Refactor derived variables

.github/workflows/data/plt00008_compare/Header

@@ -1,5 +1,5 @@
 HyperCLaw-V1.1
-25
+31
 chi
 h11
 h12
@@ -25,6 +25,12 @@ shift3
 B1
 B2
 B3
+Ham
+Mom1
+Mom2
+Mom3
+Weyl4_Re
+Weyl4_Im
 3
 0.5
 0

.github/workflows/data/plt00008_compare/Level_0/Cell_H

@@ -1,6 +1,6 @@
 1
 1
-25
+31
 0
 (4 0
 ((0,0,0) (15,15,15) (0,0,0))
@@ -10,19 +10,19 @@
 )
 4
 FabOnDisk: Cell_D_00000 0
-FabOnDisk: Cell_D_00000 819290
+FabOnDisk: Cell_D_00000 1015898
 FabOnDisk: Cell_D_00001 0
-FabOnDisk: Cell_D_00001 819291
+FabOnDisk: Cell_D_00001 1015899
 
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.github/workflows/regression-tests.yml

@@ -69,6 +69,7 @@ jobs:
         ${AMREX_HOME}/Tools/Plotfile/fcompare.gnu.ex \
         --abs_tol 1e-10 \
         --rel_tol 1e-10 \
+        --abort_if_not_all_found \
         ${GITHUB_WORKSPACE}/GRTeclyn/.github/workflows/data/plt00008_compare \
         ${BINARYBH_EXAMPLE_DIR}/plt00008
 

.github/workflows/unit-tests.yml

@@ -36,7 +36,12 @@ jobs:
       AMREX_HOME: ${{ github.workspace }}/amrex
       OMP_NUM_THREADS: 1
       TESTS_DIR: ${{ github.workspace }}/GRTeclyn/Tests
-      BUILD_CONFIG: COMP=${{ matrix.comp }} DEBUG=${{ matrix.debug}} USE_MPI=${{ matrix.mpi }} USE_OMP=${{ matrix.omp }}
+      BUILD_CONFIG: >
+        COMP=${{ matrix.comp }}
+        DEBUG=${{ matrix.debug}}
+        USE_MPI=${{ matrix.mpi }}
+        USE_OMP=${{ matrix.omp }}
+        USE_HDF5=TRUE
 
     steps:
     - name: Checkout AMReX
@@ -66,8 +71,11 @@ jobs:
 
     - name: Install dependencies
       run: |
+        PACKAGES="hdf5-tools"
         if [[ "${{ matrix.mpi }}" == "TRUE" ]]; then
-          PACKAGES="libopenmpi-dev"
+          PACKAGES="${PACKAGES} libopenmpi-dev libhdf5-openmpi-dev"
+        else
+          PACKAGES="${PACKAGES} libhdf5-dev"
         fi
         if [[ "${{ matrix.comp }}" == "llvm" && "${{ matrix.omp }}" == "TRUE" ]]; then
           PACKAGES="${PACKAGES} libomp-${{ matrix.comp-version }}-dev"
@@ -105,6 +113,11 @@ jobs:
     - name: Build Tests
       working-directory: ${{ env.TESTS_DIR }}
       run: |
+        if [[ "${{ matrix.mpi }}" == "TRUE" ]]; then
+          export HDF5_HOME=/usr/lib/x86_64-linux-gnu/hdf5/openmpi
+        else
+          export HDF5_HOME=/usr/lib/x86_64-linux-gnu/hdf5/serial
+        fi
         export OMPI_CXX=${{ steps.set-compilers.outputs.ompi_cxx }}
         make -j 4 ${{ steps.set-compilers.outputs.build_args }}
 

.gitignore

@@ -21,6 +21,7 @@ Backtrace.*
 pout.*
 *.out
 *.dat
+*.h5
 Weyl_integral*
 *ExtractionOut_*
 

.lint-ignore

@@ -8,7 +8,15 @@
 
 # These directories have yet to be ported to AMReX
 Source/AMRInterpolator/*
+Source/BoxUtils/SixthOrderDerivatives.hpp
+Source/CCZ4/GammaCalculator.hpp
+Source/InitialConditions/BlackHoles/KerrBH*
+Source/InitialConditions/ScalarFields/*
 Source/Matter/*
+Source/utils/WeylExtraction*
 Examples/KerrBH/*
 Examples/ScalarField/*
 Tests/.*
+
+# These are old files we don't want to change
+Tests/CCZ4RHSTest/*fdf5a7a*

