Merge branch 'development' into update_xrb_spherical

.codespell-ignore-words

@@ -12,4 +12,5 @@ nd
 ue
 bion
 aas
-checkin
+checkin
+indx

.github/workflows/gpu_action.yml

@@ -8,7 +8,7 @@ concurrency:
 
 jobs:
   gpu-compilation:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
         with:

CHANGES.md

@@ -1,3 +1,23 @@
+# 25.01
+
+  * address rotation source in spherical 2d coordinate (#2967)
+
+  * update scripts and input files for diffusion test  (#3012)
+
+  * update pressure via eos when transverse_use_eos=1 (#3004)
+
+  * update thermal diffusion documentation (#3011)
+
+  * rename `Opacity_dir` -> `OPACITY_DIR` (#3006)
+
+  * sync GPU CI dependencies with AMReX (#3010)
+
+  * wdmerger: update inputs for He mergers to include burn retry
+    and adjust I/O (#3008)
+
+  * fix area/vol factors for spherical when theta is close to 0 or pi
+    (#3007)
+
 # 24.12
 
   * update clang-tidy CI (#2992, #3002)
@@ -908,7 +928,7 @@
      the conversion of primitive to conserved variables (#804)
 
    * We've changed how the backup for retries is done.  Presently if
-     use_retry is enabled we make a pre-emptive copy of the StateData
+     use_retry is enabled we make a preemptive copy of the StateData
      right at the beginning of the timestep.  Now we only backup when
      we detect that a retry is needed (#812)
 

Exec/gravity_tests/DustCollapse/GNUmakefile

@@ -22,7 +22,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = ignition.net
 

Exec/gravity_tests/StarGrav/GNUmakefile

@@ -16,7 +16,7 @@ USE_REACT  = FALSE
 
 USE_MODEL_PARSER = TRUE
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/gravity_tests/evrard_collapse/GNUmakefile

@@ -18,10 +18,10 @@ USE_OMP    = FALSE
 USE_GRAV   = TRUE
 
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/gravity_tests/hse_convergence/GNUmakefile

@@ -15,7 +15,7 @@ USE_MAESTRO_INIT = FALSE
 
 CASTRO_HOME ?= ../../..
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/gravity_tests/hse_convergence_general/GNUmakefile

@@ -20,7 +20,7 @@ USE_MODEL_PARSER = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  ?= ../../..
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/gravity_tests/hydrostatic_adjust/GNUmakefile

@@ -15,7 +15,7 @@ USE_MODEL_PARSER = TRUE
 
 CASTRO_HOME ?= ../../..
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/gravity_tests/uniform_cube/GNUmakefile

@@ -20,7 +20,7 @@ USE_GRAV    ?= TRUE
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHSICS_HOME)/networks
 NETWORK_DIR ?= general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/gravity_tests/uniform_sphere/GNUmakefile

@@ -20,7 +20,7 @@ USE_GRAV    ?= TRUE
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHSICS_HOME)/networks
 NETWORK_DIR ?= general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/KH/GNUmakefile

@@ -21,7 +21,7 @@ NUMADV := 1
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     ?= gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR ?= general_null
 NETWORK_INPUTS ?= gammalaw.net
 

Exec/hydro_tests/RT/GNUmakefile

@@ -19,7 +19,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/Sedov/GNUmakefile

@@ -20,7 +20,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/Sod_stellar/GNUmakefile

@@ -18,7 +18,7 @@ USE_MHD = FALSE
 # define the location of the CASTRO top directory
 CASTRO_HOME ?= ../../..
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/hydro_tests/Vortices_LWAcoustics/GNUmakefile

@@ -18,7 +18,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/acoustic_pulse/GNUmakefile

@@ -16,7 +16,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/acoustic_pulse_general/GNUmakefile

@@ -16,7 +16,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := helmholtz
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/double_mach_reflection/GNUmakefile

@@ -17,7 +17,7 @@ CASTRO_HOME  ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/oddeven/GNUmakefile

@@ -18,7 +18,7 @@ CASTRO_HOME ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/riemann_2d/GNUmakefile

@@ -16,7 +16,7 @@ CASTRO_HOME ?= ../../..
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
 
-# This sets the network directory in $(MICROPHYSICS_HOME)/Networks
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 

Exec/hydro_tests/rotating_torus/GNUmakefile

@@ -17,7 +17,7 @@ USE_HYBRID_MOMENTUM = TRUE
 # define the location of the CASTRO top directory
 CASTRO_HOME  ?= ../../..
 
