Merge branch 'development' into make_1d_cart_mom_have_p

.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-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_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

@@ -12,7 +12,7 @@ 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 +34,7 @@ NSE_TABLE
 RADIATION
 RAD_INTERP
 REACTIONS
+RNG_STATE_INIT
 ROTATION
 SCREENING
 SHOCK_VAR

CHANGES.md

@@ -1,3 +1,22 @@
+# 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 +48,7 @@
 # 23.06
 
   * The job_info file now reports the integrator used (#2463)
-  
+
   * 1-d cylindrical geometry was fixed (#2465, #2470)
 
 # 23.05

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/FlowChart.rst

@@ -662,12 +662,13 @@ The overall evolution appears as:
 
 #. *Initialization* (``initialize_advance``)
 
-   Here we create the ``MultiFab`` s that store the needed information
+   We first do a ``clean_state`` on the old data (``S_old``).
+
+   We next create the ``MultiFab`` s that store the needed information
    at the different time nodes.  Each of the quantities below is a
    vector of size ``SDC_NODES``, whose components are the ``MultiFab``
    for that time node:
 
-
     * ``k_new`` : the current solution at this time node.
 
       Note that
@@ -700,14 +701,15 @@ SDC Single Iteration Flowchart
 
 .. index:: do_advance_sdc
 
-The update through all time nodes for a single iteration is done by
-``do_advance_sdc``.  The basic update appears as:
-
 Throughout this driver we use the ``State_Type`` ``StateData`` as
 storage for the current node.  In particular, we use the new time slot
 in the ``StateData`` (which we refer to as ``S_new``) to allow us to
 do ``FillPatch`` operations.
 
+The update through all time nodes for a single iteration is done by
+``do_advance_sdc``.  The basic update appears as:
+
+
 #. *Initialize*
 
    We allocate ``Sborder``.  Just like with the Strang CTU driver, we
@@ -756,18 +758,18 @@ do ``FillPatch`` operations.
 
        Then fill all other time nodes as: ``R_old[n]`` = ``R_old[0]``
 
-    * Do the SDC update from node ``m`` to ``m+1``.
+   * Do the SDC update from node ``m`` to ``m+1``.
 
-      We call ``do_sdc_update()`` to do the update in time to the next
-      node.  This solves the nonlinear system (when we have reactions)
-      and stores the solution in ``k_new[m+1]``.
+     We call ``do_sdc_update()`` to do the update in time to the next
+     node.  This solves the nonlinear system (when we have reactions)
+     and stores the solution in ``k_new[m+1]``.
 
 #. Store the advective terms for the next iteration.
 
    Since we are done with this iteration, we do: ``A_old[n]``
    :math:`\leftarrow` ``A_new[n]``.
 
-   We also store ``R_old`` for the next iteration.  We do this by
+#. Store ``R_old`` for the next iteration.  We do this by
    calling the reaction source one last time using the data for each
    time node.
 
@@ -777,6 +779,10 @@ do ``FillPatch`` operations.
 
    ``S_new`` :math:`\leftarrow` ``k_new[SDC_NODES-1]``
 
+#. Store the old and new sources in the State Data.
+
+#. Store the reaction information for the plotfiles.
+
 #. Call ``finalize_do_advance`` to clean up the memory.
 
 

Docs/source/Particles.rst

@@ -130,9 +130,6 @@ the same time and each line corresponds to each particle info. while
 in the other output file for the other 6 particles, 6 lines are stored
 at the same time.
 
-If ``particles.write_in_plotfile`` = 1, the particle data are stored
-in a binary file along with the main CASTRO output plotfile in
-directories ``pltXXXXX/Tracer/``.
 
 Run-time Screen Output
 ----------------------

Docs/source/Verification.rst

@@ -445,7 +445,7 @@ Light Front
 
 The light front problem tests the ability of the radiation solver to
 operate in the free-streaming limit. A radiation front is
-estabilished by initializing one end of the computational domain with
+established by initializing one end of the computational domain with
 a finite radiation field, and zero radiation field everywhere else.
 The speed of propagation of the radiation front is keep in check by
 the flux-limiters, to prevent it from exceeding :math:`c`.

Docs/source/creating_a_problem.rst

@@ -234,7 +234,7 @@ Many problem setups begin with a 1-d initial model that is mapped onto
 the grid.  The ``model_parser.H`` provides the functions that read in
 the initial model and map it on the Castro grid.  To enable this, add::
 
-  USE_CXX_MODEL_PARSER = TRUE
+  USE_MODEL_PARSER = TRUE
 
 to the problem ``GNUmakefile``.  There are 2 other parameters that can
 be set in the makefile to control the initial model storage:

Docs/source/sdc.rst

@@ -42,23 +42,13 @@ The options that affect the nonlinear solve are:
   * 3 : use VODE for the first iteration and then Newton for the
     subsequent iterations.
 
