NetworCh Documentation

NetworCh manuals: Getting started

Documentation

Common functions

Utility functions
all_segments_length.m	Return the lengths of all segments by applying PBC
find_segment.m	Find the position of a given segment within the links list
generate_connectivity.m	Generate nodal connectivity table corresponding to the links list
pbc_fold.m	Folds point(s) into the primary volume by applying PBC
pbc_position.m	Returns the closest image of a point to another by applying PBC
segment_length.m	Compute length of a given segment by applying PBC
test_structure.m	Generate test structures to test network functions
Network manipulation
chop_structure.m	Extract a slice of the network by chopping the structure in a selected direction
extract_links.m	Extract a sub-network that only contains given links from the original network
extract_nodes.m	Extract a sub-network that only contains given nodes from the original network
remove_double_links.m	Remove double-links from the network
remove_link.m	Remove a given link from the network
remove_nodes.m	Remove given nodes from the network
remove_self_loops.m	Remove self-loops from the network
replicate_volume.m	Duplicate initial network by assembling 2 periodic replica in a given direction
replicate_volume_3.m	Replicate initial network by assembling 3 periodic replica in a given direction
scale_structure.m	Rescale a structure by a scaling factor
Geometrical functions
facet_intersection.m	Find which facet of the rectangular primary volume is intersected by a given segment
facet_intersection_position.m	Determine the facet and the intersection point between the rectangular primary volume and a given segment
find_box_neighbors.m	Find neighbors of a given node based on box partitioning
outside_box.m	Check if point(s) lie(s) outside of the primary volume
partition_box.m	Sort nodes by partitioning the primary volume into boxes
segment_plane_intersection.m	Compute the intersection between a plane and a given segment
Visualization functions
plot_box.m	Plot the box delimiting the primary volume
plot_nodes.m	Plot a subset of nodes of the network
plot_segments.m	Plot a subset of segments of the network
plot_structure.m	Plot the full network structure
Export functions
export_gexf.m	Export the network in GEXF format
export_gml.m	Export the network in GML format

Functions for DD structures analysis

Utility functions
fcc_slip_system.m	Get Burgers vector and slip plane normal for a given FCC slip system
get_slip_system.m	Determine the slip system of segment with a given Burgers vector b and slip plane normal
is_junction_segment.m	Determine if a given segment (or list of segments) corresponds to a dislocation junction
structure_sanity_check.m	Perform several sanity checks on the DD structure (conservation of the Burgers vector, zero-arm nodes, self-loops, double-links, ...)
unique_slip_plane.m	Determine properties of the unique slip plane of a given segment (including the intercept coefficient)
Structure generation
generate_fcc_junction.m	Generate the initial configuration (two straight segments connected at their middle point) to form a FCC junction (Lomer, glissile, Hirth or colinear) at given angles
generate_frs.m	Generate a straight Frank-Read source in a periodic cubic volume
generate_glissile_loop.m	Generate a glissile dislocation loop
generate_infinite_line.m	Generate an infinite dislocation line in a periodic cubic volume
generate_prismatic_loop.m	Generate a prismatic dislocation loop (4 nodes)
Structure decomposition
decompose_into_loops.m	Decompose the dislocation network into loops by unzipping binary junctions
irreductible_structure.m	Fully decompose the DD structure into an irredducible core by recursively unzipping junctions and reducing the network (removing self-links, merging double-links, ...)
merge_double_links.m	Merge double-links of the DD network
physical_structure.m	Reduce the DD structure to physical nodes only by removing all discretization nodes
reduce_structure.m	Fully reduce the DD structure by recursively removing the self and double links, and the discretization nodes
Import / Export structures
read_data_files.m	List all ParaDiS data files in a given directory
read_dxa_file.m	Read dislocations from a DXA (Ovito) .ca file
read_nodes.m	Read dislocation nodes from a ParaDiS data file
write_data_file.m	Write DD structure into a ParaDiS nodal data file

Functions for MD structures analysis

read_cgsd.m	Read CGSD files (.cn and .bnd)
merge_cross_links.m	Merge cross-linked nodes into single nodes and flag them

Functions for network analysis

adjacency.m	Generate the adjacency matrix from the links/segments list
assortativity.m	Calculate the Pearson correlation coefficient that measures the assortativity of the nodes of the network
average_degree.m	Calculate the average nodes degree and the exponent of best fit power-law distribution
average_shortest_path.m	Compute the average shortest path between all pairs of nodes of the network
clustering.m	Calculate the clustering and transitivity coefficients of the network
construct_shortest_path.m	Construct the shortest path (sequence of nodes) from a source to a target node
extract_component.m	Extract a given component from the network
find_components.m	Find unconnected components of the network
link_density.m	Calculate the link density of the network
normalized_laplacian.m	Compute the normalized graph Laplacian matrix of the network
random_network.m	Generate a random network that follows a power-law degree distribution
shortest_path.m	Compute shortest path from a source to all other vertices or to a given target