polyfem::io::OutGeometryData Class Reference

Utilies related to export of geometry. More...

#include <OutData.hpp>

Collaboration diagram for polyfem::io::OutGeometryData:

Classes
struct	ExportOptions
	different export flags More...

Public Member Functions
void	init_sampler (const polyfem::mesh::Mesh &mesh, const double vismesh_rel_area)
	unitalize the ref element sampler
void	build_grid (const polyfem::mesh::Mesh &mesh, const double spacing)
	builds the grid to export the solution
void	export_data (const OutputSpace &space, const OutputFieldFunction &output_fields, const bool is_time_dependent, const double tend_in, const double dt, const ExportOptions &opts, const std::string &vis_mesh_path) const
	exports everytihng, txt, vtu, etc
void	save_vtu (const std::string &path, const OutputSpace &space, const OutputFieldFunction &output_fields, const double t, const double dt, const ExportOptions &opts) const
	saves the vtu file for time t
void	save_volume (const std::string &path, const OutputSpace &space, const OutputFieldFunction &output_fields, const double t, const double dt, const ExportOptions &opts) const
	saves the volume vtu file
void	save_surface (const std::string &export_surface, const OutputSpace &space, const OutputFieldFunction &output_fields, const double t, const double dt_in, const ExportOptions &opts) const
	saves the surface vtu file for for surface quantites, eg traction forces
void	save_contact_surface (const std::string &export_surface, const OutputSpace &space, const OutputFieldFunction &output_fields, const double t, const double dt_in, const ExportOptions &opts) const
	saves the surface vtu file for for constact quantites, eg contact or friction forces
void	save_wire (const std::string &name, const OutputSpace &space, const OutputFieldFunction &output_fields, const double t, const ExportOptions &opts) const
	saves the wireframe
void	save_points (const std::string &path, const OutputSpace &space, const OutputFieldFunction &output_fields, const ExportOptions &opts) const
	saves the nodal values
void	save_pvd (const std::string &name, const std::function< std::string(int)> &vtu_names, int time_steps, double t0, double dt, int skip_frame=1) const
	save a PVD of a time dependent simulation

Static Public Member Functions
static void	extract_boundary_mesh (const mesh::Mesh &mesh, const int n_bases, const std::vector< basis::ElementBases > &bases, const std::vector< mesh::LocalBoundary > &total_local_boundary, Eigen::MatrixXd &node_positions, Eigen::MatrixXi &boundary_edges, Eigen::MatrixXi &boundary_triangles, std::vector< Eigen::Triplet< double > > &displacement_map_entries)
	extracts the boundary mesh

Private Member Functions
void	build_vis_boundary_mesh (const mesh::Mesh &mesh, const std::vector< basis::ElementBases > &gbases, const std::vector< mesh::LocalBoundary > &total_local_boundary, Eigen::MatrixXd &boundary_vis_vertices, Eigen::MatrixXd &boundary_vis_local_vertices, Eigen::MatrixXi &boundary_vis_elements, Eigen::MatrixXi &boundary_vis_elements_ids, Eigen::MatrixXi &boundary_vis_primitive_ids, Eigen::MatrixXd &boundary_vis_normals) const
	builds the boundary mesh for visualization
void	build_vis_mesh (const mesh::Mesh &mesh, const Eigen::VectorXi &disc_orders, const std::vector< basis::ElementBases > &gbases, const std::map< int, Eigen::MatrixXd > &polys, const std::map< int, std::pair< Eigen::MatrixXd, Eigen::MatrixXi > > &polys_3d, const bool boundary_only, Eigen::MatrixXd &points, Eigen::MatrixXi &tets, Eigen::MatrixXi &el_id, Eigen::MatrixXd &discr, Eigen::MatrixXd &local_points) const
	builds visualzation mesh, upsampled mesh used for visualization the visualization mesh is a dense mesh per element all disconnected it also retuns the mapping to element id and discretization of every elment works in 2 and 3d.
void	build_high_order_vis_mesh (const mesh::Mesh &mesh, const Eigen::VectorXi &output_orders, const std::vector< basis::ElementBases > &bases, Eigen::MatrixXd &points, std::vector< paraviewo::CellElement > &elements, Eigen::MatrixXi &el_id, Eigen::MatrixXd &discr, Eigen::MatrixXd &local_points) const
	builds high-der visualzation mesh per element all disconnected it also retuns the mapping to element id and discretization of every elment works in 2 and 3d.

