setter way to set bc, better way to load mesh, setting str function (suboptimal), mises and stresses

Author: Teseo Schneider

CMakeLists.txt

@@ -1,18 +1,10 @@
 ################################################################################
 cmake_minimum_required(VERSION 3.1)
-project(PolyFEMpy)
+project(polyfempy)
 ################################################################################
 
-# Detects whether this is a top-level project
-if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
-	set(POLYFEM_PYTHON_TOPLEVEL_PROJECT ON)
-else()
-	set(POLYFEM_PYTHON_TOPLEVEL_PROJECT OFF)
-endif()
-
 set(THIRD_PARTY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/)
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
-list(APPEND CMAKE_MODULE_PATH ${THIRD_PARTY_DIR}/Catch2/contrib)
 
 # Color output
 include(UseColors)

cmake/PolyfemPythonDownloadExternal.cmake

@@ -27,7 +27,7 @@ endfunction()
 function(polyfem_python_download_polyfem)
     polyfem_python_download_project(polyfem
         GIT_REPOSITORY https://github.com/polyfem/polyfem.git
-        GIT_TAG         973ba49820be74e80cc76acc8858d39fa1e0db82
+        GIT_TAG         41005711400c3e5f0957f70d9f071b1a45d2d123
     )
 endfunction()
 

polyfempy/Settings.py

@@ -62,6 +62,8 @@ def set_solution_export_path(self, path):
 	def set_advanced_option(self, key, value):
 		self.advanced_options[key] = value
 
+	def __str__(self):
+		return json.dumps(self, default=lambda o: o.__dict__, sort_keys=True, indent=4)
 
 	def serialize(self):
-		return json.dumps(self, default=lambda o: o.__dict__, sort_keys=True, indent=4)
+		return str(self)

setup.py

@@ -79,7 +79,7 @@ def build_extension(self, ext):
 
 setup(
     name="polyfempy",
-    version="0.0.1",
+    version="0.2",
     author="Teseo Schneider",
     author_email="",
     description="Polyfem Python Bindings",

src/binding.cpp

@@ -1,6 +1,7 @@
 #include <polyfem/State.hpp>
 #include <polyfem/AssemblerUtils.hpp>
 #include <polyfem/Logger.hpp>
+#include <polyfem/MeshUtils.hpp>
 
 #include <geogram/basic/command_line.h>
 #include <geogram/basic/command_line_args.h>
@@ -12,6 +13,7 @@
 
 #include <pybind11/pybind11.h>
 #include <pybind11/eigen.h>
+#include <pybind11/functional.h>
 
 namespace py = pybind11;
 
@@ -60,10 +62,6 @@ PYBIND11_MODULE(polyfempy, m) {
 	for(auto &a : polyfem::AssemblerUtils::instance().tensor_assemblers())
 		ta.attr(a.c_str()) = a;
 
-
-	//TODO:
-	// load mesh with lambda and V, F
-
 	py::class_<polyfem::State>(m, "Solver")
 	.def(py::init<>())
 	.def("settings", [](polyfem::State &s, const std::string &json) {
@@ -81,17 +79,42 @@ PYBIND11_MODULE(polyfempy, m) {
 		init_globals();
 		s.load_mesh();
 	},																"Loads a mesh from the 'mesh' field of the json and 'bc_tag' if any bc tags")
-	.def("load_mesh", [](polyfem::State &s, std::string &path) {
+	.def("load_mesh", [](polyfem::State &s, const std::string &path) {
 		init_globals();
 		s.args["mesh"] = path;
 		s.load_mesh();
 	},																"Loads a mesh from the path and 'bc_tag' from the json if any bc tags")
-	.def("load_mesh", [](polyfem::State &s, std::string &path, std::string &bc_tag) {
+	.def("load_mesh", [](polyfem::State &s, const std::string &path, const std::string &bc_tag) {
 		init_globals();
 		s.args["mesh"] = path;
 		s.args["bc_tag"] = bc_tag;
 		s.load_mesh();
 	},																"Loads a mesh and bc_tags from path")
+	.def("set_mesh", [](polyfem::State &s, const Eigen::MatrixXd &V, const Eigen::MatrixXi &F) {
+		init_globals();
+
+		GEO::Mesh M;
+		if(V.cols() == 2)
+			polyfem::to_geogram_mesh(V, F, M);
+		else
+			polyfem::to_geogram_mesh_3d(V, F, M);
+		s.load_mesh(M, [](const polyfem::RowVectorNd&){ return -1; }, true);
+	},																"Loads a mesh from vertices and connectivity")
+
+
+	.def("set_boundary_side_set_from_bary", [](polyfem::State &s, const std::function<int(const polyfem::RowVectorNd&)> &boundary_marker) {
+		init_globals();
+		s.mesh->compute_boundary_ids(boundary_marker);
+	},																"Sets the side set for the boundary conditions, the functions takes the barycenter of the boundary (edge or face)")
+	.def("set_boundary_side_set_from_bary_and_boundary", [](polyfem::State &s, const std::function<int(const polyfem::RowVectorNd&, bool)> &boundary_marker) {
+		init_globals();
+		s.mesh->compute_boundary_ids(boundary_marker);
+	},																"Sets the side set for the boundary conditions, the functions takes the barycenter of the boundary (edge or face) and a flag that says if the element is boundary")
+	.def("set_boundary_side_set_from_v_ids", [](polyfem::State &s, const std::function<int(const std::vector<int>&, bool)> &boundary_marker) {
+		init_globals();
+		s.mesh->compute_boundary_ids(boundary_marker);
+	},																"Sets the side set for the boundary conditions, the functions takes the sorted list of vertex id and a flag that says if the element is boundary")
+
 
