NetworCh Documentation: Difference between revisions

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NetworCh manuals: Getting started
<P ALIGN="CENTER">NetworCh manuals: Getting started</P>
<P ALIGN="CENTER"><FONT SIZE="+2" color="darkred"><STRONG>
= Documentation =
NetworCh: Documentation</STRONG></font></P>
<DIV>
<P ALIGN="CENTER"><STRONG>Nicolas Bertin</STRONG></P>
</DIV>
<DIV>
<P ALIGN="CENTER">October 2016</P>
</DIV>

<HR>

This page contains a non-exhaustive list of the main Matlab functions available in the NetworCh library.


== Common functions ==
== Common functions ==


{| class="wikitable" cellpadding="2"
{| class="wikitable" cellpadding="2"
!colspan="2"|Utility functions
|-
|-
| all_segments_length.m
| all_segments_length.m
| Return the lengths of all segments by applying PBC
| Return the lengths of all segments by applying PBC
|-
|-
| chop_structure.m
| find_segment.m
| Find the position of a given segment within the links list
| Extract a slice of the network by chopping the structure in a selected direction
|-
|-
| generate_connectivity.m
| export_gexf.m
| Generate nodal connectivity table corresponding to the links list
| Export the network in GEXF format
|-
|-
| export_gml.m
| pbc_fold.m
| Folds point(s) into the primary volume by applying PBC
| Export the network in GML format
|-
| 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
|-
!colspan="2"|Network manipulation
|-
| chop_structure.m
| Extract a slice of the network by chopping the structure in a selected direction
|-
|-
| extract_links.m
| extract_links.m
Line 23: Line 49:
| extract_nodes.m
| extract_nodes.m
| Extract a sub-network that only contains given nodes from the original network
| 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
|-
!colspan="2"|Geometrical functions
|-
|-
| facet_intersection.m
| facet_intersection.m
Line 32: Line 81:
| find_box_neighbors.m
| find_box_neighbors.m
| Find neighbors of a given node based on box partitioning
| Find neighbors of a given node based on box partitioning
|-
| 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
|-
|-
| outside_box.m
| outside_box.m
Line 45: Line 88:
| Sort nodes by partitioning the primary volume into boxes
| Sort nodes by partitioning the primary volume into boxes
|-
|-
| segment_plane_intersection.m
| pbc_fold.m
| Compute the intersection between a plane and a given segment
| Folds point(s) into the primary volume by applying PBC
|-
|-
!colspan="2"|Visualization functions
| pbc_position.m
| Returns the closest image of a point to another by applying PBC
|-
|-
| plot_box.m
| plot_box.m
Line 63: Line 105:
| Plot the full network structure
| Plot the full network structure
|-
|-
!colspan="2"|Export functions
| remove_double_links.m
| Remove double-links from the network
|-
|-
| remove_link.m
| export_gexf.m
| Export the network in GEXF format
| Remove a given link from the network
|-
|-
| remove_nodes.m
| export_gml.m
| Export the network in GML format
| Remove given nodes from the network
|}

== Functions for DD structures analysis ==
{| class="wikitable" cellpadding="2"
!colspan="2"|Utility functions
|-
|-
| remove_self_loops.m
| fcc_slip_system.m
| Get Burgers vector and slip plane normal for a given FCC slip system
| Remove self-loops from the network
|-
|-
| replicate_volume.m
| get_slip_system.m
| Determine the slip system of segment with a given Burgers vector b and slip plane normal
| Duplicate initial network by assembling 2 periodic replica in a given direction
|-
|-
| replicate_volume_3.m
| is_junction_segment.m
| Determine if a given segment (or list of segments) corresponds to a dislocation junction
| Replicate initial network by assembling 3 periodic replica in a given direction
|-
|-
| structure_sanity_check.m
| scale_structure.m
| Perform several sanity checks on the DD structure (conservation of the Burgers vector, zero-arm nodes, self-loops, double-links, ...)
| Rescale a structure by a scaling factor
|-
|-
| segment_length.m
| unique_slip_plane.m
| Compute length of a given segment by applying PBC
| Determine properties of the unique slip plane of a given segment (including the intercept coefficient)
|-
|-
!colspan="2"|Structure generation
| segment_plane_intersection.m.m
| Compute the intersection between a plane and a given segment
|-
|-
| generate_fcc_junction.m
| test_structure.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 test structures to test network functions
|-
| 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)
|-
!colspan="2"|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
|-
!colspan="2"|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 DD structures analysis ==



== Functions for MD structures analysis ==
== Functions for MD structures analysis ==
Line 110: Line 194:


== Functions for network analysis ==
== Functions for network analysis ==
{| class="wikitable" cellpadding="2"
|-
| 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
|}

Latest revision as of 20:15, 31 January 2018

NetworCh manuals: Getting started

NetworCh: Documentation

Nicolas Bertin

October 2016

This page contains a non-exhaustive list of the main Matlab functions available in the NetworCh library.

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
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