Index

A

addAttributes() (pmmoto.io.evtk.xml.XmlWriter method) addComment() (pmmoto.io.evtk.xml.XmlWriter method) addComments() (pmmoto.io.evtk.vtk.VtkFile method) addData() (pmmoto.io.evtk.vtk.VtkFile method) addDeclaration() (pmmoto.io.evtk.xml.XmlWriter method) addFile() (pmmoto.io.evtk.vtk.VtkGroup method) addHeader() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) addition() (in module pmmoto.filters.morphological_operators)

addPiece() (pmmoto.io.evtk.vtk.VtkParallelFile method) addText() (pmmoto.io.evtk.xml.XmlWriter method) all_features (pmmoto.core.subdomain_features.SubdomainFeatures property) all_gather() (in module pmmoto.core.communication) all_reduce() (in module pmmoto.core.communication) appendData() (pmmoto.io.evtk.vtk.VtkFile method) appendHeader() (pmmoto.io.evtk.vtk.VtkFile method) atom_universal_force_field() (in module pmmoto.particles.atom_universal_force_field) average_image_along_axis() (in module pmmoto.analysis.average)

B

bin_distances() (in module pmmoto.domain_generation.rdf) bin_image() (in module pmmoto.core.utils) BodyCenteredCubic (class in pmmoto.domain_generation.lattice_packings)

boundary_order() (in module pmmoto.core.boundary_types) boundary_types (pmmoto.core.domain.Domain attribute) BoundaryType (class in pmmoto) box (pmmoto.core.domain.Domain attribute)

C

check_boundary_type() (pmmoto.core.subdomain.Subdomain method) check_file() (in module pmmoto.io.io_utils) check_file_path() (in module pmmoto.io.io_utils) check_folder() (in module pmmoto.io.io_utils) check_num_files() (in module pmmoto.io.io_utils) close() (pmmoto.io.evtk.xml.XmlWriter method) closeAppendedData() (pmmoto.io.evtk.vtk.VtkFile method) closeData() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) closeElement() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) (pmmoto.io.evtk.xml.XmlWriter method) closeGrid() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) closePiece() (pmmoto.io.evtk.vtk.VtkFile method) closing() (in module pmmoto.filters.morphological_operators)

collect_features() (pmmoto.core.subdomain_features.SubdomainFeatures method) collect_periodic_corrections() (pmmoto.core.subdomain_features.SubdomainFeatures method) collect_periodic_features() (pmmoto.core.subdomain_features.SubdomainFeatures method) communicate_features() (in module pmmoto.core.communication) compute_lower_face() (pmmoto.core.features.Feature method) compute_lower_neighbor() (pmmoto.core.features.Feature method) compute_upper_face() (pmmoto.core.features.Feature method) compute_upper_neighbor() (pmmoto.core.features.Feature method) connect_components() (in module pmmoto.filters.connected_components) constant_pad_img() (in module pmmoto.core.utils) convert_atoms_elements_to_ids() (in module pmmoto.particles) (in module pmmoto.particles.particles) convert_feature_id() (pmmoto.core.features.Feature method) Corner (class in pmmoto.core.features) count_label_voxels() (in module pmmoto.core.voxels) count_locations() (in module pmmoto.analysis.bins) cylinderToVTK() (in module pmmoto.io.evtk.hl)

D

DecomposedDomain (class in pmmoto.core.domain_decompose) deconstruct_img() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) determine_maximum() (in module pmmoto.core.utils) dilate() (in module pmmoto.filters.morphological_operators)

dims (pmmoto.core.domain.Domain attribute) DiscretizedDomain (class in pmmoto.core.domain_discretization) distance (pmmoto.domain_generation.porousmedia.PorousMedia property) Domain (class in pmmoto.core.domain) drainage() (in module pmmoto.filters.equilibrium_distribution)

