Dust size evolution updates

.github/workflows/pytest.yml

@@ -0,0 +1,38 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: pytest
+
+on:
+  pull_request:
+    branches: ["starforge_dev"]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Setup MPI
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: openmpi
+    - name: Install libraries
+      run: sudo apt install libhdf5-openmpi-dev libgsl-dev
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -1,5 +1,21 @@
+# Files used for gizmo compilation.
 *.o
 GIZMO
 GIZMO_config.h
 compile_time_info.cc
-Config.sh
+Config.sh
+
+# Files used for gizmo test suite.
+build/
+spcool_tables/
+TREECOOL
+spcool_tables.tgz
+test/*/*.txt
+test/*/output
+*egg-info
+*.err
+*.out
+*.hdf5
+*.tmp
+*.pyc
+*values

Makefile

@@ -103,7 +103,7 @@ FINCL =
 #----------------------------------------------------------------------------------------------
 ifeq ($(SYSTYPE),"Frontera")
 CC       =  mpicc
-CXX      =  mpicxx -std=c++11
+CXX      =  mpicxx -std=c++17
 FC       =  mpif90 -nofor_main
 OPTIMIZE = -ggdb -O2 -xCORE-AVX2 -Wno-unknown-pragmas -Wall -Wno-format-security -qopenmp
 ifeq (CHIMES,$(findstring CHIMES,$(CONFIGVARS)))
@@ -203,9 +203,11 @@ OPT     += #
 endif
 
 #----------------------------------------------------------------------------------------------
+# Environment for building GIZMO on a macbook with libraries installed via homebrew. But note
+# that the specific GSL and HDF5 versions are hardcoded here...
 ifeq ($(SYSTYPE),"MacBookCellar")
 CC       =  mpicc
-CXX      =  mpiccxx
+CXX      =  mpicxx -std=c++11
 FC       =  $(CC) #mpifort  ## change this to "mpifort" for packages requiring linking secondary fortran code, currently -only- the helmholtz eos modules do this, so I leave it un-linked for now to save people the compiler headaches
 OPTIMIZE = -O1 -funroll-loops
 OPTIMIZE += -g -Wall # compiler warnings
@@ -220,18 +222,18 @@ GSL_INCL = -I/opt/homebrew/Cellar/gsl/2.8/include #-I$(PORTINCLUDE)
 GSL_LIBS = -L/opt/homebrew/Cellar/gsl/2.8/lib #-L$(PORTLIB)
 FFTW_INCL= -I/usr/local/include
 FFTW_LIBS= -L/usr/local/lib
-HDF5INCL = -I/opt/homebrew/Cellar/hdf5/1.14.3_1/include -DH5_USE_16_API  #-I$(PORTINCLUDE) -DH5_USE_16_API
-HDF5LIB  = -L/opt/homebrew/Cellar/hdf5/1.14.3_1/lib -lhdf5 -lz  #-L$(PORTLIB)
+HDF5INCL = -I/opt/homebrew/Cellar/hdf5/1.14.6/include -DH5_USE_16_API  #-I$(PORTINCLUDE) -DH5_USE_16_API
+HDF5LIB  = -L/opt/homebrew/Cellar/hdf5/1.14.6/lib -lhdf5 -lz  #-L$(PORTLIB)
 MPICHLIB = #
 OPT     += -DDISABLE_ALIGNED_ALLOC -DCHIMES_USE_DOUBLE_PRECISION #
 endif
 