Examples/BinaryBH/BinaryBHLevel.cpp

@@ -10,11 +10,24 @@
 #include "PositiveChiAndAlpha.hpp"
 #include "PunctureTracker.hpp"
 // xxxxx #include "SixthOrderDerivatives.hpp"
+#include "Constraints.hpp"
 #include "TraceARemoval.hpp"
 #include "TwoPuncturesInitialData.hpp"
 #include "Weyl4.hpp"
 #include "WeylExtraction.hpp"
 
+void BinaryBHLevel::variableSetUp()
+{
+    BL_PROFILE("BinaryBHLevel::variableSetUp()");
+
+    // Set up the state variables
+    stateVariableSetUp();
+
+    Constraints::set_up(State_Type);
+
+    Weyl4::set_up(State_Type);
+}
+
 // Things to do during the advance step after RK4 steps
 void BinaryBHLevel::specificAdvance()
 {
@@ -221,7 +234,7 @@ void BinaryBHLevel::specificPostTimeStep()
                 bool fill_ghosts = false;
                 m_gr_amr.m_interpolator->refresh(fill_ghosts);
                 m_gr_amr.fill_multilevel_ghosts(
-                    VariableType::diagnostic, Interval(c_Weyl4_Re, c_Weyl4_Im),
+                    VariableType::derived, Interval(c_Weyl4_Re, c_Weyl4_Im),
                     min_level);
                 WeylExtraction my_extraction(m_p.extraction_params, m_dt,
                                              m_time, first_step,
@@ -238,7 +251,7 @@ void BinaryBHLevel::specificPostTimeStep()
                        m_state_new, m_state_diagnostics, EXCLUDE_GHOST_CELLS);
         if (m_level == 0)
         {
-            AMRReductions<VariableType::diagnostic> amr_reductions(m_gr_amr);
+            AMRReductions<VariableType::derived> amr_reductions(m_gr_amr);
             double L2_Ham = amr_reductions.norm(c_Ham);
             double L2_Mom = amr_reductions.norm(Interval(c_Mom1, c_Mom3));
             SmallDataIO constraints_file(m_p.data_path + "constraint_norms",
@@ -265,19 +278,3 @@ void BinaryBHLevel::specificPostTimeStep()
     }
 #endif
 }
-
-#ifdef AMREX_USE_HDF5
-// Things to do before a plot level - need to calculate the Weyl scalars
-void BinaryBHLevel::prePlotLevel()
-{
-    fillAllGhosts();
-    if (m_p.activate_extraction == 1)
-    {
-        BoxLoops::loop(
-            make_compute_pack(
-                Weyl4(m_p.extraction_params.center, m_dx, m_p.formulation),
-                Constraints(m_dx, c_Ham, Interval(c_Mom1, c_Mom3))),
-            m_state_new, m_state_diagnostics, EXCLUDE_GHOST_CELLS);
-    }
-}
-#endif /* AMREX_USE_HDF5 */

Examples/BinaryBH/BinaryBHLevel.hpp

@@ -14,6 +14,7 @@
 class BinaryBHLevel : public GRAMRLevel
 {
   public:
+    static void variableSetUp();
 
     // Inherit the contructors from GRAMRLevel
     using GRAMRLevel::GRAMRLevel;
@@ -37,11 +38,6 @@ class BinaryBHLevel : public GRAMRLevel
 
     void errorEst(amrex::TagBoxArray &tag_box_array, int clearval, int tagval,
                   amrex::Real time, int n_error_buf = 0, int ngrow = 0) final;
-
-#ifdef AMREX_USE_HDF5
-    /// Any actions that should happen just before plot files output
-    virtual void prePlotLevel() override;
-#endif /* AMREX_USE_HDF5 */
 };
 
 #endif /* BINARYBHLEVEL_HPP_ */

Examples/BinaryBH/Make.package

@@ -1,5 +1,5 @@
 GRTECLYN_CEXE_sources += BinaryBHLevel.cpp Main_BinaryBH.cpp
 
-GRTECLYN_CEXE_headers += BinaryBHLevel.hpp  DiagnosticVariables.hpp  SimulationParameters.hpp  TPAMR.hpp  UserVariables.hpp
+GRTECLYN_CEXE_headers += BinaryBHLevel.hpp  SimulationParameters.hpp  TPAMR.hpp  StateVariables.hpp
 
