Draft: Fixes to jtlaune/nu-disk

.github/workflows/ci.yml

@@ -81,14 +81,14 @@ jobs:
             --log_file=ci_cpu_log.txt
       - name: Upload logs
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: logs
           path: tst/testing/logs
           retention-days: 3
       - name: Upload figures
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: figs
           path: tst/testing/figs

.github/workflows/nightly.yml

@@ -56,14 +56,14 @@ jobs:
             --log_file=ci_cpu_log.txt
       - name: Upload CPU test log
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ci_cpu_log.txt
           path: tst/ci_cpu_log.txt
           retention-days: 3
       - name: Upload figures
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: figs
           path: tst/figs

CMakeLists.txt

@@ -119,6 +119,11 @@ if(ARTEMIS_ENABLE_ASAN)
   add_link_options(-fsanitize=address -fsanitize=undefined)
 endif()
 
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
+  # silence sprintf warnings on mac
+  add_compile_options(-Wno-deprecated-declarations)
+endif()
+
 # NOTE(@jonahm): For some reason, order still matters for including
 # parthenon and singularity. Likely has to do with project
 # includes other than Kokkos. MPI and OpenMP likely culprits.
@@ -186,7 +191,8 @@ set(ARTEMIS_SINGULARITY_INCLUDE_PATHS
     ${CMAKE_CURRENT_SOURCE_DIR}/external/singularity-eos/utils/variant/include
     ${CMAKE_CURRENT_SOURCE_DIR}/external/singularity-opac/utils
     ${CMAKE_CURRENT_SOURCE_DIR}/src
-    ${CMAKE_CURRENT_SOURCE_DIR})
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/generated>)
 
 # Set Jaybenne config options and paths
 # NOTE(@pdmullen): For the life of us, we are still not sure why we can't treat

env/bash

@@ -19,39 +19,35 @@ export ARTEMIS_HOME="${exec_dir%/env}"
 
 export MAKE_PROGRAM=${MAKE_PROGRAM:-make}
 
-export PARTITION="venado-gh"
-
 #  Identify partitions based on  SLURM_JOB_PARTITION and HOSTNAME variables
-#PARTITION="unknown"
-#if [[ $HOSTNAME == ch-fe*  ||  $SLURM_CLUSTER_NAME == "chicoma" ]]; then
-#    if [[ $SLURM_JOB_PARTITION == *gpu* ]]; then
-#        PARTITION="chicoma-gpu"
-#    else
-#        PARTITION="chicoma-cpu"
-#    fi
-#elif [[ "$HOSTNAME" =~ ^ve-rfe[1-7]$ || "$HOSTNAME" =~ ^ve-fe[1-7]$ ]]; then
-#    if [[ $SLURM_GPUS_ON_NODE > 0 || ("$HOSTNAME" =~ ^ve-rfe[1-3]$ || "$HOSTNAME" =~ ^ve-fe[1-3]$) ]]; then
-#        PARTITION="venado-gh"
-#    elif [[ $SLURM_GPUS_ON_NODE == 0 || ("$HOSTNAME" =~ ^ve-rfe[4-7]$ || "$HOSTNAME" =~ ^ve-fe[4-7]$) ]]; then
-#        PARTITION="venado-gg"
-#    fi
-#else # Catch-all for Darwin
-#    if [ -z "$SLURM_JOB_PARTITION" ]; then
-#        if [[ $HOSTNAME == darwin-fe* ]]; then
-#            echo "Do not compile on Darwin frontend nodes; use a specific partition!"
-#            echo "Supported partitions are"
-#            echo "  skylake-gold"
-#            echo "  volta-x86"
-#            echo "...setup FAILED"
-#        fi
-#    elif [[ $SLURM_JOB_PARTITION == "power9-rhel7" ]]; then
-#        PARTITION="darwin-power9-rhel7"
-#    elif [[ $SLURM_JOB_PARTITION == "skylake-gold" ]]; then
-#        PARTITION="darwin-skylake-gold"
-#    elif [[ $SLURM_JOB_PARTITION == "volta-x86" ]]; then
-#        PARTITION="darwin-volta-x86"
-#    fi
-#fi
+PARTITION="unknown"
+if [[ $HOSTNAME == ch-fe*  ||  $SLURM_CLUSTER_NAME == "chicoma" ]]; then
+    if [[ $SLURM_JOB_PARTITION == *gpu* ]]; then
+        PARTITION="chicoma-gpu"
+    else
+        PARTITION="chicoma-cpu"
+    fi
+elif [[ "$HOST" =~ ^ve-rfe[1-7]$ || "$HOST" =~ ^ve-fe[1-7]$ ]]; then
+    if [[ $SLURM_GPUS_ON_NODE > 0 || ("$HOST" =~ ^ve-rfe[1-3]$ || "$HOST" =~ ^ve-fe[1-3]$) ]]; then
+        PARTITION="venado-gh"
+    elif [[ $SLURM_GPUS_ON_NODE == 0 || ("$HOST" =~ ^ve-rfe[4-7]$ || "$HOST" =~ ^ve-fe[4-7]$) ]]; then
+        PARTITION="venado-gg"
+    fi
+else # Catch-all for Darwin
+    if [[ $HOSTNAME == darwin-fe* ]]; then
+        echo "Currently on darwin frontend node; formatting is supported but not compilation"
+        echo "Supported partitions are"
+        echo "  skylake-gold"
+        echo "  volta-x86"
+        PARTITION="darwin-fe"
+    elif [[ $SLURM_JOB_PARTITION == "power9-rhel7" ]]; then
+        PARTITION="darwin-power9-rhel7"
+    elif [[ $SLURM_JOB_PARTITION == "skylake-gold" ]]; then
+        PARTITION="darwin-skylake-gold"
+    elif [[ $SLURM_JOB_PARTITION == "volta-x86" ]]; then
+        PARTITION="darwin-volta-x86"
+    fi
+fi
 
