Merge branch 'development' into main

AMReX-Astro · Mar 1, 2021 · 5e0a1b9 · 5e0a1b9
2 parents 2499072 + 6e075fa
commit 5e0a1b9
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Showing 56 changed files with 394 additions and 7,262 deletions.
diff --git a/Exec/Make.Castro b/Exec/Make.Castro
@@ -66,12 +66,6 @@ USE_ALL_CASTRO ?= TRUE
 
 USE_AMR_CORE ?= TRUE
 
-# hack for now -- CUDA processing doesn't respect functions blocked by
-# ifdefs, so we need to define EXTRA_THERMO
-ifeq ($(USE_CUDA),TRUE)
-  DEFINES += -DEXTRA_THERMO
-endif
-
 # all Castro problems use a dimension-agnostic interface
 DIMENSION_AGNOSTIC = TRUE
 
@@ -347,16 +341,8 @@ endif
 
 include $(Bpack)
 
-ifeq ($(MEGA_FORTRAN), TRUE)
-   F90EXE_sources += mega_f.F90
-   #$(depEXETempDir)/f90.depends: mega_f.F90
-else
-   f90EXE_sources += $(ca_f90EXE_sources)
-   F90EXE_sources += $(ca_F90EXE_sources)
-endif
-
-mega_f.F90: $(ca_F90EXE_sources) $(ca_f90EXE_sources)
-	$(AMREX_HOME)/Tools/F_scripts/f90cat.py $^
+f90EXE_sources += $(ca_f90EXE_sources)
+F90EXE_sources += $(ca_F90EXE_sources)
 
 INCLUDE_LOCATIONS += $(Blocs)
 VPATH_LOCATIONS   += $(Blocs)

diff --git a/Exec/hydro_tests/rotating_torus/Prob.cpp b/Exec/hydro_tests/rotating_torus/Prob.cpp
@@ -30,9 +30,6 @@ Castro::compute_moment_of_inertia()
         // Get the Castro level
         Castro& ca_lev = getLevel(lev);
 
-        // Update the local level we're on.
-        ca_set_amr_info(lev, -1, -1, -1.0, -1.0);
-
         // Add up the moment of inertia on this level
         int idir = -1; // So we do r**2, rather than any particular direction
         moment += ca_lev.locSquaredSum("density", time, idir, local_flag);

diff --git a/Exec/reacting_tests/nse_test/convergence_simplified_sdc.sh b/Exec/reacting_tests/nse_test/convergence_simplified_sdc.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# echo the commands
+set -x
+
+EXEC=./Castro2d.gnu.MPI.SMPLSDC.ex
+RUNPARAMS="
+castro.time_integration_method=3
+"
+
+mpiexec -n 8 ${EXEC} inputs.64 ${RUNPARAMS} >& /dev/null
+mpiexec -n 8 ${EXEC} inputs.128 ${RUNPARAMS} >& /dev/null
+mpiexec -n 8 ${EXEC} inputs.256 ${RUNPARAMS} >& /dev/null
+
+RichardsonConvergenceTest2d.gnu.ex coarFile=nse_test_64_plt00080 mediFile=nse_test_128_plt00160 fineFile=nse_test_256_plt00320  >& nse_convergence_simple_sdc_lo.out
+
+mpiexec -n 8 ${EXEC} inputs.512 ${RUNPARAMS} >& /dev/null
+
+RichardsonConvergenceTest2d.gnu.ex coarFile=nse_test_128_plt00160 mediFile=nse_test_256_plt00320 fineFile=nse_test_512_plt00640 >& nse_convergence_simple_sdc_hi.out
+
+
diff --git a/Exec/reacting_tests/nse_test/create_pretty_tables.py b/Exec/reacting_tests/nse_test/create_pretty_tables.py
@@ -116,6 +116,10 @@ def read_convergence(file_lo, file_hi):
                  "rho_He4": r"$\rho X(\isotm{He}{4})$",
                  "rho_C12": r"$\rho X(\isotm{C}{12})$",
                  "rho_O16": r"$\rho X(\isotm{O}{16})$",
+                 "rho_Cr48": r"$\rho X(\isotm{Cr}{48})$",
+                 "rho_Fe52": r"$\rho X(\isotm{Fe}{52})$",
+                 "rho_Fe54": r"$\rho X(\isotm{Fe}{54})$",
+                 "rho_Ni56": r"$\rho X(\isotm{Ni}{56})$",
                  "rho_Fe56": r"$\rho X(\isotm{Fe}{56})$",
                  "rho_Ye": r"$\rho Y_e$",
                  "rho_abar": r"$\rho \bar{A}$",

diff --git a/Exec/science/rotating_star/15m_500_sec.hse.6400 b/Exec/science/rotating_star/15m_500_sec.hse.6400
diff --git a/Exec/science/rotating_star/GNUmakefile b/Exec/science/rotating_star/GNUmakefile
@@ -13,14 +13,15 @@ USE_MPI    = TRUE
 