Private Attributes
utils::RefElementSampler	ref_element_sampler
	used to sample the solution
Eigen::MatrixXd	grid_points
	grid mesh points to export solution sampled on a grid
Eigen::MatrixXi	grid_points_to_elements
	grid mesh mapping to fe elements
Eigen::MatrixXd	grid_points_bc
	grid mesh boundaries

Detailed Description

Utilies related to export of geometry.

Definition at line 23 of file OutData.hpp.

Member Function Documentation

build_grid()

void polyfem::io::OutGeometryData::build_grid	(	const polyfem::mesh::Mesh &	mesh,
		const double	spacing
	)

builds the grid to export the solution

Parameters

[in]	mesh	mesh
[in]	spacing	grid spacing, <=0 mean no grid

Definition at line 1630 of file OutData.cpp.

References polyfem::mesh::Mesh::barycentric_coords(), polyfem::mesh::Mesh::bounding_box(), polyfem::mesh::Mesh::elements_boxes(), grid_points, grid_points_bc, grid_points_to_elements, polyfem::mesh::Mesh::is_simplex(), polyfem::mesh::Mesh::is_volume(), polyfem::logger(), x, y, and z.

Referenced by polyfem::varform::VarForm::ensure_output_sampler().

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build_high_order_vis_mesh()

void polyfem::io::OutGeometryData::build_high_order_vis_mesh ( const mesh::Mesh &  mesh, const Eigen::VectorXi &  output_orders, const std::vector< basis::ElementBases > &  bases, Eigen::MatrixXd &  points, std::vector< paraviewo::CellElement > &  elements, Eigen::MatrixXi &  el_id, Eigen::MatrixXd &  discr, Eigen::MatrixXd &  local_points  ) const

private

builds high-der visualzation mesh per element all disconnected it also retuns the mapping to element id and discretization of every elment works in 2 and 3d.

if the mesh is not simplicial it gets tri/tet halized

Parameters

[in]	mesh	mesh
[in]	output_orders	output cell order per element
[in]	bases	bases used to map output reference nodes
[out]	points	mesh points
[out]	elements	mesh high-order cells
[out]	el_id	mapping from points to elements id
[out]	discr	mapping from points to discretization order

Referenced by save_volume().

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build_vis_boundary_mesh()

void polyfem::io::OutGeometryData::build_vis_boundary_mesh ( const mesh::Mesh &  mesh, const std::vector< basis::ElementBases > &  gbases, const std::vector< mesh::LocalBoundary > &  total_local_boundary, Eigen::MatrixXd &  boundary_vis_vertices, Eigen::MatrixXd &  boundary_vis_local_vertices, Eigen::MatrixXi &  boundary_vis_elements, Eigen::MatrixXi &  boundary_vis_elements_ids, Eigen::MatrixXi &  boundary_vis_primitive_ids, Eigen::MatrixXd &  boundary_vis_normals  ) const

private

builds the boundary mesh for visualization

Parameters

[in]	mesh	mesh
[in]	gbases	geometric bases
[in]	total_local_boundary	boundaries
[out]	boundary_vis_vertices	boundary visualization mesh vertices
[out]	boundary_vis_local_vertices	boundary visualization mesh vertices pre image in ref element
[out]	boundary_vis_elements	boundary visualization mesh connectivity
[out]	boundary_vis_elements_ids	boundary visualization mesh elements ids
[out]	boundary_vis_primitive_ids	boundary visualization mesh edge/face id
[out]	boundary_vis_normals	boundary visualization mesh normals

Definition at line 495 of file OutData.cpp.