 # Absolute path for conda environment can be too long
 function shorten_prompt {

inputs/radiation/rad_shock.in

@@ -14,6 +14,12 @@
 <artemis>
 problem = shock          # name of the pgen
 coordinates = cartesian  # coordinate system
+physical_units = cgs     # not scale-free
+unit_conversion = base   # [L/T/M/Temp] = 1
+time = 1.0e-10           # time unit
+length = 0.01575         # length unit
+mass = 3.906984375e-6    # mass unit (implying dunit=1.0)
+temperature = 2.18e6     # temperature unit
 
 <parthenon/job>
 problem_id = shock  # problem ID: basename of output filenames
@@ -23,65 +29,72 @@ variables = gas.prim.density,  &
             gas.prim.velocity, &
             gas.prim.sie,      &
             field.jaybenne.energy_tally
-file_type = hdf5   # HDF5 data dump
-dt        = 0.01   # time increment between outputs
+file_type = hdf5  # HDF5 data dump
+dt        = 1.0   # time increment between outputs
 
 <parthenon/time>
-nlim       = -1    # cycle limit
-tlim       = 0.05  # time limit
-integrator = rk2   # time integration algorithm
+nlim       = -1   # cycle limit
+tlim       = 6.0  # time limit
+integrator = rk2  # time integration algorithm
 
 <parthenon/mesh>
-nx1    = 512       # Number of zones in X1-direction
-x1min  = -0.01     # minimum value of X1
-x1max  = 0.01      # maximum value of X1
+nx1    = 128       # Number of zones in X1-direction
+x1min  = 0.0       # minimum value of X1
+x1max  = 1.0       # maximum value of X1
 ix1_bc = ic        # inner-X1 boundary flag
 ox1_bc = ic        # outer-X1 boundary flag
 
 nx2    = 1         # Number of zones in X2-direction
-x2min  = -0.01     # minimum value of X2
-x2max  = 0.01      # maximum value of X2
+x2min  = 0.0       # minimum value of X2
+x2max  = 1.0       # maximum value of X2
 ix2_bc = periodic  # inner-X2 boundary flag
 ox2_bc = periodic  # outer-X2 boundary flag
 
 nx3    = 1         # Number of zones in X3-direction
-x3min  = -0.01     # minimum value of X3
-x3max  = 0.01      # maximum value of X3
+x3min  = 0.0       # minimum value of X3
+x3max  = 1.0       # maximum value of X3
 ix3_bc = periodic  # inner-X3 boundary flag
 ox3_bc = periodic  # outer-X3 boundary flag
 