E

Edge (class in pmmoto.core.features) edt() (in module pmmoto.filters.distance) (in module pmmoto.filters.distance.euclidean_distance_transform) edt2d() (in module pmmoto.filters.distance) (in module pmmoto.filters.distance.euclidean_distance_transform)

edt3d() (in module pmmoto.filters.distance) (in module pmmoto.filters.distance.euclidean_distance_transform) END (pmmoto.BoundaryType attribute) erode() (in module pmmoto.filters.morphological_operators) extend_padding() (pmmoto.core.subdomain_padded.PaddedSubdomain method)

F

Face (class in pmmoto.core.features) FaceCenteredCubic (class in pmmoto.domain_generation.lattice_packings) Feature (class in pmmoto.core.features)

format() (pmmoto.core.logging.MPIFormatter method) from_discretized_domain() (pmmoto.core.domain_decompose.DecomposedDomain class method) from_domain() (pmmoto.core.domain_discretization.DiscretizedDomain class method) functionals() (in module pmmoto.analysis.minkowski)

G

gather() (in module pmmoto.core.communication) gen_img_linear() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_img_random_binary() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_img_smoothed_random_binary() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_img_to_label_map() (in module pmmoto.core.voxels) (in module pmmoto.filters.connected_components) gen_inlet_label_map() (in module pmmoto.core.voxels) gen_map() (pmmoto.core.domain_decompose.DecomposedDomain method) gen_mp_constant() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_outlet_label_map() (in module pmmoto.core.voxels) gen_pm() (in module pmmoto.domain_generation.porousmedia) gen_pm_atom_domain() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_pm_atom_file() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_pm_cylinders() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_pm_inkbottle() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_pm_spheres_domain() (in module pmmoto.domain_generation) (in module pmmoto.domain_generation.domain_generation) gen_struct_element() (in module pmmoto.filters.morphological_operators) gen_struct_ratio() (in module pmmoto.filters.morphological_operators) generate_lattice() (pmmoto.domain_generation.lattice_packings.Lattice method) get_basis_vectors() (pmmoto.domain_generation.lattice_packings.BodyCenteredCubic method) (pmmoto.domain_generation.lattice_packings.FaceCenteredCubic method) (pmmoto.domain_generation.lattice_packings.Lattice method) (pmmoto.domain_generation.lattice_packings.SimpleCubic method) get_boundary_hull() (in module pmmoto.filters.distance.euclidean_distance_transform) get_boundary_id() (in module pmmoto.core.orientation) get_boundary_type() (pmmoto.core.subdomain_features.SubdomainFeatures method) get_boundary_types() (pmmoto.core.subdomain.Subdomain method) get_boundary_voxels() (in module pmmoto.core.voxels) get_box() (pmmoto.core.subdomain.Subdomain method) get_centroid() (pmmoto.core.subdomain.Subdomain method) get_coordination_number() (pmmoto.domain_generation.lattice_packings.BodyCenteredCubic method) (pmmoto.domain_generation.lattice_packings.FaceCenteredCubic method) (pmmoto.domain_generation.lattice_packings.SimpleCubic method) get_coords() (pmmoto.core.domain_discretization.DiscretizedDomain static method) get_direction() (pmmoto.core.features.Face method) get_feature_member() (pmmoto.core.subdomain_features.SubdomainFeatures method) get_features() (pmmoto.core.subdomain_features.SubdomainFeatures method) get_global_boundary() (pmmoto.core.subdomain.Subdomain method) (pmmoto.core.subdomain_features.SubdomainFeatures method) get_id() (in module pmmoto.core.voxels) get_img_index() (pmmoto.core.subdomain.Subdomain method)