-# This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := polytrope
 
 # This sets the network directory in $(MICROPHYSICS_HOME)/networks

Exec/hydro_tests/simple_convection/GNUmakefile

@@ -0,0 +1,31 @@
+PRECISION        = DOUBLE
+PROFILE          = FALSE
+DEBUG            = FALSE
+DIM              = 2
+
+COMP	         = gnu
+
+USE_MPI          = TRUE
+USE_OMP          = FALSE
+
+USE_GRAV         = TRUE
+USE_REACT        = FALSE
+
+USE_MODEL_PARSER = TRUE
+USE_RNG_STATE_INIT = TRUE
+
+CASTRO_HOME ?= ../../..
+
+# This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
+EOS_DIR     := gamma_law
+
+# This sets the network directory in $(MICROPHYSICS_HOME)/networks
+NETWORK_DIR := general_null
+NETWORK_INPUTS = gammalaw.net
+
+PROBLEM_DIR ?= ./
+
+Bpack   := $(PROBLEM_DIR)/Make.package
+Blocs   := $(PROBLEM_DIR)
+
+include $(CASTRO_HOME)/Exec/Make.Castro

Exec/hydro_tests/simple_convection/Make.package

@@ -0,0 +1,3 @@
+CEXE_headers += initial_model.H
+
+

Exec/hydro_tests/simple_convection/README.md

@@ -0,0 +1,5 @@
+# simple_convection
+
+This is an implementation of the convection problem from pyro.
+
+

Exec/hydro_tests/simple_convection/_prob_params

@@ -0,0 +1,12 @@
+dens_base      real     10.0    y
+
+scale_height   real      4.0    y
+
+y_height       real      2.0    y
+
+thickness      real      0.25   y
+
+e_rate         real      0.1    y
+
+low_density_cutoff   real    0.01    y
+

Exec/hydro_tests/simple_convection/initial_model.H

@@ -0,0 +1,94 @@
+#ifndef INITIAL_MODEL_H
+#define INITIAL_MODEL_H
+
+#include <prob_parameters.H>
+#include <network.H>
+#include <eos.H>
+
+struct model_t {
+    amrex::Real dens_base = -1;
+    amrex::Real scale_height = -1;
+    Real xn[NumSpec] = {0.0};
+};
+
+
+
+///
+/// construct an initial model in HSE.  Note: this does not return
+/// anything, but rather updates the model_parser globals with the
+/// model information.
+///
+AMREX_INLINE
+void
+generate_initial_model(const int npts_model, const Real xmin, const Real xmax,
+                       const model_t model_params) {
+
+    model::npts = npts_model;
+    model::initialized = true;
+
+    if (npts_model > NPTS_MODEL) {
+        amrex::Error("Error: model has more than NPTS_MODEL points,  Increase MAX_NPTS_MODEL");
+    }
+
+    // compute the pressure scale height (for an isothermal, ideal-gas
+    // atmosphere)
+
+    amrex::Real pres_base = model_params.scale_height * model_params.dens_base * std::abs(gravity::const_grav);
+
+    // create the grid -- cell centers
+
+    Real dx = (xmax - xmin) / npts_model;
+
+    for (int i = 0; i < npts_model; i++) {
+        model::profile(0).r(i) = xmin + (static_cast<Real>(i) + 0.5_rt) * dx;
+    }
+
+    for (int i = 0; i < npts_model; i++) {
+
+        amrex::Real density;
+        amrex::Real pressure;
+
+        amrex::Real profile = 1.0 - (eos_rp::eos_gamma - 1.0) / eos_rp::eos_gamma * model::profile(0).r(i) / model_params.scale_height;
+
+        if (profile > 0.0) {
+            density = std::max(model_params.dens_base * std::pow(profile, 1.0/(eos_rp::eos_gamma - 1.0)),
+                               problem::low_density_cutoff);
+        } else {
+            density = problem::low_density_cutoff;
+        }
+
+        if (i == 0) {
+            pressure = pres_base;
+        } else if (density <= problem::low_density_cutoff + 1.e-30_rt) {
+            pressure = model::profile(0).state(i-1, model::ipres);
+        } else {
+            pressure = pres_base *
+                std::pow(density / model_params.dens_base, eos_rp::eos_gamma);
+        }
+
+        // initial guess
+
+        amrex::Real temp = T_guess;
+
+        eos_t eos_state;
+        eos_state.p = pressure;
+        eos_state.T = temp;
+        eos_state.rho = density;
+        for (int n = 0; n < NumSpec; n++) {
+            eos_state.xn[n] = model_params.xn[n];
+        }
+
+        eos(eos_input_rp, eos_state);
+
+        model::profile(0).state(i, model::idens) = density;
+        model::profile(0).state(i, model::ipres) = pressure;
+        model::profile(0).state(i, model::itemp) = eos_state.T;
+        for (int n = 0; n < NumSpec; n++) {
+            model::profile(0).state(i, model::ispec+n) = model_params.xn[n];
+        }
+
+    }
+
+}
+
+#endif