 #----------------------------
-ifeq ($(SYSTYPE),"PopOS")
+ifeq ($(SYSTYPE),"github-ubuntu")
 CC       =  mpicc
-CXX      =  mpiccxx
+CXX      =  mpicxx
 FC       =  $(CC)
-OPTIMIZE = -g -fcommon -O1 -ffast-math -funroll-loops -finline-functions -funswitch-loops -fpredictive-commoning -fgcse-after-reload -fipa-cp-clone  ## optimizations for gcc compilers (1/2)
+OPTIMIZE = -g -fcommon -O1 -funroll-loops -finline-functions -funswitch-loops -fpredictive-commoning -fgcse-after-reload -fipa-cp-clone  ## optimizations for gcc compilers (1/2)
 OPTIMIZE += -ftree-loop-distribute-patterns -fvect-cost-model -ftree-partial-pre   ## optimizations for gcc compilers (2/2)
 OPTIMIZE += -g -Wall # compiler warnings
 ifeq (CHIMES,$(findstring CHIMES,$(CONFIGVARS)))
@@ -256,6 +258,24 @@ OPT     += -DDISABLE_ALIGNED_ALLOC -DCHIMES_USE_DOUBLE_PRECISION
 ## to get required packages: sudo apt install libhdf5-openmpi-dev libgsl-dev libopenmpi-dev
 endif
 
+#----------------------------
+# Should work on any Flatiron institute linux cluster environment: rusty, popeye and linux workstations
+ifeq ($(SYSTYPE),"RUSTY")
+CC       =   mpicc
+ifeq (SOFTDOUBLEDOUBLE,$(findstring SOFTDOUBLEDOUBLE,$(OPT)))
+CC       =   mpicxx
+endif
+FC      = mpifort
+OPTIMIZE =  -O2 -g -Wall
+GSL_INCL = -I$(GSL_BASE)/include
+GSL_LIBS = -L$(GSL_BASE)/lib -Xlinker -R -Xlinker $(GSL_BASE) -lgsl -lgslcblas
+FFTW_INCL= -I$(FFTW3_BASE)/include
+FFTW_LIBS= -L$(FFTW3_BASE)/lib -Xlinker -R -Xlinker $(FFTW3_BASE)/lib
+MPICHLIB =
+HDF5INCL = -I$(HDF5_BASE)/include -DH5_USE_16_API
+HDF5LIB  = -L$(HDF5_BASE)/lib -Xlinker -R -Xlinker $(HDF5_BASE)/lib -lhdf5 -lz
+endif
+
 
 #----------------------------------------------------------------------------------------------
 #----------------------------------------------------------------------------------------------
@@ -329,7 +349,8 @@ SINK_OBJS = sinks/sink.o \
 RHD_OBJS =  radiation/rt_utilities.o \
 			radiation/rt_CGmethod.o \
 			radiation/rt_source_injection.o \
-			radiation/rt_chem.o 
+			radiation/rt_chem.o \
+			radiation/rt_dust_opacity.o 
 
 FOF_OBJS =	structure/fof.o \
 			structure/subfind/subfind.o \

Makefile.systype

@@ -6,50 +6,10 @@
 #
 #############
 
-SYSTYPE="Frontera"
-#SYSTYPE="BigRed200"
-#SYSTYPE="Stampede2"
-#SYSTYPE="Bridges2"
-#SYSTYPE="Anvil"
-#SYSTYPE="Wheeler"
-#SYSTYPE="CaltechHPC"
-#SYSTYPE="MacBookPro"
+SYSTYPE="github-ubuntu"
+#SYSTYPE="Frontera"
 #SYSTYPE="MacBookCellar"
-#SYSTYPE="Quest"
-#SYSTYPE="Quest-intel"
-#SYSTYPE="TSCC"
 #SYSTYPE="Expanse"
-#SYSTYPE="Iron"
+#SYSTYPE="CaltechHPC"
 #SYSTYPE="RUSTY"
-#SYSTYPE="Darter"
-#SYSTYPE="Comet"
-#SYSTYPE="Gordon"
-#SYSTYPE="odyssey"
-#SYSTYPE="antares"
-#SYSTYPE="Pleiades"
-#SYSTYPE="Mira"
-#SYSTYPE="Titan"
-#SYSTYPE="Edison"
-#SYSTYPE="SciNet"
-#SYSTYPE="Ranger_intel"
-#SYSTYPE="Ranger_pgi"
-#SYSTYPE="Darwin"
-#SYSTYPE="Magny"
-#SYSTYPE="Magny-Intel"
-#SYSTYPE="OpenSuse"
-#SYSTYPE="OpenSuse64"
-#SYSTYPE="HLRB2"
-#SYSTYPE="MPA"
-#SYSTYPE="VIP"
-#SYSTYPE="Ubuntu"
-#SYSTYPE="MBM"
-#SYSTYPE="OpteronMPA-Gnu"
-#SYSTYPE="OpteronMPA-Intel"
-#SYSTYPE="Centos5-intel"
-#SYSTYPE="Kolob"
-#SYSTYPE="Centos5-Gnu"
-#SYSTYPE="OPA-Cluster64-Intel"
-#SYSTYPE="Stampede"
-#SYSTYPE="Zwicky"
-#SYSTYPE="BlueWaters"
-#SYSTYPE="PopOS"
+#SYSTYPE="BigRed200"

