedBy:"jonholdship",lastUpdatedAt:1653303814,formattedLastUpdatedAt:"May 23, 2022",frontMatter:{id:"network",title:"Creating a Network"},sidebar:"docs",previous:{title:"Installation",permalink:"/docs/next/"},next:{title:"Model Parameters",permalink:"/docs/next/parameters"}},c={},m=[{value:"MakeRates",id:"makerates",level:2},{value:"Input",id:"input",level:2},{value:"Default Network",id:"default-network",level:2},{value:"Outputs",id:"outputs",level:2},{value:"What MakeRates Does",id:"what-makerates-does",level:2},{value:"Creating your own Network",id:"creating-your-own-network",level:2},{value:"Species list",id:"species-list",level:4},{value:"Reaction list",id:"reaction-list",level:4},{value:"Three Phase Chemistry",id:"three-phase-chemistry",level:2}],u={toc:m};function h(e){var t=e.components,a=(0,n.Z)(e,i);return(0,r.kt)("wrapper",(0,s.Z)({},u,a,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h2",{id:"makerates"},"MakeRates"),(0,r.kt)("p",null,"In order to make a chemical model flexible, the ability to solve a user supplied chemical network is a must. UCLCHEM uses a preprocessing python script to turn csv lists of species and reactions into fortran files for use in the main code. This script is called MakeRates and can be found in the Makerates subdirectory of the repository. It combines a gas phase reaction database with user supplied lists of species and additional reactions into the necessary Fortran code to run UCLCHEM. It also supplies a number of human readable outputs."),(0,r.kt)("p",null,"In the sections below, we discuss how to build your network and set the inputs for MakeRates but once that is done, you can run MakeRates with the following commands:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"cd MakeRates\npython MakeRates.py\ncd ..\npip install .\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"Note the pip install at the end of the process. Any output from MakeRates requires that the code be recompiled because MakeRates produces new source code for UCLCHEM!")),(0,r.kt)("h2",{id:"input"},"Input"),(0,r.kt)("p",null,"Makerates is controlled using a yaml file ",(0,r.kt)("inlineCode",{parentName:"p"},"Makerates/user_settings.yaml"),". By changing the values in this file, you can create different networks. The default values of this file are copied below."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-yaml"},"#Your list of all species\nspecies_file : inputFiles/default_species.csv\n\n#core reactions from gas phase database\ndatabase_reaction_file : inputFiles/umist12-ucledit.csv\ndatabase_reaction_type : UMIST\n\n#set of additional reactions: eg grain network\ncustom_reaction_file : inputFiles/default_grain_network.csv\ncustom_reaction_type : UCL\n\n#whether to automatically expand to three phase network\nthree_phase : True\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"species_file")," is a csv list of species and their properties. We provide a default list and detailed instructions below."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"database_reaction_file")," is your first reaction file, we expect most users to use UMIST12 or KIDA2014 for this but you could create your own file from an alternative database. Makerates can read files formatted in the same manner as the UMIST or KIDA databases as well as our own simple csv format, the ",(0,r.kt)("inlineCode",{parentName:"p"},"database_reaction_type")," setting lets MakeRates know which and should be set to 'UMIST', 'KIDA', or 'UCL'."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"custom_reaction_file")," is an additional reaction file. In the example file, we include all of our grain surface reactions which is the intended use of this file. "),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"three_phase")," is a toggle that tells MakeRates whether to automatically expand your network into a three phase model."),(0,r.kt)("h2",{id:"default-network"},"Default Network"),(0,r.kt)("p",null,"A basic version of each of the required file is supplied in the repository. The network that MakeRates produces from those files is also include in the source code so that a new user who simply installs UCLCHEM without running MakeRates will be using our default network. These default files serve largely as examples of how the files should be formatted and we also describe each one below so that the user can produce their own network."