References polyfem::mesh::Mesh::is_volume(), polyfem::utils::BoundarySampler::normal_for_polygon_edge(), polyfem::utils::BoundarySampler::normal_for_prism_face(), polyfem::utils::BoundarySampler::normal_for_pyramid_face(), polyfem::utils::BoundarySampler::normal_for_quad_edge(), polyfem::utils::BoundarySampler::normal_for_quad_face(), polyfem::utils::BoundarySampler::normal_for_tri_edge(), polyfem::utils::BoundarySampler::normal_for_tri_face(), polyfem::utils::RefElementSampler::num_samples(), ref_element_sampler, polyfem::utils::BoundarySampler::sample_parametric_prism_face(), polyfem::utils::BoundarySampler::sample_parametric_pyramid_face(), polyfem::utils::BoundarySampler::sample_parametric_quad_edge(), polyfem::utils::BoundarySampler::sample_parametric_quad_face(), polyfem::utils::BoundarySampler::sample_parametric_tri_edge(), polyfem::utils::BoundarySampler::sample_parametric_tri_face(), polyfem::utils::BoundarySampler::sample_polygon_edge(), and vals.

Referenced by save_surface().

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build_vis_mesh()

void polyfem::io::OutGeometryData::build_vis_mesh ( const mesh::Mesh &  mesh, const Eigen::VectorXi &  disc_orders, const std::vector< basis::ElementBases > &  gbases, const std::map< int, Eigen::MatrixXd > &  polys, const std::map< int, std::pair< Eigen::MatrixXd, Eigen::MatrixXi > > &  polys_3d, const bool  boundary_only, Eigen::MatrixXd &  points, Eigen::MatrixXi &  tets, Eigen::MatrixXi &  el_id, Eigen::MatrixXd &  discr, Eigen::MatrixXd &  local_points  ) const

private

builds visualzation mesh, upsampled mesh used for visualization the visualization mesh is a dense mesh per element all disconnected it also retuns the mapping to element id and discretization of every elment works in 2 and 3d.

if the mesh is not simplicial it gets tri/tet halized

Parameters

[in]	mesh	mesh
[in]	disc_orders	discretization orders
[in]	gbases	geometric bases
[in]	polys	polygons
[in]	polys_3d	polyhedra
[in]	boundary_only	is build only elements touching the boundary
[out]	points	mesh points
[out]	tets	mesh cells
[out]	el_id	mapping from points to elements id
[out]	discr	mapping from points to discretization order

Definition at line 721 of file OutData.cpp.

References polyfem::mesh::Mesh::dimension(), polyfem::mesh::Mesh::is_boundary_element(), polyfem::mesh::Mesh::is_cube(), polyfem::mesh::Mesh::is_prism(), polyfem::mesh::Mesh::is_pyramid(), polyfem::mesh::Mesh::is_simplex(), polyfem::mesh::Mesh::is_volume(), ref_element_sampler, and polyfem::utils::RefElementSampler::simplex_volume().

Referenced by save_volume(), and save_wire().

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export_data()

void polyfem::io::OutGeometryData::export_data	(	const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const bool	is_time_dependent,
		const double	tend_in,
		const double	dt,
		const ExportOptions &	opts,
		const std::string &	vis_mesh_path
	)		const

exports everytihng, txt, vtu, etc

Parameters

[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	is_time_dependent	if the sim is time dependent
[in]	tend_in	end time
[in]	dt	delta t
[in]	opts	export options
[in]	vis_mesh_path	vtu path

Definition at line 1124 of file OutData.cpp.

References polyfem::logger(), polyfem::io::OutputSpace::mesh, and save_vtu().

Referenced by polyfem::varform::BilaplacianVarForm::export_data(), polyfem::varform::FluidVarForm::export_data(), and polyfem::varform::ScalarVarForm::export_data().

