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| Original file line number | Diff line number | Diff line change |
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| Running phantom with APR | ||
| ======================== | ||
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| APR allows you to arbitrarily set regions of your simulation to have different local resolutions. | ||
| A description of the method and our implementation can be found in Nealon & Price 2024 (under review) and | ||
| you should cite this work if you are using APR. | ||
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| The rules of this method are: | ||
| 1. A mass factor of 2 is allowed between adjacent refinement levels (e.g. one parent 0> two children) | ||
| 2. Regions are spherical but can be nested together like a layered onion | ||
| 3. You cannot have both refinement and derefinement in the same simulation, e.g. the base refinement level has to be either the maximum or minimum | ||
| 4. Try to ensure that particles have several sound crossing times between subsequent split/merge procedures to reduce noise | ||
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| Compiling Phantom with APR | ||
| -------------------------- | ||
| Use your usual setup routine but with APR=yes. For example: | ||
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| :: | ||
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| mkdir mycalc | ||
| cd mycalc | ||
| ~/phantom/scripts/writemake.sh disc > Makefile | ||
| export APR=yes | ||
| make setup | ||
| make | ||
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| Initial conditions with APR | ||
| ------------------------- | ||
| APR does not affect any setups except SETUP=star (but for the relax procedure only). When you check your .in file it will have apr options at the bottom: | ||
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| :: | ||
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| apr_max = 3 ! number of additional refinement levels (3 -> 2x resolution) | ||
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| This option sets how many *extra* levels of refinement you want. Each level corresponds to a factor of 2 in mass. | ||
| To increase the spatial resolution by a factor of 2 you will need to use 3 levels here. | ||
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| :: | ||
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| ref_dir = 1 ! increase (1) or decrease (-1) resolution | ||
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| This chooses whether you are refining or derefining the simulation. If you are refining then the base resolution level will be 0. | ||
| If you are derefining the base level will be apr_max. | ||
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| :: | ||
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| apr_type = 2 ! 1: static, 2: moving sink, 3: create clumps | ||
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| Here you choose what kind of region you want. Current options include: | ||
| 1. A position fixed in space | ||
| 2. Tracking a particular sink particle | ||
| 3. Tracking a gravitationally bound clump (under development). | ||
| Depending on what you choose here you will get additional options to describe the properties of the region you selected. | ||
| You may need to re-run to get the right options if you alter apr_type. To add your own new region you can edit the apr_region.f90 file. | ||
| Note for now that we only allow spherical regions. | ||
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| :: | ||
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| apr_rad = 5. ! radius of innermost region | ||
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| This chooses the radius of the core of the refinement zone, where the highest/lowest refinement will be. If you think about | ||
| your refinement zone as an onion, this is the core of the onion. | ||
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| :: | ||
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| apr_drad = 10. ! size of step to next region | ||
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| This chooses the step width of the nested regions – the width of the shells as you step up your resolution. | ||
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| Running with APR | ||
| -------------------- | ||
| When APR is implemented and being used Phantom prints out the following statement in the log file: | ||
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| :: | ||
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| Adapative particle refinement is ON | ||
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| Additionally, because the particle numbers are changing each step you should see the number of | ||
| particles being updated during the steps e.g.: | ||
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| :: | ||
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| > step 2 / 16 t = 20.92159 dt = 0.072 moved 502 in 0.058 cpu-s < | np = 37902 | | ||
| > step 4 / 16 t = 21.06588 dt = 0.072 moved 1792 in 0.070 cpu-s < | ||
| > step 6 / 16 t = 21.21017 dt = 0.072 moved 319 in 0.058 cpu-s < | ||
| > step 8 / 16 t = 21.35445 dt = 0.072 moved 6175 in 0.097 cpu-s < | ||
| > step 10 / 16 t = 21.49874 dt = 0.072 moved 442 in 0.057 cpu-s < | np = 37901 | | ||
| > step 12 / 16 t = 21.64303 dt = 0.072 moved 1283 in 0.064 cpu-s < | ||
| > step 14 / 16 t = 21.78732 dt = 0.072 moved 476 in 0.058 cpu-s < | np = 37900 | | ||
| > step 16 / 16 t = 21.93160 dt = 0.072 moved 37860 in 0.31 cpu-s < | ||
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| Plotting with APR | ||
| -------------------- | ||
| APR is natively read by both splash and sarracen. The easiest way to check the method is working exactly | ||
| as you expect is to scatter plot (not render!) the mass of the particles in your simulation. This will | ||
| show you where the refinement zone is and you can confirm the geometry, it’s evolution as well as the | ||
| refinement direction. | ||
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| Analysis with APR | ||
| -------------------- | ||
| No analysis files that ship with Phantom have been updated to accommodate APR. To do this yourself, any | ||
| time you define a particle mass from the massoftype array you will need to edit it to read | ||
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| :: | ||
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| if (use_apr) then | ||
| pmassi = aprmassoftype(iamtypei,apr_level(i)) | ||
| else | ||
| pmassi = massoftype(iamtypei) | ||
| endif | ||
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| This relies on the apr_level, aprmassoftype and use_apr which can be included with | ||
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| :: | ||
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| use dim, only::use_apr | ||
| use part, only::apr_level,aprmassoftype | ||
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| Note that apr_level is integer(kind=1). |
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| Original file line number | Diff line number | Diff line change |
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@@ -19,3 +19,4 @@ This section contains the basic user guide for Phantom. | |
| hdf5 | ||
| mpi | ||
| data-curation | ||
| apr_guide | ||
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