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"We do not endorse the default network"),", we have simply produced a grain surface network that was relatively up to date in 2018. It produces reasonable ice mantle abundances for major species and ignores larger COMs. We strongly suggest any published work be based on a network in which the user has confidence. However, where the user is not greatly concerned with grain surface chemistry, the default network is a good starting point."),(0,r.kt)("h2",{id:"outputs"},"Outputs"),(0,r.kt)("p",null,"Outputs from MakeRates are automatically moved to the ",(0,r.kt)("inlineCode",{parentName:"p"},"src/")," directory so the user can ",(0,r.kt)("inlineCode",{parentName:"p"},"pip install .")," and update their installation of UCLCHEM to use their new network. However, by adding the parameter ",(0,r.kt)("inlineCode",{parentName:"p"},"output_directory")," to the yaml file, you can have all the files moved to a directory instead without copying them to your UCLCHEM src folder. If you do, the following files will be produced:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"network.f90 - Fortran arrays containing lists of species names and properties (mass, binding energy etc) as well as reaction reactants, products and rate coefficients."),(0,r.kt)("li",{parentName:"ul"},"odes.f90 - Code to calculate the rate of change of each species' abundance for the numerical solver"),(0,r.kt)("li",{parentName:"ul"},"species.csv - A list of all species in the network and their properties. Made for humans not UCLCHEM."),(0,r.kt)("li",{parentName:"ul"},"reactions.csv - A list of all reactions including reactants, products and coefficients. Made for humans not UCLCHEM.")),(0,r.kt)("h2",{id:"what-makerates-does"},"What MakeRates Does"),(0,r.kt)("p",null,"MakeRates does the following:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"Combines the two input reaction lists"),(0,r.kt)("li",{parentName:"ul"},"Filters to remove any reactions containing species not in the input species list"),(0,r.kt)("li",{parentName:"ul"},"Adds freeze out and desorption reactions for all species"),(0,r.kt)("li",{parentName:"ul"},"Creates branching reactions for Langmuir-Hinshelwood and Eley-Rideal reactions where products chemically desorb"),(0,r.kt)("li",{parentName:"ul"},"Optionally: creates additional reactions and species needed for a three phase network"),(0,r.kt)("li",{parentName:"ul"},"Does basic network consistency checks and alerts user of problems"),(0,r.kt)("li",{parentName:"ul"},"Writes fortran files for UCLCHEM"),(0,r.kt)("li",{parentName:"ul"},"Writes other output files")),(0,r.kt)("h2",{id:"creating-your-own-network"},"Creating your own Network"),(0,r.kt)("p",null,"To create your own network you need to produce a species list and a reaction list."),(0,r.kt)("h4",{id:"species-list"},"Species list"),(0,r.kt)("p",null,"The species list should simply be a list with one row per species in the network. Each row should contain the species name, mass, binding energy and enthalpy of formation. The latter two are only used for surface species so can be set to zero for the gas phase species. MakeRates will check the mass is correct for each species and alert you of discrepancies."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"C,12,0,0,0,0,0\n#CH4,16,960,0,0.7,0.667,-15.9\n")),(0,r.kt)("p",null,"In the above example, C is a gas phase species so we have set the mass but ignored the other variables. #CH4 is methane in the ice so we have additionally set a binding energy of 960 K and enthalpy of formation of -15.9 kcal/mol. The other three values (0, 0.7, 0.667) are desorption fractions that three phase chemistry networks ignore. For two phase networks, we mimic the multiple desorption events seen in TPD experiments by setting these fractions. See ",(0,r.kt)("a",{parentName:"p",href:"https://ui.adsabs.harvard.edu/abs/2004MNRAS.354.1141V/abstract"},"Viti et al. 2004")," for more information."),(0,r.kt)("p",null,"The enthalpy of formation for essentially any species can be found in chemical databases such as the ",(0,r.kt)("a",{parentName:"p",href:"https://webbook.nist.gov/"},"NIST web book"),". They're usually in kj/mol but the conversion to kcal/mol is easy enough and NIST has an option to switch values to kcal. A fantastic resource for binding energies is ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1016/j.molap.2017.01.002"},"Wakelam et al. 2017")," but these are harder to find in general. In the absolute worse case, you can sum up the binding energies of sub-groups in your molecule but this is pretty inaccurate."),(0,r.kt)("h4",{id:"reaction-list"},"Reaction list"),(0,r.kt)("p",null,"The second reaction