Template_Config.sh

@@ -503,8 +503,7 @@
 #EOS_ENFORCE_ADIABAT=(1.0)         # if set, this forces gas to lie -exactly- along the adiabat P=EOS_ENFORCE_ADIABAT*(rho^GAMMA)
 #HYDRO_REPLACE_RIEMANN_KT          # replaces the hydro Riemann solver (HLLC) with a Kurganov-Tadmor flux derived in Panuelos, Wadsley, and Kevlahan, 2019. works with MFM/MFV/fixed-grid methods [-without- MHD active, but other modules are fine]. more diffusive, but smoother, and more stable convergence results
 #SLOPE_LIMITER_TOLERANCE=1         # sets the slope-limiters used. higher=more aggressive (less diffusive, but less stable). 1=default. 0=conservative. use on problems where sharp density contrasts in poor particle arrangement may cause errors. 2=use the original GIZMO paper (more aggressive) slope-limiters. more accurate for smooth problems, but these can introduce numerical instability in problems with poorly-resolved large noise or density contrasts (e.g. multi-phase, self-gravitating flows)
-#ENERGY_ENTROPY_SWITCH_IS_ACTIVE   # enable energy-entropy switch as described in GIZMO methods paper. This can greatly improve performance on some problems where the
-                                   # the flow is very cold and highly super-sonic. it can cause problems in multi-phase flows with strong cooling, though, and is not compatible with non-barytropic equations of state
+#ENERGY_ENTROPY_SWITCH_IS_ACTIVE   # enable energy-entropy switch as described in GIZMO methods paper. This can greatly improve performance on some problems where the the flow is very cold and highly super-sonic. it can cause problems in multi-phase flows with strong cooling, though, and is not compatible with non-barytropic equations of state
 #FORCE_ENTROPIC_EOS_BELOW=(0.01)   # set (manually) the alternative energy-entropy switch which is enabled by default in MFM/MFV: if relative velocities are below this threshold, it uses the entropic EOS
 #HYDRO_KERNEL_SURFACE_VOLCORR      # attempt to correct SPH/MFM/MFV cell volumes for free-surface effects, using the estimated boundary correction for the Wendland C2 kernel (works with others but most accurate for this) based on asymmetry of neighbors within kernel, as calibrated in Reinhardt & Stadel 2017 (arXiv:1701.08296), see e.g. their Fig 3
 #DISABLE_SURFACE_VOLCORR           # disables HYDRO_KERNEL_SURFACE_VOLCORR if it would be set by default (e.g. if EOS_ELASTIC is enabled)
@@ -582,6 +581,7 @@
 #GRAIN_RDI_TESTPROBLEM             # top-level flag to enable a variety of test problem behaviors, customized for the idealized studies of dust dynamics in Moseley et al 2019MNRAS.489..325M, Seligman et al 2019MNRAS.485.3991S, Steinwandel et al arXiv:2111.09335, Ji et al arXiv:2112.00752, Hopkins et al 2020MNRAS.496.2123H and arXiv:2107.04608, Squire et al 2022MNRAS.510..110S. Cite these if used.
 #GRAIN_RDI_TESTPROBLEM_ACCEL_DEPENDS_ON_SIZE    # Make the idealized external grain acceleration grain size-dependent; equivalent to assuming an absorption efficiency Q=1. Cite GRAIN_RDI_TESTPROBLEM papers.
 #GRAIN_RDI_TESTPROBLEM_LIVE_RADIATION_INJECTION # Enables idealized radiation injection by a source population designed to set up outflow test problems with live radiation-hydrodynamics as in Hopkins et al., arXiv:2107.04608. Cite that paper if this module is used.
+#IO_DUST_NOT_IN_ICFILE              # special flag needed if restarting from a snapshot (flag=2) with no dust. Will set dust species via params arguments and assume an MRN size distribution, if GALSF_ISMDUSTCHEM_MODEL is active 
 # --------------------
 # ----- MPI & Parallel-FFTW De-Bugging
 #DOUBLEPRECISION_FFTW               # FFTW in double precision to match libraries
@@ -591,6 +591,22 @@
 #ALLOW_IMBALANCED_GASPARTICLELOAD   # increases All.MaxPartGas to All.MaxPart: can allow better load-balancing in some cases, but uses more memory. But use me if you run into errors where it can't fit the domain (where you would increase PartAllocFac, but can't for some reason)
 ####################################################################################################
 
