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update polyfem #14

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0d8cb2c
update polyfem
Huangzizhou Jun 30, 2024
fe02e7e
fix set_log_level
Huangzizhou Jun 30, 2024
96420e6
separate classes into separate folders
Huangzizhou Jun 30, 2024
5d713ba
polyfem_command
Huangzizhou Jul 1, 2024
a5de325
command line tool
Huangzizhou Jul 1, 2024
d317a58
shape derivative python interface
Huangzizhou Jul 2, 2024
94b57c5
fix memory issue, support multiple states
Huangzizhou Jul 2, 2024
6433fec
python binding for adjoint form
Huangzizhou Jul 26, 2024
1c0de74
Update README.md
Huangzizhou Jul 26, 2024
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command line tool
  • Loading branch information
@Huangzizhou
Huangzizhou committed Jul 1, 2024
commit a5de325da0f9cb689a911c40cac8f441947e8ac5
82 changes: 16 additions & 66 deletions polyfempy/command.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,80 +6,30 @@ def polyfem():
parser = argparse.ArgumentParser()

parser.add_argument("-j", "--json", type=str,
default="", help="Simulation json file")
parser.add_argument("-m", "--mesh", type=str, default="", help="Mesh path")
parser.add_argument("-b", "--febio", type=str,
default="", help="FEBio file path")
default="", help="Simulation JSON file")

parser.add_argument("--n_refs", type=int, default=0,
help="Number of refinements")
parser.add_argument("--not_norm", type=bool, default=True,
help="Skips mesh normalization")
parser.add_argument("-y", "--yaml", type=str,
default="", help="Simulation YAML file")

parser.add_argument("--problem", type=str,
default="", help="Problem name")
parser.add_argument("--sform", type=str,
default="", help="Scalar formulation")
parser.add_argument("--tform", type=str,
default="", help="Tensor formulation")
parser.add_argument("--max_threads", type=int, default=1,
help="Maximum number of threads")

parser.add_argument("--solver", type=str, default="", help="Solver to use")
parser.add_argument("-s", "--strict_validation", action='store_true',
help="Enables strict validation of input JSON")

parser.add_argument("-q", "-p", type=int, default=1,
help="Discretization order")
parser.add_argument("--p_ref", type=bool,
default=False, help="Use p refimenet")
# parser.add_argument("--spline", use_splines, "Use spline for quad/hex meshes");
parser.add_argument("--count_flipped_els", type=bool,
default=False, help="Count flippsed elements")
parser.add_argument("--lin_geom", type=bool, default=False,
help="Force use linear geometric mapping")
# parser.add_argument("--isoparametric", isoparametric, "Force use isoparametric basis");
# parser.add_argument("--serendipity", serendipity, "Use of serendipity elements, only for Q2");
# parser.add_argument("--stop_after_build_basis", stop_after_build_basis, "Stop after build bases");
parser.add_argument("--vis_mesh_res", type=float,
default=-1.0, help="Vis mesh resolution")
parser.add_argument("--project_to_psd", type=bool,
default=False, help="Project local matrices to psd")
parser.add_argument("--n_incr_load", type=int, default=-
1, help="Number of incremeltal load")

parser.add_argument("--output", type=str, default="",
help="Output json file")
parser.add_argument("--vtu", type=str, default="", help="Vtu output file")

parser.add_argument("--quiet", type=bool, default=False,
help="Disable cout for logging")
parser.add_argument("--log_file", type=str,
default="", help="Log to a file")
parser.add_argument("--log_level", type=int, default=1,
help="Log level 1 debug 2 info")

parser.add_argument("--export_material_params", type=bool,
default=False, help="Export material parameters")
parser.add_argument("-o", "--output_dir", type=str,
default="", help="Directory for output files")

args = parser.parse_args()

polyfem_command(
args.json,
args.febio,
args.mesh,
args.problem,
args.sform,
args.tform,
args.n_refs,
args.not_norm,
args.solver,
args.q,
args.p_ref,
args.count_flipped_els,
args.lin_geom,
args.vis_mesh_res,
args.project_to_psd,
args.n_incr_load,
args.output,
args.vtu,
args.log_level,
args.log_file,
args.quiet,
args.export_material_params)
json=args.json,
yaml=args.yaml,
log_level=args.log_level,
strict_validation=args.strict_validation,
max_threads=args.max_threads,
output_dir=args.output_dir
)
52 changes: 33 additions & 19 deletions src/state/state.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -571,24 +571,41 @@ void define_solver(py::module_ &m)
s.assemble_rhs();
s.assemble_mass_mat();

s.solve_export_to_file = false;
s.solution_frames.clear();
Eigen::MatrixXd sol, pressure;
s.solve_problem(sol, pressure);
s.solve_export_to_file = true;

s.compute_errors(sol);

s.save_json(sol);
s.export_data(sol, pressure);

return py::make_tuple(sol, pressure);
},
"solve the pde")
.def(
"init_timestepping",
[](State &s, const double t0, const double dt) {
init_globals(s);
s.stats.compute_mesh_stats(*s.mesh);
"build_basis",
[](State &s) {
if (!s.mesh)
throw std::runtime_error("Load mesh first!");

s.build_basis();
},
"build finite element basis")
.def(
"assemble",
[](State &s) {
if (s.bases.size() == 0)
throw std::runtime_error("Call build_basis() first!");

s.assemble_rhs();
s.assemble_mass_mat();
},
"assemble RHS and mass matrix if needed")
.def(
"init_timestepping",
[](State &s, const double t0, const double dt) {
if (!s.solve_data.rhs_assembler || s.mass.size() == 0)
throw std::runtime_error("Call assemble() first!");

s.solution_frames.clear();
Eigen::MatrixXd sol, pressure;
Expand Down Expand Up @@ -639,23 +656,19 @@ void define_solver(py::module_ &m)

.def(
"compute_errors",
[](State &s, Eigen::MatrixXd &sol) {
init_globals(s);
// py::scoped_ostream_redirect output;

s.compute_errors(sol);
},
[](State &s, Eigen::MatrixXd &sol) { s.compute_errors(sol); },
"compute the error", py::arg("solution"))

// .def("export_data", [](State &s) {
// py::scoped_ostream_redirect output; s.export_data(); }, "exports all
// data specified in the settings")
.def(
"export_data",
[](State &s, const Eigen::MatrixXd &sol,
const Eigen::MatrixXd &pressure) { s.export_data(sol, pressure); },
"exports all data specified in the settings")
.def(
"export_vtu",
[](State &s, const Eigen::MatrixXd &sol,
const Eigen::MatrixXd &pressure, const double time,
const double dt, std::string &path, bool boundary_only) {
// py::scoped_ostream_redirect output;
s.args["output"]["advanced"]["vis_boundary_only"] = boundary_only;
s.out_geom.save_vtu(
s.resolve_output_path(path), s, sol, pressure, time, dt,
Expand Down Expand Up @@ -1142,7 +1155,8 @@ void define_solve(py::module_ &m)
: load_yaml(yaml_file, in_args);

if (!ok)
log_and_throw_error(fmt::format("unable to open {} file", json_file));
throw std::runtime_error(
fmt::format("unable to open {} file", json_file));

json tmp = json::object();
tmp["/output/log/level"_json_pointer] = int(log_level);
Expand All @@ -1163,7 +1177,7 @@ void define_solve(py::module_ &m)

// Mesh was not loaded successfully; load_mesh() logged the error.
if (state.mesh == nullptr)
log_and_throw_error("Failed to load the mesh!");
throw std::runtime_error("Failed to load the mesh!");

state.stats.compute_mesh_stats(*state.mesh);

Expand Down
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