 	.def("set_rhs", [](polyfem::State &s, std::string &path) {
 		init_globals();
@@ -143,7 +166,39 @@ PYBIND11_MODULE(polyfempy, m) {
 
 		s.interpolate_function(points.rows(), s.sol, fun, boundary_only);
 		return  py::make_tuple(points, tets, fun);
-	}, 																					"returns the solution on a densly sampled mesh, use 'vismesh_rel_area' to control density",
-	py::arg("boundary_only") = bool(false));
+	}, "returns the solution on a densly sampled mesh, use 'vismesh_rel_area' to control density", py::arg("boundary_only") = bool(false))
+	.def("get_stresses", 	[](polyfem::State &s,  bool boundary_only) {
+		Eigen::MatrixXd points;
+		Eigen::MatrixXi tets;
+		Eigen::MatrixXd discr;
+		Eigen::MatrixXd fun;
+
+		s.build_vis_mesh(points, tets, discr);
+		s.compute_tensor_value(points.rows(), s.sol, fun, boundary_only);
+
+		return fun;
+	}, "returns the stress tensor on a densly sampled mesh, use 'vismesh_rel_area' to control density", py::arg("boundary_only") = bool(false))
+	.def("get_sampled_mises", 	[](polyfem::State &s,  bool boundary_only) {
+		Eigen::MatrixXd points;
+		Eigen::MatrixXi tets;
+		Eigen::MatrixXd discr;
+		Eigen::MatrixXd fun;
+
+		s.build_vis_mesh(points, tets, discr);
+		s.compute_scalar_value(points.rows(), s.sol, fun, boundary_only);
+
+		return fun;
+	}, "returns the von mises stresses on a densly sampled mesh, use 'vismesh_rel_area' to control density", py::arg("boundary_only") = bool(false))
+	.def("get_sampled_mises_avg", 	[](polyfem::State &s,  bool boundary_only) {
+		Eigen::MatrixXd points;
+		Eigen::MatrixXi tets;
+		Eigen::MatrixXd discr;
+		Eigen::MatrixXd fun, tfun;
+
+		s.build_vis_mesh(points, tets, discr);
+		s.average_grad_based_function(points.rows(), s.sol, fun, tfun, boundary_only);
+
+		return py::make_tuple(fun, tfun);
+	}, "returns the von mises stresses and stress tensor averaged around a vertex on a densly sampled mesh, use 'vismesh_rel_area' to control density", py::arg("boundary_only") = bool(false));
 
 }

tests/bending.py

@@ -35,7 +35,7 @@ def test_run(self):
 
 		solver = pf.Solver()
 
-		solver.settings(settings.serialize())
+		solver.settings(str(settings))
 		solver.load_mesh(mesh_path, tag_path)
 
 		solver.solve()

tests/inflation.py

@@ -29,7 +29,7 @@ def test_run(self):
 
 
 
-		solver.settings(settings.serialize())
+		solver.settings(settings)
 		solver.load_mesh(mesh_path)
 
 		solver.solve()

tests/torsion.py

@@ -37,7 +37,7 @@ def test_run(self):
 		solver = pf.Solver()
 
 
-		solver.settings(settings.serialize())
+		solver.settings(str(settings))
 		solver.load_mesh(mesh_path)
 
 		solver.solve()