Merge branch 'development' into ppm_source_tracing

.clang-tidy

@@ -38,4 +38,4 @@ Checks: >
      mpi-*,
      openmp-*
 
-HeaderFilterRegex: '(/Source/*/|/Util/model_parser_cxx|^\./|^tmp_build_dir/castro_sources/*/).*\.H$'
+HeaderFilterRegex: '(/Source/*/|/Util/model_parser|^\./|^tmp_build_dir/castro_sources/*/).*\.H$'

.github/workflows/c-linter.yml

@@ -52,7 +52,7 @@ jobs:
           python3 external/cpp-linter-action/run_on_changed_files.py ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} \
           -ignore-files="amrex|Microphysics" \
           -config-file="${GITHUB_WORKSPACE}/.clang-tidy" \
-          -header-filter='/Source/|/Util/model_parser_cxx|^\./' \
+          -header-filter='/Source/|/Util/model_parser|^\./' \
           -run-linter
 
       - name: Archive clang tidy report

.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-params.yml

@@ -0,0 +1,46 @@
+name: check runtime params
+
+on:
+  push:
+    branches:
+      - development
+      - main
+  pull_request:
+    branches:
+      - development
+
+jobs:
+  check-runtime-params:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          cd ../..
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - 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-params
+        run: |
+          PYTHONPATH=external/Microphysics/util/build_scripts python .github/workflows/check_params.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)
+
+
+

.github/workflows/check_params.py

@@ -0,0 +1,76 @@
+import argparse
+import importlib
+import os
+import re
+from pathlib import Path
+import sys
+
+# some parameters that are not defined in _cpp_parameters
+
+whitelist = ["castro.lo_bc",
+             "castro.hi_bc",
+             "gravity.abs_tol",
+             "gravity.rel_tol"]
+
+# we don't have all of the radiation parametrs in the _cpp_parameters
+# yet, so we won't check these namespaces
+
+namespace_ignore = ["radiation", "radsolve"]
+
+def doit(castro_dir):
+
+    castro = Path(os.path.abspath(castro_dir))
+
+    # import the module that defines the Castro runtime params
+    sys.path.append(str(castro / "Source" / "driver/"))
+    import parse_castro_params
+
+    # read in the parameters defined in _cpp_parameters
+    param_file = castro / "Source" / "driver" / "_cpp_parameters"
+    params = parse_castro_params.read_param_file(str(param_file))
+
+    namespaces = set(p.namespace for p in params)
+    runtime_parameters = [f"{p.namespace}.{p.name}" for p in params]
+
+    pattern = re.compile(r"[A-Za-z0-9_]+\.[A-Za-z0-9_]+", re.IGNORECASE)
+
+    # loop over all the inputs files
+    exec_path = castro / "Exec"
+    for f in exec_path.glob("**/inputs*"):
+
+        if os.path.isdir(f):
+            continue
+
+        # find all the params in each namespace
+        with open(f) as infile:
+            print(f"working on {f}")
+            for line in infile:
+                # remove comments
+                idx = line.find("#")
+                if idx > 0:
+                    line = line[idx:]
+
+                found_param = pattern.match(line)
+                if not found_param:
+                    continue
+
+                p = found_param.group(0)
+                nm = p.split(".")[0]
+                if nm in namespaces and nm not in namespace_ignore:
+                    if not (p in runtime_parameters or p in whitelist):
+                        sys.exit(f"Error: {p} not valid")
+
+
+if __name__ == "__main__":
+
+    # we need the top-level Castro directory
+
+    p = argparse.ArgumentParser()
+    p.add_argument("castro_dir", type=str, nargs=1,
+                   help="top level Castro directory")
+
+    args = p.parse_args()
+
+    doit(args.castro_dir[0])
+
+

.github/workflows/good_defines.txt

@@ -5,14 +5,13 @@ AMREX_USE_CUDA
 AMREX_USE_GPU
 AMREX_USE_OMP
 AUX_THERMO
-AUX_UPDATE
 BL_FORT_USE_LOWERCASE
 BL_FORT_USE_UNDERSCORE
 BL_FORT_USE_UPPERCASE
 BL_LANG_FORT
 BL_LAZY
 BL_USE_SETBUF
-CXX_MODEL_PARSER
+MODEL_PARSER
 DIFFUSION
 DO_PROBLEM_POST_INIT
 DO_PROBLEM_POST_RESTART
@@ -34,6 +33,7 @@ NSE_TABLE
 RADIATION
 RAD_INTERP
 REACTIONS
+RNG_STATE_INIT
 ROTATION
 SCREENING
 SHOCK_VAR

CHANGES.md

@@ -1,3 +1,56 @@
+# 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
+    and now uses the same ODE code path as simplified-SDC.  This means
+    we don't need our own custom VODE righthand side functions (#2559,
+    #2560, #2567, #2578, #2580, #2584)
+
+  * The true SDC runtime parameter `sdc_solve_for_rhoe` has been
+    removed. (#2572)
+
+  * The true SDC runtime parameters `sdc_solver_tol_spec`,
+    `sdc_solver_tol_ener`, `sdc_solver_atol` have been removed.
+    Instead the Microphysics integration tolerance parameters should
+    be used. (#2571)
+
+  * The true SDC runtime parameter `sdc_newton_use_analytic_jac` has
+    been removed.  Instead the Microphysics integrator `jacobian`
+    parameter should be used (#2573)
+
 # 23.08
 
   * Time evolution without subcycling on the fine levels, which is enabled via
@@ -29,7 +82,7 @@
 # 23.06
 
   * The job_info file now reports the integrator used (#2463)
-  
+
   * 1-d cylindrical geometry was fixed (#2465, #2470)
 
 # 23.05

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

Diagnostics/Sedov/main.cpp

@@ -45,8 +45,9 @@ std::pair<Real, Real> get_coord_info(const Array<Real, AMREX_SPACEDIM>& p,
     AMREX_ASSERT(coord == 2);
 
     r_zone = p[0] - center[0];
-    Real r_r = problo[0]+static_cast<Real>(i+1)*dx_level[0];
-    Real r_l = problo[0]+static_cast<Real>(i)*dx_level[0];
+
+    Real r_r = p[0] + 0.5_rt * dx_level[0];
+    Real r_l = p[0] - 0.5_rt * dx_level[0];
     vol = (4.0_rt/3.0_rt) * M_PI * dx_level[0] *
         (r_r*r_r + r_l*r_r + r_l*r_l);
 

Docs/source/AMR.rst

@@ -148,6 +148,8 @@ fine cell data above it.)
 
 The synchronization consists of two parts:
 
+.. index:: castro.do_reflux
+
 -  Step 1: Hyperbolic reflux
 
    In the hyperbolic reflux step, we update the conserved variables with
@@ -159,7 +161,7 @@ The synchronization consists of two parts:
    where :math:`V` is the volume of the cell and the correction from
    :math:`\delta\Fb` is supported only on coarse cells adjacent to fine grids.
 
-   Note: this can be enabled/disabled via castro.do_reflux. Generally,
+   Note: this can be enabled/disabled via ``castro.do_reflux``. Generally,
    it should be enabled (1).
 
    Also note that for axisymmetric or 1D spherical coordinates, the