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mainpage.txt
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mainpage.txt
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/**
@mainpage Nautilus documentation
@verbatim
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~~~~~~~~~~~~~~~~~~~~~~~~~~~|^"~~~~~~~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~~
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_______________________|_______\________________
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/
@endverbatim
@tableofcontents
@section section1 Introduction
A fast 1D gas-grain chemical model by FH (2008). Based upon the OSU gas-grain chemical model. Updated from gg_osu_2006v1d by RTG/VW.
Rate equations from Hasegawa & Herbst (1992). Modified rates following Caselli et al. (1998)\n\n
Stiff solver for sparse Jacobians: LSODES/ODEPACK (Hindmarsh 1983)\n
Turbulent mixing implemented through first order operator splitting\n
The simulation binary is <b>nautilus</b>. The binary to be used for ASCII output generation is <b>nautilus_outputs</b>.
@section section_example How To Use
A folder containing an example simulation is available in example_simulation/
To use the code, my advice would be to have one folder for the code, in a specific location. Then, in another location, you can
create as many folders as you want, with one specific simulation in each folder.
In my case, I always put my programs in a folder named <b>~/bin</b>.
Then, to easily access your program, you can modify your commandline preferences by editing your bash profile <b>~/.bashrc</b>.
To easily go to your program directory via :
@verbatim
cd $nautilus
@endverbatim
add the following line to your bash profile :
@code
export nautilus="$HOME/bin/nautilus"
@endcode
To launch Nautilus wherever you want in your server via :
@verbatim
nautilus
@endverbatim
add the following line to your bash profile :
@code
alias nautilus="$HOME/bin/nautilus/nautilus"
@endcode
Keep in mind that typing
@verbatim
> cd -
@endverbatim
in your Terminal, you will go back to the previous directory (not the parent one, the previous one). Typing this command several
times allow you to switch easily between two folders.
@section section_commands Basic commands
Compile <b>nautilus</b>
@code
Makefile.py
@endcode
See all compilation options
@code
Makefile.py help
@endcode
Compile <b>nautilus_outputs</b>
@code
Makefile.py output
@endcode
Generate Doxygen documentation (all errors will be stored in a <b>doxygen.log</b> file)
@code
doxygen doxygen.conf 2>doxygen.log
@endcode
@section section_input Input files
Input files have a <b>*.in</b> extension. All parameters file can have comments, either a full line or the end of a line. The comment character being the '!' character.
Blanck lines are ignored
@li <b>parameters.in</b> : parameter file of the code, with various flags
@li <b>abundances.in</b> : Give initial abundances for a set of species (a reduced number or all. Default minimum values are applied
for those that do not exist in this file.
@li <b>element.in</b> : name and mass in AMU of all elemental species existing in the simulation
@li <b>gas_reactions.in</b> : Reaction that occurs in gas phase
@li <b>gas_species.in</b> : species that are involved in gas phase reactions
@li <b>grain_reactions.in</b> : Reactions that occurs on grain surface
@li <b>grain_species.in</b> : Species that are involved in grain surface reactions
@li <b>activation_energies.in</b> : Activation energy for endothermic reactions
@li <b>surface_parameters.in</b> : various energies and parameters for diffusion and movements on the grain surface
@section section_output Output files
<b>*.out</b> files are output files. <b>*.tmp</b> files are file that are generated at each timestep, either to continue a
simulation or check if there is a problem
<b>*.ab</b> files are ASCII files generated by nautilus_outputs from the binaries <b>abundances.*.out</b>.
One file per species in a folder named <b>ab</b>.
@li <b>abundances.*.out</b> : writing in binary format the abundances of all species at each timestep (one file per timestep-output)
@li <b>abundances.tmp</b> : writing in ASCII format the abundances of all species at the current timestep-output
@li <b>rates.*.out</b> : writing in binary format the critical reactions rates
@li <b>info.out</b> : writing information on the code, in particular about the code version (commit ID and branch)
@li <b>species.out</b> : Writing the list of species and their corresponding index
@li <b>elemental_abundances.tmp/out</b> : writing information about prime elements, their total abundances and mass
@section section_errors Errors
Error 1: Missing input file.