list is intended to contain your surface network but can also be used to augment the gas phase databases by including additional gas phase reactions. The reaction list should be a list with one row per reaction and each row should be a comma separated list of 3 reactants, 4 products, three coefficients (alpha,beta,gamma) and a minimum and maximum temperature. Any missing values such as a third reactant can be left blank. In particular, the temperatures are optional but can be useful when you include multiple versions of the same reaction. In that case, UCLCHEM will only use each one within its specified temperature range."),(0,r.kt)("p",null,"The third reactant can be used as a keyword to tell MakeRates what kind of reaction is occuring. In the absence of a keyword, MakeRates and UCLCHEM will treat any reaction as a gas-phase two body reaction. Two keywords the user may wish to use are ER and LH for Eley-Rideal and Langmuir-Hinshelwood reactions respectively (see ",(0,r.kt)("a",{parentName:"p",href:"grain/"},"Grain Chemisty"),"). If a keyword is not added, UCLCHEM will assume a reaction between two surface reactions follows a Kooji-Arrhenius equation."),(0,r.kt)("p",null,"Two other useful reactions types to include are FREEZE and DESORB. Makerates adds freeze out and desorption reactions for every species, assuming they remain unchanged by the process. For example, CO in the gas becomes #CO on the grain. If you would instead like to specify the products, you can include a reaction:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"H3O+,FREEZE,,#H2O,H,,,1,0,0,,,\n#HPN,DESORB,,HPN+,,,,1,0,0,,,\n")),(0,r.kt)("p",null,"which will override the desorption or freeze out products of a species. "),(0,r.kt)("h2",{id:"three-phase-chemistry"},"Three Phase Chemistry"),(0,r.kt)("p",null,"The input ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," controls whether the ices are treated as a single phase or the surface is treated separated to the bulk. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to true, the chemical network will have gas, grain surface, and bulk ice chemistry. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to false, the chemical network will have gas and grain surface chemistry."),(0,r.kt)("p",null,"When true, MakeRates will create the bulk ice chemistry by duplicating the surface species and reactions in your input files. The difference will be that, unless you specifically override the bulk binding energy, every species in the bulk has a binding energy equal to the H2O binding energy. It will also add terms to the ODEs to allow transfer between the bulk and the surface. See the chemistry sections for more information."),(0,r.kt)("p",null,'You can override the binding energy of material in the bulk by explicitly including the bulk species in your species file rather than allowing MakeRates to automatically add it. Bulk species are designated with an "@". For example, "H2O" is gas phase H',(0,r.kt)("span",{parentName:"p",className:"math 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If you set the binding energy to "Inf", the species will not leave the grains during thermal desorption. This allows you to model refractory species in the bulk.'))}h.isMDXComponent=!0}}]); \ No newline at end of file diff --git a/assets/js/d26b1119.e35bc5a5.js b/assets/js/d26b1119.e35bc5a5.js new file mode 100644 index 00000000..13254e9f --- /dev/null +++ b/assets/js/d26b1119.e35bc5a5.js @@ -0,0 +1 @@ +"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[3053],{3905:(e,t,a)=>{a.d(t,{Zo:()=>c,kt:()=>h});var s=a(7294);function n(e,t,a){return t in e?Object.defineProperty(e,t,{value:a,enumerable:!0,configurable:!0,writable:!0}):e[t]=a,e}function r(e,t){var a=Object.keys(e);if(Object.getOwnPropertySymbols){var s=Object.getOwnPropertySymbols(e);t&&(s=s.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),a.push.apply(a,s)}return a}function i(e){for(var t=1;t=0||(n[a]=e[a]);return n}(e,t);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);for(s=0;s=0||Object.prototype.propertyIsEnumerable.call(e,a)&&(n[a]=e[a])}return n}var l=s.createContext({}),p=function(e){var t=s.useContext(l),a=t;return e&&(a="function"==typeof e?e(t):i(i({},t),e)),a},c=function(e){var t=p(e.components);return s.createElement(l.Provider,{value:t},e.children)},m={inlineCode:"code",wrapper:function(e){var t=e.children;return s.createElement(s.Fragment,{},t)}},u=s.forwardRef((function(e,t){var a=e.components,n=e.mdxType,r=e.originalType,l=e.parentName,c=o(e,["components","mdxType","originalType","parentName"]),u=p(a),h=n,d=u["".concat(l,".").concat(h)]||u[h]||m[h]||r;return