get_index() (pmmoto.core.subdomain.Subdomain static method) get_inlet() (pmmoto.core.subdomain.Subdomain method) get_length() (pmmoto.core.domain.Domain method) (pmmoto.core.subdomain.Subdomain method) get_logger() (in module pmmoto.core.logging) get_maximum() (in module pmmoto.analysis.stats) get_maximum_diameter() (pmmoto.core.subdomain_verlet.VerletSubdomain method) get_minimum() (in module pmmoto.analysis.stats) get_nearest_boundary_index() (in module pmmoto.core.voxels) get_neighbor_ranks() (pmmoto.core.domain_decompose.DecomposedDomain method) get_origin() (pmmoto.core.domain.Domain method) (pmmoto.core.subdomain.Subdomain method) get_outlet() (pmmoto.core.subdomain.Subdomain method) get_own_voxels() (pmmoto.core.subdomain.Subdomain method) (pmmoto.core.subdomain_padded.PaddedSubdomain method) get_packing_efficiency() (pmmoto.domain_generation.lattice_packings.BodyCenteredCubic method) (pmmoto.domain_generation.lattice_packings.FaceCenteredCubic method) (pmmoto.domain_generation.lattice_packings.SimpleCubic method) get_padded_box() (pmmoto.core.subdomain_padded.PaddedSubdomain method) get_padded_start() (pmmoto.core.subdomain_padded.PaddedSubdomain static method) get_padded_voxels() (pmmoto.core.subdomain_padded.PaddedSubdomain method) get_padding() (pmmoto.core.subdomain_padded.PaddedSubdomain method) get_pc() (pmmoto.domain_generation.multiphase.Multiphase static method) get_periodic_correction() (pmmoto.core.features.Corner method) (pmmoto.core.features.Edge method) (pmmoto.core.features.Face method) get_probe_radius() (pmmoto.domain_generation.multiphase.Multiphase static method) get_radius() (pmmoto.core.subdomain.Subdomain method) (pmmoto.domain_generation.lattice_packings.BodyCenteredCubic method) (pmmoto.domain_generation.lattice_packings.FaceCenteredCubic method) (pmmoto.domain_generation.lattice_packings.Lattice method) (pmmoto.domain_generation.lattice_packings.SimpleCubic method) get_reservoir_padding() (pmmoto.core.subdomain_padded.PaddedSubdomain method) get_resolution() (pmmoto.core.domain_discretization.DiscretizedDomain method) get_saturation() (pmmoto.domain_generation.multiphase.Multiphase method) get_sizes() (in module pmmoto.filters.porosimetry) get_slice() (pmmoto.core.features.Face method) get_start() (pmmoto.core.subdomain.Subdomain static method) get_strides() (pmmoto.core.features.Face method) get_verlet_box() (pmmoto.core.subdomain_verlet.VerletSubdomain method) get_verlet_centroid() (pmmoto.core.subdomain_verlet.VerletSubdomain method) get_verlet_loop() (pmmoto.core.subdomain_verlet.VerletSubdomain method) get_verlet_voxels() (pmmoto.core.subdomain_verlet.VerletSubdomain method) get_volume() (pmmoto.core.domain.Domain method) get_volume_fraction() (pmmoto.domain_generation.multiphase.Multiphase method) get_voxels() (pmmoto.core.features.Feature method) (pmmoto.core.subdomain.Subdomain static method) getFileName() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) gridToVTK() (in module pmmoto.io.evtk.hl)

I

imageToVTK() (in module pmmoto.io.evtk.hl) initialize() (in module pmmoto) (in module pmmoto.core.pmmoto) initialize_atoms() (in module pmmoto.particles) (in module pmmoto.particles.particles) initialize_cylinders() (in module pmmoto.particles.particles) initialize_spheres() (in module pmmoto.particles) (in module pmmoto.particles.particles)

inlet (pmmoto.core.domain.Domain attribute) inlet_connected_img() (in module pmmoto.filters.connected_components) inlet_outlet_connected_img() (in module pmmoto.filters.connected_components) INTERNAL (pmmoto.BoundaryType attribute) is_periodic() (pmmoto.core.features.Feature method) isolated_img() (in module pmmoto.filters.connected_components)

L

Lattice (class in pmmoto.domain_generation.lattice_packings)

length (pmmoto.core.domain.Domain attribute) linesToVTK() (in module pmmoto.io.evtk.hl)