Error 2: Species name in reaction do not match expected list of species
Error 3: More elements than NB_PRIME_ELEMENTS
Error 4: When reordering reactions, it seems that some reactions misses or not expected
Error 5: In parameter file, IS_DIFFUSIVITY has a value that is not recognized by the code
Error 6: The number of prime elements in input files *_species.in do not match with the real one coming from element.in
Error 7: The file "time_evolution.dat" does not exist.
Error 8: Grain temperature cannot be read from "structure_evolution.dat" if the "structure_evolution" flag is not activated.
Error 9: IS_STRUCTURE_EVOLUTION has an undefined value.
Error 10: GRAIN_TEMPERATURE_TYPE is not 'table' and the grain temperature column exist in 'structure_evolution.dat'.
Error 11: Error in subroutine DICHO of dust_temperature.f90: the sign of the function doesn't change in the interval:"
Error 12: OUTPUT_TYPE has an undefined value.
Error 13: A species is expected to be on grains (starting with 'J'), but is not.
Error 14: One species have no production or destruction reaction.
Error 15: One reaction is not well defined (either prime elements or electric charge, or temperature range).
Error 16: At least one reaction has alpha = 0, please change alpha or comment the reaction.
Error 17: Two reactions with the same ID have different reactants or product, or incompatible temperature ranges
Error 18: One gas species has no grain equivalent
Error 19: One gas species has no adsorption reaction (ITYPE=99)
Error 20: One surface species has no desorption reaction (either ITYPE=15,16,66,67)
Error 21: STRUCTURE_TYPE has a value that is not defined in the code
Error 22: In 0D, we can't have 1D_sample>1
Error 23: You can't have 1D structure and time evolution (read from a data file) of that structure at the same time.
Error 24: Problem occured while inside the sorting array procedure 'get_sorted_index'
Error 25: The file where 1D data are expected doesn't exist.
@section section_itype Reactions Types
ITYPE 0: Gas phase reactions with GRAINS
ITYPE 1: Photodissoc/ionisation with cosmic rays
ITYPE 2: Gas phase photodissociations/ionisations by secondary UV photons generated by CR
ITYPE 3: Gas phase photodissociations/ionisations by UV
ITYPE 4-8: Bimolecular gas phase reactions - several possible formula
ITYPE 10-11: H2 formation on the grains when IS_GRAIN_REACTIONS eq 0
ITYPE 14: Grain surface reactions
ITYPE 15: Thermal evaporation
ITYPE 16: Cosmic-ray evaporation
ITYPE 17: Photodissociations by Cosmic rays on grain surfaces
ITYPE 18: Photodissociations by Cosmic rays on grain surfaces
ITYPE 19-20: Photodissociations by UV photons on grain surfaces
ITYPE 21: Grain surface reactions
ITYPE 66: Photodesorption by external UV
ITYPE 67: Photodesorption by CR generated UV
ITYPE 98: storage of H2S under a refractory form
ITYPE 99: Adsorption on grains
@section section_warning Warnings
A lot of warnings are launched by the ODEPACK files. Some of them are more problematic than others that are just deprecated feature
(even though this is a problem for readability).
The most problematic is a call of DPREP in the subroutine DIPREP, in opkda1.
The error returned is the following:
@verbatim
LYH), RWORK(LSAVF), RWORK(LEWT), RWORK(LACOR), IA, JA, IC, JC, RWORK(LWM), RWOR
1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)
opkda1.f90:1214.93:
, RWORK(LYH), RWORK(LSAVF), RWORK(LEWT), RWORK(LACOR), IA, JA, RWORK(LWM), RWOR
1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)
@endverbatim
*/