a?s.createElement(d,i(i({ref:t},c),{},{components:a})):s.createElement(d,i({ref:t},c))}));function h(e,t){var a=arguments,n=t&&t.mdxType;if("string"==typeof e||n){var r=a.length,i=new Array(r);i[0]=u;var o={};for(var l in t)hasOwnProperty.call(t,l)&&(o[l]=t[l]);o.originalType=e,o.mdxType="string"==typeof e?e:n,i[1]=o;for(var p=2;p{a.r(t),a.d(t,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>o,metadata:()=>p,toc:()=>m});var s=a(7462),n=a(3366),r=(a(7294),a(3905)),i=["components"],o={id:"network",title:"Creating a Network"},l=void 0,p={unversionedId:"network",id:"network",title:"Creating a Network",description:"MakeRates",source:"@site/docs/start-network.md",sourceDirName:".",slug:"/network",permalink:"/docs/next/network",draft:!1,tags:[],version:"current",lastUpdatedBy:"Gijs Vermari\xebn",lastUpdatedAt:1697189829,formattedLastUpdatedAt:"Oct 13, 2023",frontMatter:{id:"network",title:"Creating a Network"},sidebar:"docs",previous:{title:"Installation",permalink:"/docs/next/"},next:{title:"Model Parameters",permalink:"/docs/next/parameters"}},c={},m=[{value:"MakeRates",id:"makerates",level:2},{value:"Input",id:"input",level:2},{value:"Default Network",id:"default-network",level:2},{value:"Outputs",id:"outputs",level:2},{value:"What MakeRates Does",id:"what-makerates-does",level:2},{value:"Creating your own Network",id:"creating-your-own-network",level:2},{value:"Species list",id:"species-list",level:4},{value:"Reaction list",id:"reaction-list",level:4},{value:"Three Phase Chemistry",id:"three-phase-chemistry",level:2}],u={toc:m};function h(e){var t=e.components,a=(0,n.Z)(e,i);return(0,r.kt)("wrapper",(0,s.Z)({},u,a,{components:t,mdxType:"MDXLayout"}),(0,r.kt)("h2",{id:"makerates"},"MakeRates"),(0,r.kt)("p",null,"In order to make a chemical model flexible, the ability to solve a user supplied chemical network is a must. UCLCHEM uses a preprocessing python script to turn csv lists of species and reactions into fortran files for use in the main code. This script is called MakeRates and can be found in the Makerates subdirectory of the repository. It combines a gas phase reaction database with user supplied lists of species and additional reactions into the necessary Fortran code to run UCLCHEM. It also supplies a number of human readable outputs."),(0,r.kt)("p",null,"In the sections below, we discuss how to build your network and set the inputs for MakeRates but once that is done, you can run MakeRates with the following commands:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-bash"},"cd MakeRates\npython MakeRates.py\ncd ..\npip install -e . \n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"Note the pip install at the end of the process. Any output from MakeRates requires that the code be recompiled because MakeRates produces new source code for UCLCHEM!")),(0,r.kt)("h2",{id:"input"},"Input"),(0,r.kt)("p",null,"Makerates is controlled using a yaml file ",(0,r.kt)("inlineCode",{parentName:"p"},"Makerates/user_settings.yaml"),". By changing the values in this file, you can create different networks. The default values of this file are copied below."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre",className:"language-yaml"},"#Your list of all species\nspecies_file : inputFiles/default_species.csv\n\n#core reactions from gas phase database\ndatabase_reaction_file : inputFiles/umist12-ucledit.csv\ndatabase_reaction_type : UMIST\n\n#set of additional reactions: eg grain network\ncustom_reaction_file : inputFiles/default_grain_network.csv\ncustom_reaction_type : UCL\n\n#whether to automatically expand to three phase network\nthree_phase : True\n")),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"species_file")," is a csv list of species and their properties. We provide a default list and detailed instructions below."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"database_reaction_file")," is your first reaction file, we expect most users to use UMIST12 or KIDA2014 for this but you could create your own file from an alternative database. Makerates can read files formatted in the same manner as the UMIST or KIDA databases as well as our own simple csv format, the ",(0,r.kt)("inlineCode",{parentName:"p"},"database_reaction_type")," setting lets MakeRates know which and should be set to 'UMIST', 'KIDA', or 'UCL'."