Merge branch 'development' into ppm_T

.github/workflows/check-makefiles.yml

@@ -0,0 +1,38 @@
+name: check makefiles
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  check-ifdefs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          # this path is specific to Ubuntu
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Run check-ifdefs
+        run: |
+          python .github/workflows/check_makefiles.py
+

.github/workflows/check_makefiles.py

@@ -0,0 +1,46 @@
+import re
+import sys
+from pathlib import Path
+
+correct_params = {
+    "DEBUG": "FALSE",
+    "USE_MPI": "TRUE",
+    "USE_OMP": "FALSE",
+    "COMP": "gnu",
+    "USE_CUDA": "FALSE",
+    "USE_HIP": "FALSE",
+    "PRECISION": "DOUBLE",
+    "PROFILE": "FALSE"}
+
+
+def find_source_files():
+    p = Path("./Exec")
+    files = list(p.glob(r"**/GNUmakefile"))
+    return files
+
+def check_makefile(makefile):
+
+    with open(makefile) as mf:
+        for _line in mf:
+            if idx := _line.find("#") >= 0:
+                line = _line[:idx]
+            else:
+                line = _line
+
+            for key in correct_params:
+                if key in line:
+                    try:
+                        k, v = re.split(":=|\?=|=", line)
+                    except ValueError:
+                        sys.exit(f"invalid line: {line}")
+
+                    if not v.strip() == correct_params[key]:
+                        sys.exit(f"invalid param {key} in {makefile}")
+
+if __name__ == "__main__":
+
+    for f in find_source_files():
+        check_makefile(f)
+
+
+

CHANGES.md

@@ -1,9 +1,37 @@
 # 23.11
 
+  * Problem GNUmakefiles have been standardized and now allow for the
+    problem to be compiled elsewhere (#2640, #2641, #2642, #2643)
+
+  * The true-SDC Newton solver has been made more robust and faster
+    (#2586, #2602, #2605, #2606)
+
+  * Several problems that required the initial model grid spacing to
+    be specified in the inputs file now automatically compute it as
+    needed, including `flame_wave` (#2610), `convective_flame`,
+    `bubble_convergence`, and `hse_convergence` (#2624), `double_bubble`,
+    `gamma_law_bubble`, and `hse_convergence_general` (#2612)
+
+  * Outflow boundary conditions for the 4th order solver have been changed
+    to no longer use the one-sided stencil (#2607)
+
+  * The ca_rad_source hook in Fortran has been removed. The existing
+    problem_rad_source() hook in C++ can be used instead. (#2626)
+
   * The compile option USE_AUX_UPDATE has been removed. If you want to
     manually update the auxiliary parameters, you can use an external
     source term or you can use the problem post-timestep hook. (#2614)
 
+  * The pressure is now always included in the x-momentum flux in 1-d
+    Cartesian, and this fixes an issue at jumps in refinement with the
+    pressure gradient (#2468)
+
+  * A bug was fixed in the 4th order diffusion operator that was introduced
+    when it was originally converted to C++ (#2592)
+
+  * The 2nd order Radau integrator had the wrong quadrature weights
+    (#2594)
+
 # 23.10
 
   * True-SDC no longer evolves density as part of the reaction system

Diagnostics/DustCollapse/GNUmakefile

@@ -23,7 +23,7 @@ Bpack   := ./Make.package
 Blocs   := .
 # EXTERN_SEARCH = .
 
-CASTRO_HOME := ../..
+CASTRO_HOME ?= ../..
 
 INCLUDE_LOCATIONS += $(AMREX_HOME)/Src/Extern/amrdata
 include $(AMREX_HOME)/Src/Extern/amrdata/Make.package

Diagnostics/Radiation/GNUmakefile

@@ -28,7 +28,7 @@ Bpack   := ./Make.package
 Blocs   := .
 # EXTERN_SEARCH = .
 
-CASTRO_HOME := ../..
+CASTRO_HOME ?= ../..
 
 INCLUDE_LOCATIONS += $(AMREX_HOME)/Src/Extern/amrdata
 include $(AMREX_HOME)/Src/Extern/amrdata/Make.package

Diagnostics/Sedov/GNUmakefile

@@ -23,7 +23,7 @@ Bpack   := ./Make.package
 Blocs   := .
 # EXTERN_SEARCH = .
 