 USE_GRAV   = TRUE
 USE_REACT  = TRUE
+USE_NSE    = TRUE
 
 USE_CXX_MODEL_PARSER = TRUE
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks
-NETWORK_DIR := aprox21
+NETWORK_DIR := aprox19
 
 INTEGRATOR_DIR := VODE
 

diff --git a/Exec/science/rotating_star/probin b/Exec/science/rotating_star/probin
@@ -1,6 +1,6 @@
 &fortin
 
-  model_name =  "15m_500_sec.hse.6400"
+  model_name =  "15m_aprox19.6400"
 
 /
 
@@ -19,7 +19,7 @@
   max_tempgrad_lev   = -1
 
   dengrad            = 1.e18
-  denerr             = 0.5e9
+  denerr             = 0.5e5
 
   velgrad            = 1.e18
   velerr             = 1.e18

diff --git a/Exec/science/wdmerger/Prob.cpp b/Exec/science/wdmerger/Prob.cpp
@@ -99,8 +99,6 @@ Castro::wd_update (Real time, Real dt)
 
     for (int lev = 0; lev <= parent->finestLevel(); lev++) {
 
-      ca_set_amr_info(lev, -1, -1, -1.0, -1.0);
-
       Castro& c_lev = getLevel(lev);
 
       GeometryData geomdata = c_lev.geom.data();
@@ -276,8 +274,6 @@ Castro::wd_update (Real time, Real dt)
 
     }
 
-    ca_set_amr_info(level, -1, -1, -1.0, -1.0);
-
     // Compute effective radii of stars at various density cutoffs
 
     bool local_flag = true;
@@ -421,8 +417,6 @@ void Castro::volInBoundary (Real time, Real& vol_P, Real& vol_S, Real rho_cutoff
 
     for (int lev = 0; lev <= parent->finestLevel(); lev++) {
 
-      ca_set_amr_info(lev, -1, -1, -1.0, -1.0);
-
       Castro& c_lev = getLevel(lev);
 
       const auto dx = c_lev.geom.CellSizeArray();
@@ -502,8 +496,6 @@ void Castro::volInBoundary (Real time, Real& vol_P, Real& vol_S, Real rho_cutoff
     if (!local)
       amrex::ParallelDescriptor::ReduceRealSum({vol_P, vol_S});
 
-    ca_set_amr_info(level, -1, -1, -1.0, -1.0);
-
 }
 
 

diff --git a/Exec/science/wdmerger/inputs_2d b/Exec/science/wdmerger/inputs_2d
@@ -179,6 +179,12 @@ castro.dual_energy_eta1 = 1.0e-3
 # Threshold for when to use (E - K) in updating internal energy
 castro.dual_energy_eta2 = 1.0e-4
 
+# Use Coulomb corrections in Helmholtz EOS
+eos.use_eos_coulomb = 1
+
+# Keep EOS inputs constant after EOS evaluation
+eos.eos_input_is_constant = 1
+
 ############################################################################################
 # Reactions/Network
 ############################################################################################
@@ -201,6 +207,38 @@ castro.react_rho_min = 1.0e6
 # Maximum density for allowing nuclear burning
 castro.react_rho_max = 1.0e12
 
+# Smallest allowable mass fraction
+network.small_x = 1.0e-12
+
+# Burn at constant volume
+integrator.do_constant_volume_burn = 1
+
+# Evaluate the RHS during the burn
+integrator.call_eos_in_rhs = 1
+
+# Integration tolerances
+integrator.rtol_spec = 1.0e-6
+integrator.atol_spec = 1.0e-6
+
+integrator.rtol_temp = 1.0e-6
+integrator.atol_temp = 1.0e-6
+
+integrator.rtol_enuc = 1.0e-6
+integrator.atol_enuc = 1.0e-6
+
+# Do not abort or retry on a failed burn (Castro will handle this)
+integrator.abort_on_failure = 0
+integrator.retry_burn = 0
+
+# Renormalize abundances during the burn
+integrator.renormalize_abundances = 1
+
+# Maximum temperature allowed in the burn
+integrator.MAX_TEMP = 1.0e10
+
+# Use tabular rate evaluation when availble
+network.use_tables = 1
+
 ############################################################################################
 # Gravity
 ############################################################################################

diff --git a/Exec/science/wdmerger/inputs_3d b/Exec/science/wdmerger/inputs_3d
@@ -182,6 +182,12 @@ castro.dual_energy_eta1 = 1.0e-3
 # Threshold for when to use (E - K) in updating internal energy
 castro.dual_energy_eta2 = 1.0e-4
 
+# Use Coulomb corrections in Helmholtz EOS
+eos.use_eos_coulomb = 1
+
+# Keep EOS inputs constant after EOS evaluation
+eos.eos_input_is_constant = 1
+
 ############################################################################################
 # Reactions/Network
 ############################################################################################
@@ -204,6 +210,38 @@ castro.react_rho_min = 1.0e6
 # Maximum density for allowing nuclear burning
 castro.react_rho_max = 1.0e12
 