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extract_boundary_mesh()

void polyfem::io::OutGeometryData::extract_boundary_mesh ( const mesh::Mesh &  mesh, const int  n_bases, const std::vector< basis::ElementBases > &  bases, const std::vector< mesh::LocalBoundary > &  total_local_boundary, Eigen::MatrixXd &  node_positions, Eigen::MatrixXi &  boundary_edges, Eigen::MatrixXi &  boundary_triangles, std::vector< Eigen::Triplet< double > > &  displacement_map_entries  )

static

extracts the boundary mesh

Parameters

[in]	mesh	mesh
[in]	n_bases	number of bases
[in]	bases	bases
[in]	total_local_boundary	mesh boundaries
[out]	node_positions	nodes positions
[out]	boundary_edges	edges
[out]	boundary_triangles	triangles
[out]	displacement_map	map of collision mesh vertices to nodes, empty if identity

Definition at line 95 of file OutData.cpp.

References polyfem::basis::Basis::global(), polyfem::mesh::Mesh::has_poly(), polyfem::mesh::Mesh::is_conforming(), polyfem::mesh::Mesh::is_cube(), polyfem::mesh::Mesh::is_prism(), polyfem::mesh::Mesh::is_pyramid(), polyfem::mesh::Mesh::is_simplex(), polyfem::mesh::Mesh::is_simplicial(), polyfem::mesh::Mesh::is_volume(), polyfem::logger(), and polyfem::mesh::Mesh::n_faces().

Referenced by polyfem::varform::NonlinearElasticVarForm::build_collision_mesh().

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init_sampler()

void polyfem::io::OutGeometryData::init_sampler	(	const polyfem::mesh::Mesh &	mesh,
		const double	vismesh_rel_area
	)

unitalize the ref element sampler

Parameters

[in]	mesh	mesh
[in]	vismesh_rel_area	relative sampling size

Definition at line 1625 of file OutData.cpp.

References polyfem::utils::RefElementSampler::init(), polyfem::mesh::Mesh::is_volume(), polyfem::mesh::Mesh::n_elements(), and ref_element_sampler.

Referenced by polyfem::varform::VarForm::ensure_output_sampler().

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save_contact_surface()

void polyfem::io::OutGeometryData::save_contact_surface	(	const std::string &	export_surface,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const double	t,
		const double	dt_in,
		const ExportOptions &	opts
	)		const

saves the surface vtu file for for constact quantites, eg contact or friction forces

Parameters

[in]	export_surface	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	t	time
[in]	dt_in	delta_t
[in]	opts	export options

Definition at line 1472 of file OutData.cpp.

References polyfem::io::OutputSample::cell_count, polyfem::io::OutputSpace::collision_mesh, polyfem::io::OutputSample::Contact, polyfem::io::OutputSample::domain, polyfem::io::OutputSample::dt, polyfem::io::OutputSample::points, polyfem::io::OutputSample::time, and polyfem::io::OutGeometryData::ExportOptions::use_hdf5.

Referenced by save_vtu().

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save_points()

void polyfem::io::OutGeometryData::save_points	(	const std::string &	path,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const ExportOptions &	opts
	)		const

saves the nodal values

Parameters

[in]	path	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	opts	export options

Definition at line 1563 of file OutData.cpp.

References polyfem::io::OutputSample::cell_count, polyfem::mesh::Mesh::dimension(), polyfem::io::OutputSpace::dirichlet_nodes, polyfem::io::OutputSpace::dirichlet_nodes_position, polyfem::io::OutputSample::domain, polyfem::io::OutGeometryData::ExportOptions::export_field(), polyfem::mesh::Mesh::get_node_id(), polyfem::io::OutputSpace::mesh, polyfem::io::OutputSample::node_ids, polyfem::io::OutputSample::Points, polyfem::io::OutputSample::points, and polyfem::io::OutGeometryData::ExportOptions::use_hdf5.

Referenced by save_vtu().