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"custom_reaction_file")," is an additional reaction file. In the example file, we include all of our grain surface reactions which is the intended use of this file. "),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"three_phase")," is a toggle that tells MakeRates whether to automatically expand your network into a three phase model."),(0,r.kt)("h2",{id:"default-network"},"Default Network"),(0,r.kt)("p",null,"A basic version of each of the required file is supplied in the repository. The network that MakeRates produces from those files is also include in the source code so that a new user who simply installs UCLCHEM without running MakeRates will be using our default network. These default files serve largely as examples of how the files should be formatted and we also describe each one below so that the user can produce their own network."),(0,r.kt)("p",null,(0,r.kt)("strong",{parentName:"p"},"We do not endorse the default network"),", we have simply produced a grain surface network that was relatively up to date in 2018. It produces reasonable ice mantle abundances for major species and ignores larger COMs. We strongly suggest any published work be based on a network in which the user has confidence. However, where the user is not greatly concerned with grain surface chemistry, the default network is a good starting point."),(0,r.kt)("h2",{id:"outputs"},"Outputs"),(0,r.kt)("p",null,"Outputs from MakeRates are automatically moved to the ",(0,r.kt)("inlineCode",{parentName:"p"},"src/")," directory so the user can ",(0,r.kt)("inlineCode",{parentName:"p"},"pip install .")," and update their installation of UCLCHEM to use their new network. However, by adding the parameter ",(0,r.kt)("inlineCode",{parentName:"p"},"output_directory")," to the yaml file, you can have all the files moved to a directory instead without copying them to your UCLCHEM src folder. If you do, the following files will be produced:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"network.f90 - Fortran arrays containing lists of species names and properties (mass, binding energy etc) as well as reaction reactants, products and rate coefficients."),(0,r.kt)("li",{parentName:"ul"},"odes.f90 - Code to calculate the rate of change of each species' abundance for the numerical solver"),(0,r.kt)("li",{parentName:"ul"},"species.csv - A list of all species in the network and their properties. Made for humans not UCLCHEM."),(0,r.kt)("li",{parentName:"ul"},"reactions.csv - A list of all reactions including reactants, products and coefficients. Made for humans not UCLCHEM.")),(0,r.kt)("h2",{id:"what-makerates-does"},"What MakeRates Does"),(0,r.kt)("p",null,"MakeRates does the following:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},"Combines the two input reaction lists"),(0,r.kt)("li",{parentName:"ul"},"Filters to remove any reactions containing species not in the input species list"),(0,r.kt)("li",{parentName:"ul"},"Adds freeze out and desorption reactions for all species"),(0,r.kt)("li",{parentName:"ul"},"Creates branching reactions for Langmuir-Hinshelwood and Eley-Rideal reactions where products chemically desorb"),(0,r.kt)("li",{parentName:"ul"},"Optionally: creates additional reactions and species needed for a three phase network"),(0,r.kt)("li",{parentName:"ul"},"Does basic network consistency checks and alerts user of problems"),(0,r.kt)("li",{parentName:"ul"},"Writes fortran files for UCLCHEM"),(0,r.kt)("li",{parentName:"ul"},"Writes other output files")),(0,r.kt)("h2",{id:"creating-your-own-network"},"Creating your own Network"),(0,r.kt)("p",null,"To create your own network you need to produce a species list and a reaction list."),(0,r.kt)("h4",{id:"species-list"},"Species list"),(0,r.kt)("p",null,"The species list should simply be a list with one row per species in the network. Each row should contain the species name, mass, binding energy and enthalpy of formation. The latter two are only used for surface species so can be set to zero for the gas phase species. MakeRates will check the mass is correct for each species and alert you of discrepancies."),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"C,12,0,0,0,0,0\n#CH4,16,960,0,0.7,0.667,-15.9\n")),(0,r.kt)("p",null,"In the above example, C is a gas phase species so we have set the mass but ignored the other variables. #CH4 is methane in the ice so we have additionally set a binding energy of 960 K and enthalpy of formation of -15.9 kcal/mol. The other three values (0, 0.7, 0.667) are desorption fractions that three phase chemistry networks ignore. For two phase networks, we mimic the multiple desorption events seen in TPD experiments by setting