-CASTRO_HOME := ../..
+CASTRO_HOME ?= ../..
 
 #INCLUDE_LOCATIONS += $(AMREX_HOME)/Src/Extern/amrdata
 #include $(AMREX_HOME)/Src/Extern/amrdata/Make.package

Docs/source/reactions.rst

@@ -57,8 +57,32 @@ in the inputs file. Reactions are enabled by setting::
 the efficiency).
 
 It is possible to set the maximum and minimum temperature and density for allowing
-reactions to occur in a zone using the parameters ``castro.react_T_min``,
-``castro.react_T_max``, ``castro.react_rho_min`` and ``castro.react_rho_max``.
+reactions to occur in a zone using the parameters:
+
+* ``castro.react_T_min`` and ``castro.react_T_max`` for temperature
+
+* ``castro.react_rho_min`` and ``castro.react_rho_max`` for density
+
+.. index:: castro.disable_shock_burning, USE_SHOCK_VAR
+
+Burning can also be disabled inside shocks.  This requires that the code be
+compiled with::
+
+  USE_SHOCK_VAR = TRUE
+
+in the ``GNUmakefile``.  This will allocate storage for a shock flag in the conserved
+state array.  This flag is computed via a multidimensional shock detection algorithm
+that looks for compression (:math:`\nabla \cdot \ub < 0`) along with a pressure jump
+in the direction of compression.  The runtime parameter::
+
+   castro.disable_shock_burning = 1
+
+will skip reactions in a zone where we've detected a shock.
+
+.. note::
+
+   Both the compilation with ``USE_SHOCK_VAR = TRUE`` and the runtime parameter
+   ``castro.disable_shock_burning = 1`` are needed to turn off burning in shocks.
 
 Reactions Flowchart
 ===================

Exec/Make.Castro

@@ -97,11 +97,19 @@ endif
 
 # need to put any build suffices before Make.defs
 ifeq ($(USE_SIMPLIFIED_SDC), TRUE)
-  USERSuffix = .SMPLSDC
+  ifneq ($(USERSuffix),)
+    USERSuffix := .SMPLSDC$(USERSuffix)
+  else
+    USERSuffix = .SMPLSDC
+  endif
 endif
 
 ifeq ($(USE_TRUE_SDC), TRUE)
-  USERSuffix = .TRUESDC
+  ifneq ($(USERSuffix),)
+    USERSuffix := .TRUESDC$(USERSuffix)
+  else
+    USERSuffix = .TRUESDC
+  endif
 endif
 
 USE_MLMG = FALSE

Exec/gravity_tests/DustCollapse/GNUmakefile

@@ -17,7 +17,7 @@ USE_MHD = FALSE
 
 
 # define the location of the CASTRO top directory
-CASTRO_HOME  := ../../..
+CASTRO_HOME  ?= ../../..
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/EOS
 EOS_DIR     := gamma_law
@@ -26,7 +26,9 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS = ignition.net
 
-Bpack	:= ./Make.package
-Blocs	:= .
+PROBLEM_DIR ?= ./
+
+Bpack	:= $(PROBLEM_DIR)/Make.package
+Blocs	:= $(PROBLEM_DIR)
 
 include $(CASTRO_HOME)/Exec/Make.Castro

Exec/gravity_tests/StarGrav/GNUmakefile

@@ -1,4 +1,4 @@
-CASTRO_HOME := ../../..
+CASTRO_HOME ?= ../../..
 
 PRECISION  = DOUBLE
 PROFILE    = FALSE
@@ -23,7 +23,9 @@ EOS_DIR     := helmholtz
 NETWORK_DIR := general_null
 NETWORK_INPUTS = ignition_wdconvect.net
 
-Bpack   := ./Make.package
-Blocs   := .
+PROBLEM_DIR ?= ./
+
+Bpack   := $(PROBLEM_DIR)/Make.package
+Blocs   := $(PROBLEM_DIR)
 
 include $(CASTRO_HOME)/Exec/Make.Castro

Exec/gravity_tests/advecting_white_dwarf/GNUmakefile

@@ -23,7 +23,7 @@ NETWORK_DIR ?= general_null
 
 NETWORK_INPUTS = ignition.net
 
-PROBLEM_DIR ?= $(CASTRO_HOME)/Exec/gravity_tests/advecting_white_dwarf
+PROBLEM_DIR ?= ./
 
 Blocs = $(PROBLEM_DIR)
 Bpack = $(PROBLEM_DIR)/Make.package

Exec/gravity_tests/evrard_collapse/GNUmakefile

@@ -1,12 +1,7 @@
 # Define the location of the CASTRO top directory,
 # if not already defined by an environment variable.
 