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save_pvd()

void polyfem::io::OutGeometryData::save_pvd	(	const std::string &	name,
		const std::function< std::string(int)> &	vtu_names,
		int	time_steps,
		double	t0,
		double	dt,
		int	skip_frame = 1
	)		const

save a PVD of a time dependent simulation

Parameters

[in]	name	filename
[in]	vtu_names	names of the vtu files
[in]	time_steps	total time stesp
[in]	t0	initial time
[in]	dt	delta t
[in]	skip_frame	every which frame to skip

Definition at line 1617 of file OutData.cpp.

Referenced by polyfem::varform::VarForm::save_timestep().

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save_surface()

void polyfem::io::OutGeometryData::save_surface	(	const std::string &	export_surface,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const double	t,
		const double	dt_in,
		const ExportOptions &	opts
	)		const

saves the surface vtu file for for surface quantites, eg traction forces

Parameters

[in]	export_surface	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	t	time
[in]	dt_in	delta_t
[in]	opts	export options

Definition at line 1401 of file OutData.cpp.

References build_vis_boundary_mesh(), polyfem::io::OutputSample::cell_count, polyfem::io::OutputSample::domain, polyfem::io::OutputSample::dt, polyfem::io::OutputSample::element_ids, polyfem::io::OutGeometryData::ExportOptions::export_field(), polyfem::io::OutputSpace::geometry_bases, polyfem::mesh::Mesh::get_boundary_id(), polyfem::mesh::Mesh::is_volume(), polyfem::io::OutputSample::local_points, polyfem::io::OutputSpace::mesh, polyfem::mesh::Mesh::n_elements(), polyfem::io::OutputSample::normals, polyfem::io::OutputSpace::output_orders, polyfem::io::OutputSample::points, polyfem::io::OutputSample::primitive_ids, polyfem::io::OutputSample::Surface, polyfem::io::OutputSample::time, polyfem::io::OutputSpace::total_local_boundary, and polyfem::io::OutGeometryData::ExportOptions::use_hdf5.

Referenced by save_vtu().

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save_volume()

void polyfem::io::OutGeometryData::save_volume	(	const std::string &	path,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const double	t,
		const double	dt,
		const ExportOptions &	opts
	)		const

saves the volume vtu file

Parameters

[in]	path	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	t	time
[in]	dt	delta t
[in]	opts	export options

Definition at line 1248 of file OutData.cpp.

References polyfem::io::OutGeometryData::ExportOptions::boundary_only, build_high_order_vis_mesh(), build_vis_mesh(), polyfem::io::OutputSample::cell_count, polyfem::mesh::Mesh::dimension(), polyfem::io::OutGeometryData::ExportOptions::discretization_order, polyfem::io::OutputSample::domain, polyfem::io::OutputSample::dt, polyfem::io::OutputSample::element_ids, polyfem::io::OutGeometryData::ExportOptions::export_field(), polyfem::io::OutputSpace::geometry_bases, polyfem::mesh::Obstacle::get_edge_connectivity(), polyfem::mesh::Obstacle::get_face_connectivity(), polyfem::mesh::Obstacle::get_vertex_connectivity(), polyfem::io::OutputSample::Grid, grid_points, grid_points_bc, grid_points_to_elements, polyfem::mesh::Mesh::is_volume(), polyfem::io::OutputSample::local_points, polyfem::io::OutputSpace::mesh, polyfem::mesh::Mesh::n_elements(), polyfem::mesh::Obstacle::n_vertices(), polyfem::io::OutputSpace::obstacle, polyfem::io::OutputSpace::output_orders, polyfem::io::OutputField::Point, polyfem::io::OutputSample::points, polyfem::io::OutputSpace::polys, polyfem::io::OutputSpace::polys_3d, polyfem::io::OutputSample::requested_fields, polyfem::io::OutGeometryData::ExportOptions::sol_on_grid, polyfem::io::OutputSample::time, polyfem::io::OutGeometryData::ExportOptions::use_hdf5, polyfem::io::OutGeometryData::ExportOptions::use_sampler, polyfem::mesh::Obstacle::v(), polyfem::io::OutputSample::Volume, and polyfem::io::write_matrix().