these fractions. See ",(0,r.kt)("a",{parentName:"p",href:"https://ui.adsabs.harvard.edu/abs/2004MNRAS.354.1141V/abstract"},"Viti et al. 2004")," for more information."),(0,r.kt)("p",null,"The enthalpy of formation for essentially any species can be found in chemical databases such as the ",(0,r.kt)("a",{parentName:"p",href:"https://webbook.nist.gov/"},"NIST web book"),". They're usually in kj/mol but the conversion to kcal/mol is easy enough and NIST has an option to switch values to kcal. A fantastic resource for binding energies is ",(0,r.kt)("a",{parentName:"p",href:"https://dx.doi.org/10.1016/j.molap.2017.01.002"},"Wakelam et al. 2017")," but these are harder to find in general. In the absolute worse case, you can sum up the binding energies of sub-groups in your molecule but this is pretty inaccurate."),(0,r.kt)("h4",{id:"reaction-list"},"Reaction list"),(0,r.kt)("p",null,"The second reaction list is intended to contain your surface network but can also be used to augment the gas phase databases by including additional gas phase reactions. The reaction list should be a list with one row per reaction and each row should be a comma separated list of 3 reactants, 4 products, three coefficients (alpha,beta,gamma) and a minimum and maximum temperature. Any missing values such as a third reactant can be left blank. In particular, the temperatures are optional but can be useful when you include multiple versions of the same reaction. In that case, UCLCHEM will only use each one within its specified temperature range."),(0,r.kt)("p",null,"The third reactant can be used as a keyword to tell MakeRates what kind of reaction is occuring. In the absence of a keyword, MakeRates and UCLCHEM will treat any reaction as a gas-phase two body reaction. Two keywords the user may wish to use are ER and LH for Eley-Rideal and Langmuir-Hinshelwood reactions respectively (see ",(0,r.kt)("a",{parentName:"p",href:"grain/"},"Grain Chemisty"),"). If a keyword is not added, UCLCHEM will assume a reaction between two surface reactions follows a Kooji-Arrhenius equation."),(0,r.kt)("p",null,"Two other useful reactions types to include are FREEZE and DESORB. Makerates adds freeze out and desorption reactions for every species, assuming they remain unchanged by the process. For example, CO in the gas becomes #CO on the grain. If you would instead like to specify the products, you can include a reaction:"),(0,r.kt)("pre",null,(0,r.kt)("code",{parentName:"pre"},"H3O+,FREEZE,,#H2O,H,,,1,0,0,,,\n#HPN,DESORB,,HPN+,,,,1,0,0,,,\n")),(0,r.kt)("p",null,"which will override the desorption or freeze out products of a species. "),(0,r.kt)("h2",{id:"three-phase-chemistry"},"Three Phase Chemistry"),(0,r.kt)("p",null,"The input ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," controls whether the ices are treated as a single phase or the surface is treated separated to the bulk. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to true, the chemical network will have gas, grain surface, and bulk ice chemistry. If ",(0,r.kt)("inlineCode",{parentName:"p"},"three_phase")," is set to false, the chemical network will have gas and grain surface chemistry."),(0,r.kt)("p",null,"When true, MakeRates will create the bulk ice chemistry by duplicating the surface species and reactions in your input files. The difference will be that, unless you specifically override the bulk binding energy, every species in the bulk has a binding energy equal to the H2O binding energy. It will also add terms to the ODEs to allow transfer between the bulk and the surface. See the chemistry sections for more information."),(0,r.kt)("p",null,'You can override the binding energy of material in the bulk by explicitly including the bulk species in your species file rather than allowing MakeRates to automatically add it. Bulk species are designated with an "@". 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For example, you could introduce a new procedure that is valid Fortran but does not do what you want it to do. In these cases, you'll have to hunt the problem down yourself. We recommend running the test cases in ",(0,a.kt)("inlineCode",{parentName:"p"},"scripts/run_uclchem_tests.py")," and comparing the output to the ones in the example using the plot created by ",(0,a.kt)("inlineCode",{parentName:"p"},"scripts/plot_uclchem_tests.py"),". Sometimes, they'll be different because you introduced a change that you know will effect the chemistry. For example, you might have changed a desorption process and find the ice abundances change which is totally fine. However, if you see a change that is unexpected, you can investigate."),(0,a.kt)("p",null,"There's no better way to debug these errors than to simply print a lot of things to screen. 