The makefile

Important

The required config.mk, makefile, and params.dat files are provided as templates. To set up your simulation:

  1. Copy config.mk and makefile from 3D-PDR/templates/1D/ or 3D-PDR/templates/3D/ into your src/ directory, based on your simulation type (1D or 3D).

  2. Copy the params.dat file from the same template directory into the 3D-PDR/ home directory.

The main flags of the code are specified in the config.mk file. This file is then called within the makefile.

In config.mk, the flags are divided into two main sections:

  1. Compiler options

  2. Chemistry and density options

First Section (Compiler Options)

F90               = gfortran
CC                = gcc
CPPFLAGS          = -cpp
OPENMP            = 1
OPTIMISE          = 3
PYWRAP            = 0

  • F90 Specifies the Fortran compiler. The default compiler is gfortran. No other Fortran compilers have been tested, so change this only if you are willing to debug potential issues yourself.

  • CC Specifies the C compiler. For macOS users, you may need to use gcc-14 or mp-gcc-14 (or equivalent) instead of gcc. It is strongly recommended to use GCC versions later than 7.3.0.

  • CPPFLAGS Specifies the C preprocessor flag, which should be -cpp.

  • OPENMP Controls whether the code runs in parallel (OPENMP = 1) or serial mode (OPENMP = 0). It is recommended to always use OPENMP = 1 unless there is a specific reason not to.

  • OPTIMISE Defines the compiler optimization level. Flags 0 and 1 are for development and debugging, while 2 and 3 are used for production runs. The recommended value is OPTIMISE = 3 for normal use. A flag 4 also exists but is not recommended, as it may lower precision and cause instability.

  • PYWRAP Enables Python wrapper compilation (PYWRAP = 1) for the py3DPDR.py interface. See the Jupyter notebook HandsOn_1Dexamples.ipynb for usage examples.

Second Section (Chemistry and Density Options)

DIMENSIONS        = 1
RAYTHEIA          = 0
XYZ               = 0
NETWORK           = REDUCED
XRAYS             = 0
DUST              = HTT91
GUESS_TEMP        = 1
THERMALBALANCE    = 1
FORCECONVERGENCE  = 1
GRAINRECOMB       = 0
SUPRATHERMAL      = 0
H2FORM            = CT02
CRATTENUATION     = 0
RESTART           = 0
OUTRAYINFO        = 0

  • DIMENSIONS: Specifies the dimensionality of the model.

    • DIMENSIONS = 1 — for one-dimensional models.

    • DIMENSIONS = 3 — for three-dimensional models.

  • RAYTHEIA: Activates the new ray-tracing algorithm implemented for 3D models in 3D-PDR. This self-consistent algorithm performs fast ray tracing to compute column densities, line emission, and escape probabilities.

    • RAYTHEIA = 1 — uses memory-optimized mode (slower but minimal RAM usage).

    • RAYTHEIA = 2 — faster mode without memory optimization (higher RAM usage; not recommended above 64³ resolution).

    • RAYTHEIA = 0 — uses the original method from Bisbas et al. (2012).

    Note

    For 1D models, always set RAYTHEIA = 0.

  • XYZ: Defines the format of the 3D density distribution (use XYZ = 0 for 1D models).

    • XYZ = 0 — z changes fastest.

    • XYZ = 1 — x changes fastest.

    See the Three-dimensional Density Distributions section for more details.

  • NETWORK: Selects the chemical network based on the UMIST database.

    • REDUCED — 33 species, 331 reactions.

    • MEDIUM — 77 species, 1158 reactions (due to B. Gaches).

    • FULL — 215 species, 2926 reactions.

    More complex networks increase runtime. See the The species_[network].d section on how to specify the initial elemental abundances.

  • XRAYS: Enables X-ray chemistry (currently experimental). Works in limited cases for NETWORK = REDUCED only. Set XRAYS = 0 in all other cases.

  • DUST: Determines how dust temperature is treated.

  • GUESS_TEMP: Sets the initial gas temperature used to start iterations.

    • 1 — uses an approximate function based on FUV intensity (recommended).

    • 0 — uniform temperature across the cloud.

  • THERMALBALANCE: Determines whether the model solves for thermal balance or not.

    • THERMALBALANCE = 1 — switch on thermal balance.

    • THERMALBALANCE = 0 — isothermal runs.

    Note

    For isothermal models, also set GUESS_TEMP = 0 and specify temperature in params.dat

  • FORCECONVERGENCE: Accelerates convergence by restricting variable changes after several iterations. Recommended value: FORCECONVERGENCE = 1.

  • GRAINRECOMB: Enables electron recombination on dust grains. GRAINRECOMB = 1 uses the treatment from Weingartner & Draine (2001). Some issues remain for the FULL network.

  • SUPRATHERMAL: Enables suprathermal formation of CO via CH⁺. See Visser et al. (2009) and Bisbas et al. (2019). Values for the critical A_V and Alfvén velocity are set in params.dat.

  • H2FORM: Specifies the H₂ formation recipe:

    • CT02 — Cazaux & Tielens (2002, 2004); see detailed description here.

    • SIMPLE — simplified function (see makefile comments).

    • R07 — Röllig et al. (2007) benchmark function.

  • CRATTENUATION: Enables cosmic-ray attenuation.

    • 1 — uses Padovani et al. (2018; 2024) low/high models. Replace CRIR value in params.dat with L, H or U.

    • 0 — uses constant CR ionization rate throughout the cloud.

  • RESTART Allows resuming an interrupted run (RESTART = 1). Writes a binary file restart.bin in the working directory. To restart after a crash or timeout, simply rerun the code.

    Note

    Delete any old restart.bin before starting a new model. Works only with THERMALBALANCE = 1.

  • OUTRAYINFO: Saves information for each ray in separate files. Default: OUTRAYINFO = 0.