-CASTRO_HOME := ../../..
-
-# Location of this directory. Useful if
-# you're trying to compile this from another location.
-
-TEST_DIR = $(CASTRO_HOME)/Exec/gravity_tests/evrard_collapse
+CASTRO_HOME ?= ../../..
 
 PRECISION  = DOUBLE
 PROFILE    = FALSE
@@ -17,7 +12,7 @@ DIM        = 3
 
 COMP	   = gnu
 
-USE_MPI    = FALSE
+USE_MPI    = TRUE
 USE_OMP    = FALSE
 
 USE_GRAV   = TRUE
@@ -30,7 +25,9 @@ EOS_DIR     := gamma_law
 NETWORK_DIR := general_null
 NETWORK_INPUTS = gammalaw.net
 
-Bpack   += $(TEST_DIR)/Make.package
-Blocs   += $(TEST_DIR)
+PROBLEM_DIR ?= ./
+
+Bpack   += $(PROBLEM_DIR)/Make.package
+Blocs   += $(PROBLEM_DIR)
 
 include $(CASTRO_HOME)/Exec/Make.Castro

Exec/gravity_tests/hse_convergence/GNUmakefile

@@ -13,7 +13,7 @@ USE_MODEL_PARSER = TRUE
 
 USE_MAESTRO_INIT = FALSE
 
-CASTRO_HOME = ../../..
+CASTRO_HOME ?= ../../..
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz
@@ -22,7 +22,9 @@ EOS_DIR     := helmholtz
 NETWORK_DIR := general_null
 NETWORK_INPUTS := triple_alpha_plus_o.net
 
-Bpack   := ./Make.package
-Blocs   := .
+PROBLEM_DIR ?= ./
+
+Bpack   := $(PROBLEM_DIR)/Make.package
+Blocs   := $(PROBLEM_DIR)
 
 include $(CASTRO_HOME)/Exec/Make.Castro

Exec/gravity_tests/hse_convergence/_prob_params

@@ -1,6 +1,4 @@
 
-nx_model        integer        128          y
-
 dens_base       real           1.0_rt       y
 
 temp_base       real           1.0_rt       y

Exec/gravity_tests/hse_convergence/inputs.ppm.128

@@ -78,7 +78,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 128
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/inputs.ppm.256

@@ -78,7 +78,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 256
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/inputs.ppm.512

@@ -78,7 +78,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 512
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/inputs.ppm.64

@@ -78,7 +78,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 64
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/inputs.sdc2-pslope-reflect.testsuite

@@ -78,7 +78,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 256
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/inputs.sdc4-reflect.testsuite

@@ -77,7 +77,5 @@ amr.derive_plot_vars = ALL
 problem.dens_base = 1.e7
 problem.temp_base = 1.0e8
 
-problem.nx_model = 256
-
 # MICROPHYSICS
 network.small_x = 1.e-10

Exec/gravity_tests/hse_convergence/problem_initialize.H

@@ -6,6 +6,7 @@
 #include <model_parser.H>
 #include <initial_model.H>
 #include <network.H>
+#include <global.H>
 
 AMREX_INLINE
 void problem_initialize ()
@@ -38,10 +39,19 @@ void problem_initialize ()
 
     int nbuf = 8;
 
+    // we use the fine grid dx for the model resolution
+    auto fine_geom = global::the_amr_ptr->Geom(global::the_amr_ptr->maxLevel());
+
+    auto dx = fine_geom.CellSizeArray();
+    auto dx_model = dx[AMREX_SPACEDIM-1];
+
+    int nx_model = static_cast<int>((probhi[AMREX_SPACEDIM-1] -
+                                     problo[AMREX_SPACEDIM-1] + 1.e-8_rt) / dx_model);
+
     // generate the initial model -- it will be stored in the model
     // parser global data
 
-    generate_initial_model(problem::nx_model,
+    generate_initial_model(nx_model,
                            problo[AMREX_SPACEDIM-1], probhi[AMREX_SPACEDIM-1],
                            model_params, nbuf);