 

Examples/KerrBH/UserVariables.hpp → Examples/BinaryBH/StateVariables.hpp

@@ -3,12 +3,12 @@
  * Please refer to LICENSE in GRTeclyn's root directory.
  */
 
-#ifndef USERVARIABLES_HPP
-#define USERVARIABLES_HPP
+#ifndef STATEVARIABLES_HPP
+#define STATEVARIABLES_HPP
 
 #include "ArrayTools.hpp"
-#include "CCZ4UserVariables.hpp"
-#include "DiagnosticVariables.hpp"
+#include "BCParity.hpp"
+#include "CCZ4Variables.hpp"
 
 /// This enum gives the index of every variable stored in the grid
 enum
@@ -18,12 +18,11 @@ enum
     NUM_VARS = NUM_CCZ4_VARS,
 };
 
-namespace UserVariables
+namespace StateVariables
 {
-static const std::array<std::string, NUM_VARS> variable_names =
-    ccz4_variable_names;
-} // namespace UserVariables
+static const amrex::Vector<std::string> names = CCZ4Variables::names;
 
-#include "UserVariables.inc.hpp"
+static const std::array<BCParity, NUM_VARS> parities = CCZ4Variables::parities;
+} // namespace StateVariables
 
-#endif /* USERVARIABLES_HPP */
+#endif /* STATEVARIABLES_HPP */

Examples/BinaryBH/inputs.test

@@ -91,16 +91,6 @@ isPeriodic = 0 0 0
 hi_boundary = 1 1 1
 lo_boundary = 1 1 2
 
-# if reflective boundaries selected, must set
-# parity of all vars (in order given by UserVariables.hpp)
-# 0 = even
-# 1,2,3 = odd x, y, z
-# 7     = odd xyz
-vars_parity = 0 0 4 6 0 5 0  0 0 4 6 0 5 0  0 1 2 3          0 1 2 3 1 2 3
-              #chi and hij   K and Aij      Theta and Gamma  Gauge
-vars_parity_diagnostic = 0 1 2 3       0 7
-                         #Ham and Mom  Weyl
-
 # if sommerfeld boundaries selected, must select
 # non zero asymptotic values
 num_nonzero_asymptotic_vars = 5
@@ -164,8 +154,8 @@ extraction_levels = 0
 num_points_phi = 24
 num_points_theta = 37
 num_modes = 3
-modes = 2 0 # l m for spherical harmonics
-        2 1
+modes = 2 0 \
+        2 1 \
         2 2
 # integral_file_prefix = "Weyl4_mode_"
 
@@ -184,4 +174,4 @@ amrex.fpe_trap_zero=1
 amrex.fpe_trap_overflow=1
 
 amr.plot_vars = chi # The default is to plot all state variables
-amr.derive_plot_vars = Ham Mom # The default is none for derived variables.
+amr.derive_plot_vars = constraints # The default is none for derived variables.

Examples/BinaryBH/params.txt

@@ -95,28 +95,13 @@ isPeriodic = 0 0 0
 hi_boundary = 1 1 1
 lo_boundary = 1 1 2
 
-# if reflective boundaries selected, must set
-# parity of all vars (in order given by UserVariables.hpp)
-# 0 = even
-# 1,2,3 = odd x, y, z
-# 4,5,6 = odd xy, yz, xz
-# 7     = odd xyz
-vars_parity            = 0 0 4 6 0 5 0    #chi and hij
-                         0 0 4 6 0 5 0    #K and Aij
-                         0 1 2 3          #Theta and Gamma
-                         0 1 2 3 1 2 3    #lapse shift and B
-vars_parity_diagnostic = 0 1 2 3          #Ham and Mom
-                         0 7              #Weyl
-
 # if sommerfeld boundaries selected, must select
 # asymptotic values
-num_nonzero_asymptotic_vars = 5
 nonzero_asymptotic_vars = chi h11 h22 h33 lapse
 nonzero_asymptotic_values = 1.0 1.0 1.0 1.0 1.0
 
 # if you are using extrapolating BC:
 # extrapolation_order = 1
-# num_extrapolating_vars = -1
 # extrapolating_vars =
 
 #################################################