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That prints a statement of your choice as well as many of the parameters."),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-fortran"},'!do some processing\nCALL myNewSubroutine\nCALL simpleDebug("Param values after myNewSubroutine")\n')),(0,a.kt)("h2",{id:"common-error-sources"},"Common Error Sources"),(0,a.kt)("h3",{id:"variable-reset"},"Variable Reset"),(0,a.kt)("p",null,"If you notice errors that only occur when you run the code more than once in a python script, then a common source is the initial value that variables take in the code. Variable initialization done at the declaration stage of a module only happens once. That is why the vast majority of variables that are not fortran parameters (constants) are set to an initial value by defaultparameters.f90 or in the initialization subroutines of the physics-core, chemistry, and physics modules."),(0,a.kt)("p",null,"It's very common when editing the code or adding new variables to forget to do this and then to see unusual behaviour when you run multiple models in a row in python."))}h.isMDXComponent=!0}}]); \ No newline at end of file diff --git a/assets/js/fe21a616.8e43114f.js b/assets/js/fe21a616.8e43114f.js deleted file mode 100644 index 9be91237..00000000 --- a/assets/js/fe21a616.8e43114f.js +++ /dev/null @@ -1 +0,0 @@ -"use strict";(self.webpackChunk=self.webpackChunk||[]).push([[6982],{3905:(e,t,n)=>{n.d(t,{Zo:()=>c,kt:()=>h});var r=n(7294);function o(e,t,n){return t in e?Object.defineProperty(e,t,{value:n,enumerable:!0,configurable:!0,writable:!0}):e[t]=n,e}function a(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),n.push.apply(n,r)}return n}function i(e){for(var t=1;t=0||(o[n]=e[n]);return o}(e,t);if(Object.getOwnPropertySymbols){var a=Object.getOwnPropertySymbols(e);for(r=0;r=0||Object.prototype.propertyIsEnumerable.call(e,n)&&(o[n]=e[n])}return o}var l=r.createContext({}),u=function(e){var t=r.useContext(l),n=t;return e&&(n="function"==typeof e?e(t):i(i({},t),e)),n},c=function(e){var t=u(e.components);return r.createElement(l.Provider,{value:t},e.children)},p={inlineCode:"code",wrapper:function(e){var t=e.children;return r.createElement(r.Fragment,{},t)}},d=r.forwardRef((function(e,t){var n=e.components,o=e.mdxType,a=e.originalType,l=e.parentName,c=s(e,["components","mdxType","originalType","parentName"]),d=u(n),h=o,m=d["".concat(l,".").concat(h)]||d[h]||p[h]||a;return n?r.createElement(m,i(i({ref:t},c),{},{components:n})):r.createElement(m,i({ref:t},c))}));function h(e,t){var n=arguments,o=t&&t.mdxType;if("string"==typeof e||o){var a=n.length,i=new Array(a);i[0]=d;var s={};for(var l in t)hasOwnProperty.call(t,l)&&(s[l]=t[l]);s.originalType=e,s.mdxType="string"==typeof e?e:o,i[1]=s;for(var u=2;u{n.r(t),n.d(t,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>s,metadata:()=>u,toc:()=>p});var r=n(7462),o=n(3366),a=(n(7294),n(3905)),i=["components"],s={id:"dev-python-wrap",title:"Writing The Python Interface"},l=void 0,u={unversionedId:"dev-python-wrap",id:"version-v3.3.0/dev-python-wrap",title:"Writing The Python Interface",description:"The python interface is a relatively complex bit of code, a lot of work is put on the development side to make the user side a smooth experience. Writing the core of UCLCHEM in Fortran gives great performance benefits but compiling it to python with F2PY has its peculiarities. Here, we discuss the steps needed to adjust the code.",source:"@site/versioned_docs/version-v3.3.0/dev-python-wrap.md",sourceDirName:".",slug:"/dev-python-wrap",permalink:"/docs/dev-python-wrap",draft:!1,tags:[],version:"v3.3.0",frontMatter:{id:"dev-python-wrap",title:"Writing The Python Interface"},sidebar:"docs",previous:{title:"Overview of the Code",permalink:"/docs/dev-overview"},next:{title:"Debugging",permalink:"/docs/dev-debugging"}},c={},p=[{value:"The Fortran Side",id:"the-fortran-side",level:2},{value:"The Python Side",id:"the-python-side",level:2},{value:"Tips and Tricks",id:"tips-and-tricks",level:2}],d={toc:p};function h(e){var t=e.components,n=(0,o.Z)(e,i);return(0,a.kt)("wrapper",(0,r.Z)({},d,n,{components:t,mdxType:"MDXLayout"}),(0,a.kt)("p",null,"The python interface is a relatively complex bit of code, a lot of work is put on the development side to make the user side a smooth experience. Writing the core of UCLCHEM in Fortran