+# Smallest allowable mass fraction
+network.small_x = 1.0e-12
+
+# Burn at constant volume
+integrator.do_constant_volume_burn = 1
+
+# Evaluate the RHS during the burn
+integrator.call_eos_in_rhs = 1
+
+# Integration tolerances
+integrator.rtol_spec = 1.0e-6
+integrator.atol_spec = 1.0e-6
+
+integrator.rtol_temp = 1.0e-6
+integrator.atol_temp = 1.0e-6
+
+integrator.rtol_enuc = 1.0e-6
+integrator.atol_enuc = 1.0e-6
+
+# Do not abort or retry on a failed burn (Castro will handle this)
+integrator.abort_on_failure = 0
+integrator.retry_burn = 0
+
+# Renormalize abundances during the burn
+integrator.renormalize_abundances = 1
+
+# Maximum temperature allowed in the burn
+integrator.MAX_TEMP = 1.0e10
+
+# Use tabular rate evaluation when availble
+network.use_tables = 1
+
 ############################################################################################
 # Gravity
 ############################################################################################

diff --git a/Exec/science/wdmerger/probin b/Exec/science/wdmerger/probin
@@ -94,43 +94,4 @@
 
 &extern
 
-  ! Note that some of the parameters in this
-  ! namelist are specific to the default EOS,
-  ! network, and/or integrator used in the 
-  ! makefile. If you try a different set of 
-  ! microphysics routines be sure to check that
-  ! the parameters in here are consistent, as
-  ! Fortran does not like seeing unknown variables
-  ! in the namelist.
-
-  small_x = 1.d-12
-
-  use_eos_coulomb = T
-  eos_input_is_constant = T
-
-  do_constant_volume_burn = T
-  call_eos_in_rhs = T
-
-  rtol_spec = 1.d-6
-  atol_spec = 1.d-6
-
-  rtol_temp = 1.d-6
-  atol_temp = 1.d-6
-
-  rtol_enuc = 1.d-6
-  atol_enuc = 1.d-6
-
-  abort_on_failure = F
-  retry_burn = F
-
-  renormalize_abundances = T
-
-  MAX_TEMP = 1.d10
-
-  ! Note that not every network has tabular
-  ! rates enabled, so for some networks the
-  ! following option will have no effect.
-
-  use_tables = T
-
 /
diff --git a/Exec/science/wdmerger/sum_integrated_quantities.cpp b/Exec/science/wdmerger/sum_integrated_quantities.cpp
@@ -102,10 +102,6 @@ Castro::sum_integrated_quantities ()
     for (int lev = 0; lev <= finest_level; lev++)
     {
 
-      // Update the local level we're on.
-
-      ca_set_amr_info(lev, -1, -1, -1.0, -1.0);
-
       // Get the current level from Castro
 
       Castro& ca_lev = getLevel(lev);
@@ -148,10 +144,6 @@ Castro::sum_integrated_quantities ()
 
     }
 
-    // Return to the original level.
-
-    ca_set_amr_info(level, -1, -1, -1.0, -1.0);
-
     // Do the reductions.
 
     int nfoo_sum = 18;

diff --git a/Exec/science/wdmerger/tests/tde/inputs.test b/Exec/science/wdmerger/tests/tde/inputs.test
@@ -124,6 +124,12 @@ castro.small_temp = 1.e5
 # Minimum allowable density (g / cm**3)
 castro.small_dens = 1.e-5
 
+# Use Coulomb corrections in Helmholtz EOS
+eos.use_eos_coulomb = 1
+
+# Keep EOS inputs constant after EOS evaluation
+eos.eos_input_is_constant = 1
+
 ############################################################################################
 # Gravity
 ############################################################################################

diff --git a/Exec/science/wdmerger/tests/tde/probin b/Exec/science/wdmerger/tests/tde/probin
@@ -42,43 +42,4 @@
 
 &extern
 
-  ! Note that some of the parameters in this
-  ! namelist are specific to the default EOS,
-  ! network, and/or integrator used in the 
-  ! makefile. If you try a different set of 
-  ! microphysics routines be sure to check that
-  ! the parameters in here are consistent, as
-  ! Fortran does not like seeing unknown variables
-  ! in the namelist.
-
-  small_x = 1.d-12
-
-  use_eos_coulomb = T
-  eos_input_is_constant = T
-
-  do_constant_volume_burn = T
-  call_eos_in_rhs = T
-
-  rtol_spec = 1.d-6
-  atol_spec = 1.d-6
-
-  rtol_temp = 1.d-6
-  atol_temp = 1.d-6
-
-  rtol_enuc = 1.d-6
-  atol_enuc = 1.d-6
-
-  abort_on_failure = F
-  retry_burn = F
-
-  renormalize_abundances = T
-
-  MAX_TEMP = 1.d10
-
-  ! Note that not every network has tabular
-  ! rates enabled, so for some networks the
-  ! following option will have no effect.
-
-  use_tables = T
-
 /