+############################################################################################################################-
+#------------------ ISM Dust Chemical Evolution Models (follow growth, destruction, and size evolution of different grain species)
+#----------------- Users of any of these modules should cite Choban et al., 2022/25 for the methods/implementation in GIZMO and FIRE
+############################################################################################################################-
+#GALSF_ISMDUSTCHEM_MODEL=(1+2)              #- enable live dust evolution model (value deteremines the dust species tracked). Use GALSF_ISMDUSTCHEM_SILICATE_COMPOSITION to set the silicate composition.
+                                            #- model = 1: Track silicates and carbonaceous dust.
+                                            #- model = 2: Track metallic iron dust.
+                                            #- model = 4: Track oxygen bearing dust species which is a simple match to observations of MW oxygen depletion.
+                                            #- model = 8: Track metallic iron nanoparticles with set fraction assumed to be locked in silicate dust as inclusions based on Zhukovska+(2018). Requires GALSF_ISMDUSTCHEM_MODEL=2.
+#GALSF_ISMDUSTCHEM_SILICATE_COMPOSITION=(1+2+8)   #- set the silicate dust chemical composition. This changes the production, growth, and destruction rates of silicate dust, and the max depletions of Mg, Fe, Si, and O in the gas phase.
+                                            #- model = 1 (default): olivine-pyroxene mix [(Fe_0.571 Mg_1.06) Si O_3.63]
+                                            #- model = 2: add 2 extra O atoms to better match O depletions.
+                                            #- model = 4: add 1 extra Fe atom to better match Fe depletions.
+                                            #- model = 8: remove all Fe. Use with additional metallic iron species to avoid Fe limiting silicate growth.
+#GALSF_ISMDUSTCHEM_GRAINSIZEEVO=16          #- enable grain size evolution model w/ N number of logarithmically spaced bins (must also turn on GALSF_ISMDUSTCHEM_MODEL= 1 or (1 + 2) only and GALSF_ISMDUSTCHEM_SILICATE_COMPOSITION)
+############################################################################################################################-
 
 
 