 <parthenon/swarm>
-ix1_bc = jaybenne_reflecting
-ox1_bc = jaybenne_reflecting
-ix2_bc = periodic
-ox2_bc = periodic
-ix3_bc = periodic
-ox3_bc = periodic
+ix1_bc = jaybenne_reflecting  # inner-X1 boundary flag for swarms
+ox1_bc = jaybenne_reflecting  # outer-X1 boundary flag for swarms
+ix2_bc = periodic  # inner-X2 boundary flag for swarms
+ox2_bc = periodic  # outer-X2 boundary flag for swarms
+ix3_bc = periodic  # inner-X3 boundary flag for swarms
+ox3_bc = periodic  # outer-X3 boundary flag for swarms
 
 <parthenon/meshblock>
-nx1 = 64  # Number of cells in each MeshBlock, X1-dir
-nx2 = 1   # Number of cells in each MeshBlock, X2-dir
-nx3 = 1   # Number of cells in each MeshBlock, X3-dir
+nx1 = 128  # Number of cells in each MeshBlock, X1-dir
+nx2 = 1    # Number of cells in each MeshBlock, X2-dir
+nx3 = 1    # Number of cells in each MeshBlock, X3-dir
 
 <physics>
-gas = true
-radiation = true
+gas = true        # enable gas hydrodynamics
+radiation = true  # enable IMC radiation
 
 <gas>
-gamma = 1.666666  # adiabatic index
-cv = 1.5          # specific heat
-cfl = 0.8
-reconstruct = plm
-riemann = hllc
-dfloor = 1.0e-10
-siefloor = 1.0e-10
+gamma = 1.666666    # adiabatic index
+mu = 1.008          # mean molecular weight
+cfl = 0.8           # CFL number
+reconstruct = plm   # reconstruction algorithm
+riemann = hllc      # Riemann solver
 
 <gas/opacity/absorption>
-opacity_model = shocktube_a  # absorption opacity model
-coef_kappa_a = 577.35  # kappa_a,0 constant
-rho_exp = -1.0         # dens exponent for opacity powerlaw
-temp_exp = 0.0         # temp exponent for opacity powerlaw
+opacity_model = powerlaw  # absorption opacity model
+coef_kappa_a = 577.0      # kappa_a,0 constant (must be passed in cgs)
+rho_exp = -1.0            # dens exponent for opacity powerlaw
+temp_exp = 0.0            # temp exponent for opacity powerlaw
 
 <jaybenne>
-num_particles = 10000
-use_ddmc = false
+num_particles = 100000  # particle resolution
+use_ddmc = false        # use DDMC?
+
+<problem>
+rhol = 5.69      # density (left)
+rhor = 17.1      # density (right)
+vxl = 0.329524   # x-velocity (left)
+vxr = 0.109841   # x-velocity (right)
+tl = 1.0         # gas and radiation temp (left)
+tr = 3.66055     # gas and radiation temp (right)
+xdisc = 0.828571 # discontinuity position

inputs/radiation/thermalization.in

@@ -13,6 +13,8 @@
 
 <artemis>
 problem = thermalization  # name of the pgen
+physical_units = cgs
+unit_conversion = base
 coordinates = cartesian   # coordinate system
 
 <parthenon/job>
@@ -24,12 +26,12 @@ variables = gas.prim.density,  &
             gas.prim.sie,      &
             field.jaybenne.energy_tally
 file_type = hdf5   # HDF5 data dump
-dt        = 0.01   # time increment between outputs
+dt        = 1.0e-9 # time increment between outputs
 
 <parthenon/time>
-nlim       = -1    # cycle limit
-tlim       = 5.0   # time limit
-integrator = rk2   # time integration algorithm
+nlim       = -1      # cycle limit
+tlim       = 6.0e-8  # time limit
+integrator = rk1     # time integration algorithm
 
 <parthenon/mesh>
 nx1    = 4         # Number of zones in X1-direction
@@ -60,22 +62,23 @@ gas = true
 radiation = true
 
 <gas>
-gamma = 2.0  # adiabatic index
-cv = 8.0     # specific heat
+gamma = 1.4  # adiabatic index
+mu = 28.96   # mean molecular weight
 cfl = 0.8
 reconstruct = plm
 riemann = hllc
 dfloor = 1.0e-10
 siefloor = 1.0e-10
 