Referenced by save_vtu().

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save_vtu()

void polyfem::io::OutGeometryData::save_vtu	(	const std::string &	path,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const double	t,
		const double	dt,
		const ExportOptions &	opts
	)		const

saves the vtu file for time t

Parameters

[in]	path	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	t	time
[in]	dt	delta t
[in]	opts	export options

Definition at line 1183 of file OutData.cpp.

References polyfem::io::OutputSpace::collision_mesh, polyfem::io::OutGeometryData::ExportOptions::contact_forces, polyfem::io::OutGeometryData::ExportOptions::export_field(), polyfem::io::OutGeometryData::ExportOptions::fields, polyfem::io::OutGeometryData::ExportOptions::file_extension(), polyfem::io::OutGeometryData::ExportOptions::friction_forces, polyfem::logger(), polyfem::io::OutputSpace::mesh, polyfem::io::OutGeometryData::ExportOptions::normal_adhesion_forces, polyfem::io::OutGeometryData::ExportOptions::points, save_contact_surface(), save_points(), save_surface(), save_volume(), save_wire(), polyfem::io::OutGeometryData::ExportOptions::surface, polyfem::io::OutGeometryData::ExportOptions::tangential_adhesion_forces, polyfem::io::OutGeometryData::ExportOptions::volume, and polyfem::io::OutGeometryData::ExportOptions::wire.

Referenced by export_data(), polyfem::varform::VarForm::save_subsolve(), and polyfem::varform::VarForm::save_timestep().

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save_wire()

void polyfem::io::OutGeometryData::save_wire	(	const std::string &	name,
		const OutputSpace &	space,
		const OutputFieldFunction &	output_fields,
		const double	t,
		const ExportOptions &	opts
	)		const

saves the wireframe

Parameters

[in]	name	filename
[in]	space	output geometry data
[in]	output_fields	callback appending physics-specific fields
[in]	t	time
[in]	opts	export options

Definition at line 1512 of file OutData.cpp.

References build_vis_mesh(), polyfem::io::OutputSample::cell_count, polyfem::io::OutputSample::domain, polyfem::io::OutputSample::element_ids, polyfem::io::OutputSpace::geometry_bases, polyfem::io::OutputSample::local_points, polyfem::io::OutputSpace::mesh, polyfem::mesh::Mesh::n_elements(), polyfem::io::OutputSpace::output_orders, polyfem::io::OutputSample::points, polyfem::io::OutputSpace::polys, polyfem::io::OutputSpace::polys_3d, polyfem::io::OutputSample::time, polyfem::io::OutGeometryData::ExportOptions::use_hdf5, and polyfem::io::OutputSample::Wire.

Referenced by save_vtu().

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Member Data Documentation

grid_points

Eigen::MatrixXd polyfem::io::OutGeometryData::grid_points

private

grid mesh points to export solution sampled on a grid

Definition at line 209 of file OutData.hpp.

Referenced by build_grid(), and save_volume().

grid_points_bc

Eigen::MatrixXd polyfem::io::OutGeometryData::grid_points_bc

private

grid mesh boundaries

Definition at line 213 of file OutData.hpp.

Referenced by build_grid(), and save_volume().

grid_points_to_elements

Eigen::MatrixXi polyfem::io::OutGeometryData::grid_points_to_elements

private

grid mesh mapping to fe elements

Definition at line 211 of file OutData.hpp.

Referenced by build_grid(), and save_volume().

ref_element_sampler

utils::RefElementSampler polyfem::io::OutGeometryData::ref_element_sampler

private

used to sample the solution

Definition at line 206 of file OutData.hpp.

Referenced by build_vis_boundary_mesh(), build_vis_mesh(), and init_sampler().

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The documentation for this class was generated from the following files:

• src/polyfem/io/OutData.hpp
• src/polyfem/io/OutData.cpp