@@ -615,49 +631,4 @@
 #USE_TIMESTEP_DILATION_FOR_ZOOMS            #- enable time dilation modules, need to customize for applications, cannot be simply generically turned on without coding how they will work
 #DILATION_FOR_STELLAR_KINEMATICS_ONLY       #- special version of time dilation designed for stellar kinematics in e.g. dense star clusters or galaxy centers
 #SINK_RIAF_SUBEDDINGTON_MODEL=(0.01)        #- enable an arbitrary modular variation in the radiative efficiency of BHs as a function of eddington ratio or other particle properties, with the critical transition to the jet mode at this eddington ratio (defined in terms of mdot/mdot_crit)
-####################################################################################################-
-
-############################################################################################################################-
-#------------------ ISM Dust Chemical Evolution Models (follow growth, destruction, and size evolution of different grain types)
-#----------------- Users of any of these modules should cite Choban et al., 2022/25 for the methods/implementation in GIZMO and FIRE
-############################################################################################################################-
-#GALSF_ISMDUSTCHEM_MODEL=(2+4+8)    #- enable live dust evolution model (must select either elemental or species or other model codes as well)
-                                    #- model = 1: "dust by element" dust evolution model based off Bekki(2013)/McKinnon+(2016). Track generalized silicates and carbonaceous dust.
-                                    #- model = 2: "dust by species" dust evolution model based off Zhukovska+(2008/2016/2018). Tracks silicates (set composition), carbonaceous, SiC, and metallic iron dust along with optional iron nanoparticles and/or O reservoir dust species.
-                                    #- model = 4: additional metallic iron dust nano-particles with set fraction assumed to be locked in silicate dust as inclusions based on Zhukovska+(2018)
-                                    #- model = 8: additional oxygen bearing dust species which is a simple match to observations of MW oxygen depletion since they cannot be explained with purely silicate dust
-                                    #- model = 16: modified "dust by species" model to be used with GALSF_ISMDUSTCHEM_GRAINSIZEEVO. Tracks size evolution of silicates (set composition), carbonaceous, and metallic iron
-                                    #- model = 32: modified "dust by species" model to be used with GALSF_ISMDUSTCHEM_GRAINSIZEEVO. Tracks size evolution of silicates w/ extra O and Fe (set composition) and carbonaceous
-#GALSF_ISMDUSTCHEM_PASSIVE          #- decouples dust evolution from dust physics, chemisty, and feedback. Dust will evolve passively, with any physics or chemistry involving dust using constant, preset values (typically D/Z=0.4) 
-# Options for grain size evolution model
-#GALSF_ISMDUSTCHEM_GRAINSIZEEVO=16     #- enable grain size evolution model w/ N number of logarithmically spaced bins (must also turn on GALSF_ISMDUSTCHEM_MODEL= 2 + (16 or 32) only)
-#IO_GRAINSIZEEVO_BINS_IN_SNAPSHOT=2 # Allows you to restart from a snapshot with a SMALLER number of grain size bins only. Set to the number of bins in the snapshot.
-#IO_DUST_NOT_IN_ICFILE     # special flag needed if restarting from a snapshot (flag=2) with no dust. Will set dust species via params arguments and assume an MRN size distrubtion
-#INIT_DUST_SIZES_LOGNORM # flag if the initalized dust population has a lognormal size distribution. Otherwise power-law MRN is assumed.
-# Extra output options
-#OUTPUT_GRAIN_BIN_SLOPES # Outputs the slopes of each grain size bin in addition to the total number and mass.
-#OUTPUT_SHATCOAG_MASSRATE # Outputs the mass transfer rate from shattering and coagulation processes in each grain size bin.
-#GALSF_ISMDUSTCHEM_SUPERSONIC_GRAIN_VELOCITY # Assumes supersonic turbulence for determining grain velocities. Default is Kolmogorov.
-# Flags to turn off certain dust processes
-#COAGULATION_DENSE_GAS_ENHANCEMENT_TURNOFF # Turnoff enhancement of gas density for sub-resolved coagulation. 
-#AGBDUST_TURNOFF
-#SNEDUST_TURNOFF
-#DUSTDIFFUSION_TURNOFF
-#DUSTSPUTTERING_TURNOFF
-#DUSTACCRETION_TURNOFF
-#COULOMB_ENHANCEMENT_TURNOFF
-#DUSTSNEDEST_TURNOFF
-#DUSTCOAGULATION_TURNOFF
-#DUSTSHATTERING_TURNOFF
-#DUSTPHOTODESTRUCTION_TURNON # Not included in fiducial model
-# Options below are for testing the integration of dust evolution with all the dust physics included in FIRE
-#PHOTOELECTRIC_TURNOFF
-#MOLECULARFRACTION_TURNOFF
-#RADIATIONTRANSPORT_TURNOFF # This will also affect the dust temperature calculations in FIRE-3 since these are determined from rad transport and the optically thick heating which uses rt kappa
-#METALLINECOOLING_TURNOFF
-#LOWTEMP_TURNOFF
-#FREEELECTRON_TURNOFF
-#HII_TURNOFF
-#HIGHTTEMP_TURNOFF
-############################################################################################################################-
-
+####################################################################################################-