gives great performance benefits but compiling it to python with F2PY has its peculiarities. Here, we discuss the steps needed to adjust the code."),(0,a.kt)("h2",{id:"the-fortran-side"},"The Fortran Side"),(0,a.kt)("p",null,"The fortran side is the more difficult. We define a module in ",(0,a.kt)("inlineCode",{parentName:"p"},"src/fortran_src/wrap.f90")," which is a Fortran module that F2PY will turn into a python module. Any subroutine declared in ",(0,a.kt)("inlineCode",{parentName:"p"},"wrap.f90")," will become a function in the Python module."),(0,a.kt)("p",null,"The most likely change you'll want to make is to add a physics module so we'll look at cloud as an example. In ",(0,a.kt)("inlineCode",{parentName:"p"},"wrap.f90")," cloud is declared:"),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-fortran"}," SUBROUTINE cloud(dictionary, outSpeciesIn,abundance_out,successFlag)\n USE cloud_mod\n\n CHARACTER(LEN=*) :: dictionary, outSpeciesIn\n DOUBLE PRECISION :: abundance_out(500)\n INTEGER :: successFlag\n !f2py intent(in) dictionary,outSpeciesIn\n !f2py intent(out) abundance_out,successFlag\n ...\n END SUBROUTINE\n")),(0,a.kt)("p",null,"where we've dropped the bulk of the code since we only care about the declaration. Once compiled, you will be able to call this function using ",(0,a.kt)("inlineCode",{parentName:"p"},"uclchem.wrap.cloud(dictionary,outSpeciesIn)"),"."),(0,a.kt)("p",null,"This works because we've done two things. First, we've declared both the two inputs and the two outputs as arguments in Fortran in the normal way. Both inputs and outputs of a subroutine are declared as arguments in Fortran, usually with an ",(0,a.kt)("inlineCode",{parentName:"p"},"INTENT(IN)")," or ",(0,a.kt)("inlineCode",{parentName:"p"},"INTENT(OUT)")," statement, although that is unnecessary. We then declare the intent of those argument for F2PY using the comments that start ",(0,a.kt)("inlineCode",{parentName:"p"},"!f2py")," to tell F2PY which arguments should be arguments of the corresponding python function and which should be outputs."),(0,a.kt)("h2",{id:"the-python-side"},"The Python Side"),(0,a.kt)("p",null,"We could leave it at that. However, for ease of use, we write pure python functions in the uclchem module which call the underlying wrap functions rather than having users directly access the f2py functions. For example, in ",(0,a.kt)("inlineCode",{parentName:"p"},"uclchem.model"),", we define a cloud function which calls ",(0,a.kt)("inlineCode",{parentName:"p"},"wrap.cloud"),":"),(0,a.kt)("pre",null,(0,a.kt)("code",{parentName:"pre",className:"language-python"},'\ndef cloud(param_dict=None, out_species=None):\n """Run cloud model from UCLCHEM\n\n Args:\n param_dict (dict,optional): A dictionary of parameters where keys are any of the variables in defaultparameters.f90 and values are value for current run.\n out_species (list, optional): A list of species for which final abundance will be returned. If None, no abundances will be returned.. Defaults to None.\n\n Returns:\n int,list: A integer which is negative if the model failed to run, or a list of abundances of all species in `outSpecies`\n """\n n_out,param_dict,out_species=_reform_inputs(param_dict,out_species)\n abunds, success_flag = wrap.cloud(dictionary=param_dict, outspeciesin=out_species)\n if success_flag < 0 or n_out == 0:\n return success_flag\n else:\n return abunds[: n_out]\n')),(0,a.kt)("p",null,"This allows us to make some arguments optional using python's keyword arguments. It also lets us write docstrings from which we can generate documentation for the functions. Finally, it lets us tidy up the output! For example, arrays passed too and from the Fortran subroutines must be of fixed length so in this function, we cut the output abundance array down to just the elements the user actually wanted."),(0,a.kt)("h2",{id:"tips-and-tricks"},"Tips and Tricks"),(0,a.kt)("ul",null,(0,a.kt)("li",{parentName:"ul"},(0,a.kt)("p",{parentName:"li"},"Once imported, all values are initialized in UCLCHEM. Calling a subroutine multiple times does not reset variables. That is to say that if your Fortran modules declare variables with an initial value, those variables will not return to those initial values. Instead, you'll notice all our modules reset their variables manually in the initialize functions such as initializePhysics.")),(0,a.kt)("li",{parentName:"ul"},(0,a.kt)("p",{parentName:"li"},"Debugging your fortran code can be greatly complicated by the F2PY interface. 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