-* ``sdc_solver_tol_dens`` : the relative error on the density in solving the nonlinear system.
+  The tolerances for both the Newton and VODE solver are controlled by
+  the usual Microphysics parameters: ``integrator.rtol_spec``,
+  ``integrator.atol_spec``, ``integrator.rtol_enuc``,
+  ``integrator.atol_enuc``.
 
-* ``sdc_solver_tol_spec`` : the relative error on the partial densities, :math:`(\rho X_k)`
-  in the nonlinear solve.
-
-* ``sdc_solver_tol_ener`` : the relative error of the energy in the nonlinear solve.
-
-* ``sdc_solver_atol`` : the absolute error in the mass fractions during the nonlinear solve.
-
-* ``sdc_solver_relax_factor`` : the factor by which to relax the
-  tolerances (i.e. increase them) for earlier iterations.  We reach
-  the desired tolerances on the final iteration.
-
-* ``sdc_solve_for_rhoe`` : whether we solve the system in terms of :math:`(\rho e)` or :math:`(\rho E)`.
-
-* ``sdc_newton_use_analytic_jac`` : whether we use the analytic Jacobian when doing Newton iterations for
-  the reaction part of the system or compute it numerically.
+  In all cases, the type of Jacobian (analytic or numerical) is determined by
+  ``integrator.jacobian``.
 
 
 

Docs/source/software.rst

@@ -622,7 +622,7 @@ get a sense of these is to look at the ``.H`` files in the
 ------------------
 
 There is a ``Geometry`` object, ``geom`` for each level as part of
-the ``Castro`` object (this is inhereted through ``AmrLevel``).
+the ``Castro`` object (this is inherited through ``AmrLevel``).
 
 ``ParmParse`` class
 -------------------

Exec/Make.Castro

@@ -89,6 +89,12 @@ ifeq ($(USE_SDC), TRUE)
   $(error USE_SDC is no longer supported.  Use with USE_SIMPLIFIED_SDC or USE_TRUE_SDC)
 endif
 
+ifeq ($(USE_SIMPLIFIED_SDC), TRUE)
+  ifeq ($(USE_TRUE_SDC), TRUE)
+    $(error USE_SIMPLIFIED_SDC cannot be combined with USE_TRUE_SDC)
+  endif
+endif
+
 # need to put any build suffices before Make.defs
 ifeq ($(USE_SIMPLIFIED_SDC), TRUE)
   USERSuffix = .SMPLSDC
@@ -161,9 +167,13 @@ endif
 MAX_NPTS_MODEL ?= 10000
 NUM_MODELS ?= 1
 
-ifeq ($(USE_CXX_MODEL_PARSER), TRUE)
-  Bdirs += Util/model_parser_cxx
-  DEFINES += -DCXX_MODEL_PARSER -DNPTS_MODEL=$(MAX_NPTS_MODEL) -DNUM_MODELS=$(NUM_MODELS)
+ifeq ($(USE_MODEL_PARSER), TRUE)
+  Bdirs += Util/model_parser
+  DEFINES += -DMODEL_PARSER -DNPTS_MODEL=$(MAX_NPTS_MODEL) -DNUM_MODELS=$(NUM_MODELS)
+endif
+
+ifeq ($(USE_RNG_STATE_INIT), TRUE)
+  DEFINES += -DRNG_STATE_INIT
 endif
 
 # add / define any special physics we need
@@ -298,8 +308,6 @@ Bpack	+= $(foreach dir, $(Pdirs), $(AMREX_HOME)/Src/$(dir)/Make.package)
 # directory
 NETWORK_OUTPUT_PATH = $(CASTRO_AUTO_SOURCE_DIR)
 
-USE_CXX_EOS := TRUE
-
 include $(MICROPHYSICS_HOME)/Make.Microphysics_extern
 
 Bpack += $(foreach dir, $(EXTERN_CORE), $(dir)/Make.package)

Exec/gravity_tests/StarGrav/GNUmakefile

@@ -14,7 +14,7 @@ USE_MPI    = TRUE
 USE_GRAV   = TRUE
 USE_REACT  = FALSE
 
-USE_CXX_MODEL_PARSER = TRUE
+USE_MODEL_PARSER = TRUE
 
 # This sets the EOS directory in $(MICROPHYSICS_HOME)/eos
 EOS_DIR     := helmholtz

Exec/gravity_tests/advecting_white_dwarf/GNUmakefile

@@ -12,7 +12,7 @@ DIM ?= 3
 
 USE_GRAV ?= TRUE
 
-USE_CXX_MODEL_PARSER = TRUE
+USE_MODEL_PARSER = TRUE
 NUM_MODELS = 1
 
 COMP ?= gnu