Save Jacobian to file - #3464
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- PetscPreconditioner saves Jacobian using PETSc binary or ASCII format. - Solver saves metadata: A Jacobian global index offset field to the dmp files, and a JSON file with the variable information. - SNES solver outputs Jacobian if `save_jacobian = true`. An option `jacobian_export_kind` select whether the Jacobian is calculated using the nonlinear system being solved (that depends on timestep and scaling), the scaled RHS function (that depends on variable scaling), or the raw `rhs` function is saved.
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| .withDefault("jacobian")), | ||
| jacobian_export_format((*options)["jacobian_export_format"] | ||
| .doc("Format for saved Jacobian matrices: binary, ascii") | ||
| .withDefault(PetscMatrixExportFormat::binary)) {} |
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warning: no header providing "PetscMatrixExportFormat" is directly included [misc-include-cleaner]
src/solver/impls/snes/snes.cxx:1:
+ #include "bout/petsc_preconditioner.hxx"|
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| PetscErrorCode ComputeJacobianDefaultMaybeExport(SNES snes, Vec x1, Mat Jac, Mat Jac_new, | ||
| void* ctx) { | ||
| PetscErrorCode err = SNESComputeJacobianDefault(snes, x1, Jac, Jac_new, ctx); |
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warning: variable 'err' of type 'PetscErrorCode' (aka 'int') can be declared 'const' [misc-const-correctness]
| PetscErrorCode err = SNESComputeJacobianDefault(snes, x1, Jac, Jac_new, ctx); | |
| ctx) {const |
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| Field3D Solver::jacobianIndexBase(int localStart) { return globalIndex(localStart); } | ||
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| std::vector<Solver::JacobianVariableMetadata> Solver::getJacobianMetadata2D() const { |
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warning: no header providing "std::vector" is directly included [misc-include-cleaner]
src/solver/solver.cxx:59:
+ #include <vector>Saves to same directory as the dmp file outputs, using `Options::root()["datadir"]`
Started a test to check the output Jacobian
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| }; | ||
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| BOUTMAIN(TestSolver); |
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warning: variable 'init_err' of type 'int' can be declared 'const' [misc-const-correctness]
BOUTMAIN(TestSolver);
^Additional context
include/bout/physicsmodel.hxx:430: expanded from macro 'BOUTMAIN'
int init_err = BoutInitialise(argc, argv); \
^Checks that the Jacobian can be read in either sparse or dense format, and that the values are as expected.
Utility that extracts the block of the Jacobian corresponding to rows of variable A and columns of variable B.
Adds docstrings and user manual on writing the Jacobian from SNES and read it into Python.
Documentation includes a table of settings, and examples.
| jacobian_export_format( | ||
| (*options)["jacobian_export_format"] | ||
| .doc("PETSc MatView format for saved Jacobians: binary or ascii") | ||
| .withDefault(PetscMatrixExportFormat::binary)), |
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warning: no header providing "PetscMatrixExportFormat" is directly included [misc-include-cleaner]
src/solver/impls/cvode/cvode.cxx:27:
- #include <cstddef>
+ #include "bout/petsc_preconditioner.hxx"
+ #include <cstddef>| #if BOUT_HAS_PETSC | ||
| std::string CvodeSolver::getJacobianExportStem(JacobianExportKind kind) { | ||
| const std::string datadir = Options::root()["datadir"]; | ||
| return fmt::format("{}/{}_{}_{:06d}", datadir, jacobian_export_prefix, toString(kind), |
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warning: no header providing "fmt::format" is directly included [misc-include-cleaner]
src/solver/impls/cvode/cvode.cxx:30:
+ #include "fmt/format.h"| jacobian_metadata_written = true; | ||
| } | ||
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| PetscCall(PetscPreconditioner::saveMatrix(jacobian, getJacobianMatrixFilename(stem), |
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warning: no header providing "PetscPreconditioner" is directly included [misc-include-cleaner]
^| save_vars(xdata); | ||
| PetscCall(VecRestoreArray(x, &xdata)); | ||
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| PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0); |
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warning: variable 'ierr' of type 'PetscErrorCode' (aka 'int') can be declared 'const' [misc-const-correctness]
| PetscErrorCode ierr = saveDiagnosticJacobian(JacobianExportKind::rhs, x, t, 0.0); | |
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| if (selected_precon == CvodePreconMethod::Auto) { | ||
| if (hasPreconditioner()) { | ||
| selected_precon = CvodePreconMethod::user; | ||
| } else if (bout::build::has_petsc) { |
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warning: no header providing "bout::build::has_petsc" is directly included [misc-include-cleaner]
src/solver/impls/cvode/cvode.cxx:26:
- #include "bout/build_defines.hxx"
+ #include "bout/build_config.hxx"
+ #include "bout/build_defines.hxx"| PetscCall(VecGetArray(f, &fdata)); | ||
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| try { | ||
| s->rhs(s->petsc_t, const_cast<BoutReal*>(xdata), s->petsc_rhs_tmp.data(), true); |
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warning: do not use const_cast to remove const qualifier [cppcoreguidelines-pro-type-const-cast]
{
^| } | ||
| }; | ||
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| BOUTMAIN(TestSolver); |
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warning: variable 'init_err' of type 'int' can be declared 'const' [misc-const-correctness]
BOUTMAIN(TestSolver);
^Additional context
include/bout/physicsmodel.hxx:430: expanded from macro 'BOUTMAIN'
int init_err = BoutInitialise(argc, argv); \
^Use of prefix for the metadata file was inconsistent. Since it's always the same, always use the same name.
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Formatting errors are from |
1 participant
Utilities for saving the solver Jacobian from the SNES and CVODE solvers.
save_jacobian = true. An optionjacobian_export_kindselect whether the Jacobian is calculated using the nonlinear system being solved (that depends on timestep and scaling), the scaled RHS function (that depends on variable scaling), or the rawrhsfunction is saved.A python utility
read_jacobian.pyuses PETSc'sPetscBinaryIO.pyto read the binary output files. This is used in the integrated tests. In future this utility could be merged intoboutdataorxBOUT.