 <gas/opacity/absorption>
-opacity_model = thermalization
-kappa_a = 1.0
+opacity_model = constant
+kappa_a = 2.0
 
 # <gas/opacity/scattering>
 # scattering_model = constant
 # kappa_s = 10.0
 
 <jaybenne>
-dt = 0.01
+dt = 1.0e-10
 num_particles = 1000
+use_ddmc = true

src/CMakeLists.txt

@@ -64,7 +64,6 @@ set (SRC_LIST
   pgen/conduction.hpp
   pgen/constant.hpp
   pgen/disk.hpp
-  pgen/nu_disk.hpp
   pgen/gaussian_bump.hpp
   pgen/linear_wave.hpp
   pgen/pgen.hpp
@@ -145,8 +144,15 @@ if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
    message(STATUS "Standalone mode. Adding artemis executable")
    add_executable(artemis main.cpp)
    target_link_libraries(artemis PRIVATE artemislib)
-   add_custom_command(TARGET artemis POST_BUILD
-                      COMMAND ${CMAKE_COMMAND} -E copy
-                              ${CMAKE_BINARY_DIR}/rebound/librebound.so
-                              $<TARGET_FILE_DIR:artemis>)
+
+   # Bake in rpath to rebound on mac
+   if(${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
+    set_target_properties(artemis PROPERTIES
+      BUILD_RPATH "${CMAKE_BINARY_DIR}/rebound"
+    )
+    add_custom_command(TARGET artemis POST_BUILD
+      COMMAND install_name_tool -add_rpath @executable_path/../rebound $<TARGET_FILE:artemis>
+      COMMAND install_name_tool -change librebound.so @rpath/librebound.so $<TARGET_FILE:artemis>
+    )
+   endif()
 endif()

src/artemis.cpp

@@ -101,7 +101,7 @@ Packages_t ProcessPackages(std::unique_ptr<ParameterInput> &pin) {
   if (do_nbody) packages.Add(NBody::Initialize(pin.get(), constants));
   if (do_gravity) packages.Add(Gravity::Initialize(pin.get(), constants, packages));
   if (do_gas) packages.Add(Gas::Initialize(pin.get(), units, constants, packages));
-  if (do_dust) packages.Add(Dust::Initialize(pin.get()));
+  if (do_dust) packages.Add(Dust::Initialize(pin.get(), units));
   if (do_rotating_frame) packages.Add(RotatingFrame::Initialize(pin.get()));
   if (do_cooling) packages.Add(Gas::Cooling::Initialize(pin.get()));
   if (do_drag) packages.Add(Drag::Initialize(pin.get()));

src/artemis_params.yaml

@@ -33,13 +33,13 @@ artemis:
     cgs:
       _type: opt
       _description: "CGS unit system"
-  unit_conversion:
+  unit_specifier:
     _type: "string"
     _default: "base"
     _description: "How to provide unit conversions between code and physical units"
     base:
       _type: opt
-      _description: "Provide base unit conversions (length, time, mass)"
+      _description: "Provide base unit conversions (length, time, mass, temperature)"
     ppd:
       _type: opt
       _description: "AU, Year/(2 pi), solar mass units for protoplanetary disks"
@@ -55,6 +55,10 @@ artemis:
     _type: "Real"
     _default: "1.0"
     _description: "Physical units value of mass equal to 1 code unit"
+  temperature:
+    _type: "Real"
+    _default: "1.0"
+    _description: "Physical units value of temperature equal to 1 code unit"
 
 
 physics:

src/drag/drag.cpp

@@ -42,6 +42,7 @@ std::shared_ptr<StateDescriptor> Initialize(ParameterInput *pin) {
   params.Add("x2max", pin->GetReal("parthenon/mesh", "x2max"));
   params.Add("x3max", pin->GetReal("parthenon/mesh", "x3max"));
 
+  params.Add("profile",pin->GetString("problem", "profile"));
   params.Add("dslope",pin->GetReal("problem", "dslope"));
   params.Add("tslope",pin->GetReal("problem", "tslope"));
   params.Add("h0",pin->GetReal("problem", "h0"));