M

map_to_index() (pmmoto.core.features.Face method) match_global_boundary_voxels() (in module pmmoto.core.voxels) match_neighbor_boundary_voxels() (in module pmmoto.core.voxels) max_distance (pmmoto.domain_generation.porousmedia.PorousMedia property) module pmmoto pmmoto.analysis pmmoto.analysis.average pmmoto.analysis.bins pmmoto.analysis.minkowski pmmoto.analysis.stats pmmoto.core pmmoto.core.boundary_types pmmoto.core.communication pmmoto.core.domain pmmoto.core.domain_decompose pmmoto.core.domain_discretization pmmoto.core.features pmmoto.core.logging pmmoto.core.orientation pmmoto.core.pmmoto pmmoto.core.subdomain pmmoto.core.subdomain_features pmmoto.core.subdomain_padded pmmoto.core.subdomain_verlet pmmoto.core.utils pmmoto.core.voxels pmmoto.domain_generation pmmoto.domain_generation.domain_generation pmmoto.domain_generation.lattice_packings pmmoto.domain_generation.multiphase pmmoto.domain_generation.porousmedia pmmoto.domain_generation.rdf pmmoto.filters pmmoto.filters.connected_components pmmoto.filters.distance pmmoto.filters.distance.euclidean_distance_transform pmmoto.filters.equilibrium_distribution pmmoto.filters.morphological_operators pmmoto.filters.porosimetry pmmoto.io pmmoto.io.data_read pmmoto.io.evtk pmmoto.io.evtk.evtk pmmoto.io.evtk.hl pmmoto.io.evtk.vtk pmmoto.io.evtk.xml pmmoto.io.io_utils pmmoto.io.output pmmoto.particles pmmoto.particles.atom_universal_force_field pmmoto.particles.particles

MPIFormatter (class in pmmoto.core.logging) Multiphase (class in pmmoto.domain_generation.multiphase)

O

openAppendedData() (pmmoto.io.evtk.vtk.VtkFile method) openData() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) openElement() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) (pmmoto.io.evtk.xml.XmlWriter method)

openGrid() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkParallelFile method) opening() (in module pmmoto.filters.morphological_operators) openPiece() (pmmoto.io.evtk.vtk.VtkFile method) outlet (pmmoto.core.domain.Domain attribute) outlet_connected_img() (in module pmmoto.filters.connected_components) own_img() (in module pmmoto.core.utils)

P

PaddedSubdomain (class in pmmoto.core.subdomain_padded) PERIODIC (pmmoto.BoundaryType attribute) periodic (pmmoto.core.domain.Domain attribute) periodic_check() (pmmoto.core.domain.Domain method) (pmmoto.core.subdomain.Subdomain method) phase_count() (in module pmmoto.filters.connected_components) phase_exists() (in module pmmoto.core.utils) plot_pore_size_distribution() (in module pmmoto.filters.porosimetry) pmmoto module pmmoto.analysis module pmmoto.analysis.average module pmmoto.analysis.bins module pmmoto.analysis.minkowski module pmmoto.analysis.stats module pmmoto.core module pmmoto.core.boundary_types module pmmoto.core.communication module pmmoto.core.domain module pmmoto.core.domain_decompose module pmmoto.core.domain_discretization module pmmoto.core.features module pmmoto.core.logging module pmmoto.core.orientation module pmmoto.core.pmmoto module pmmoto.core.subdomain module pmmoto.core.subdomain_features module pmmoto.core.subdomain_padded module pmmoto.core.subdomain_verlet module pmmoto.core.utils module pmmoto.core.voxels module pmmoto.domain_generation module pmmoto.domain_generation.domain_generation module

pmmoto.domain_generation.lattice_packings module pmmoto.domain_generation.multiphase module pmmoto.domain_generation.porousmedia module pmmoto.domain_generation.rdf module pmmoto.filters module pmmoto.filters.connected_components module pmmoto.filters.distance module pmmoto.filters.distance.euclidean_distance_transform module pmmoto.filters.equilibrium_distribution module pmmoto.filters.morphological_operators module pmmoto.filters.porosimetry module pmmoto.io module pmmoto.io.data_read module pmmoto.io.evtk module pmmoto.io.evtk.evtk module pmmoto.io.evtk.hl module pmmoto.io.evtk.vtk module pmmoto.io.evtk.xml module pmmoto.io.io_utils module pmmoto.io.output module pmmoto.particles module pmmoto.particles.atom_universal_force_field module pmmoto.particles.particles module pointsToVTK() (in module pmmoto.io.evtk.hl) pointsToVTKAsTIN() (in module pmmoto.io.evtk.hl) polyLinesToVTK() (in module pmmoto.io.evtk.hl) pore_size_distribution() (in module pmmoto.filters.porosimetry) porosimetry() (in module pmmoto.filters.porosimetry) porosity (pmmoto.domain_generation.porousmedia.PorousMedia property) PorousMedia (class in pmmoto.domain_generation.porousmedia) py_read_lammps_atoms() (in module pmmoto.io) (in module pmmoto.io.data_read)

R

read_atom_map() (in module pmmoto.io) (in module pmmoto.io.data_read) read_binned_distances_rdf() (in module pmmoto.io) (in module pmmoto.io.data_read) read_lammps_atoms() (in module pmmoto.io) (in module pmmoto.io.data_read)

read_rdf() (in module pmmoto.io) (in module pmmoto.io.data_read) read_sphere_pack_xyzr_domain() (in module pmmoto.io) (in module pmmoto.io.data_read) rectilinearToVTK() (in module pmmoto.io.evtk.hl) renumber_image() (in module pmmoto.core.voxels)

S

save() (pmmoto.io.evtk.vtk.VtkFile method) (pmmoto.io.evtk.vtk.VtkGroup method) (pmmoto.io.evtk.vtk.VtkParallelFile method) save_extended_img_data_parallel() (in module pmmoto.io) (in module pmmoto.io.output) save_img() (in module pmmoto.io) (in module pmmoto.io.output) save_particle_data() (in module pmmoto.io) (in module pmmoto.io.output)

set_distance() (pmmoto.domain_generation.porousmedia.PorousMedia method) set_feature_voxels() (pmmoto.core.subdomain_features.SubdomainFeatures method) set_porosity() (pmmoto.domain_generation.porousmedia.PorousMedia method) set_wall_bcs() (pmmoto.core.subdomain.Subdomain method) setup_logger() (in module pmmoto.core.logging) SimpleCubic (class in pmmoto.domain_generation.lattice_packings) structuredToVTK() (in module pmmoto.io.evtk.hl) Subdomain (class in pmmoto.core.subdomain) SubdomainFeatures (class in pmmoto.core.subdomain_features) subtraction() (in module pmmoto.filters.morphological_operators)

U

uff_radius() (in module pmmoto.particles) (in module pmmoto.particles.particles) unpad() (in module pmmoto.core.utils)

unstructuredGridToVTK() (in module pmmoto.io.evtk.hl) update_buffer() (in module pmmoto.core.communication) update_img() (pmmoto.domain_generation.multiphase.Multiphase method) update_reservoir() (pmmoto.core.subdomain_padded.PaddedSubdomain method)

V

VerletSubdomain (class in pmmoto.core.subdomain_verlet) volume (pmmoto.core.domain.Domain attribute) VtkCellType (class in pmmoto.io.evtk.vtk) VtkDataType (class in pmmoto.io.evtk.vtk)

VtkFile (class in pmmoto.io.evtk.vtk) VtkFileType (class in pmmoto.io.evtk.vtk) VtkGroup (class in pmmoto.io.evtk.vtk) VtkParallelFile (class in pmmoto.io.evtk.vtk) VtkParallelFileType (class in pmmoto.io.evtk.vtk)

W

WALL (pmmoto.BoundaryType attribute) writeArraysToFile() (in module pmmoto.io.evtk.evtk) writeArrayToFile() (in module pmmoto.io.evtk.evtk)

writeBlockSize() (in module pmmoto.io.evtk.evtk) writeParallelPoints() (in module pmmoto.io.evtk.hl) writeParallelVTKGrid() (in module pmmoto.io.evtk.hl)

X

XmlWriter (class in pmmoto.io.evtk.xml)