NetworCh Introduction and examples - Revision history

Nbertin: Nbertin moved page Introduction and examples to NetworCh Introduction and examples

2018-01-31T20:12:00Z

Nbertin moved page Introduction and examples to NetworCh Introduction and examples

← Older revision	Revision as of 20:12, 31 January 2018
(No difference)

Nbertin at 20:10, 31 January 2018

2018-01-31T20:10:35Z

@@ Line 1: / Line 1: @@
-NetworCh manuals: Getting started
+<P ALIGN="CENTER">NetworCh manuals: Getting started</P>
-= Introduction and examples =
+NetworCh: Introduction and examples</STRONG></font></P>
 == NetworCh basics ==
@@ Line 91: / Line 117: @@
 <pre>
-[rn,links] = random_network(n,alpha,bounds);
+[rn,links] = random_network(n,P,bounds);
 </pre>
-will generate a network of <tt>n</tt> nodes whose degree distribution (number of connections per node) will satisfy a power-law distribution of exponent alpha. The algorithm to generate such network is based on the configuration model, with the additional constraint that links must join nodes that are in the spatial vicinity of one another.
+will generate a network of <tt>n</tt> nodes randomly positionned within <tt>bounds</tt>, and whose degree distribution (number of connections per node) is specified with array <tt>P</tt>. The algorithm to generate such a network is based on the configuration model, with the additional constraint that links must join nodes that are in the spatial vicinity of one another.
 == Exporting networks ==

Nbertin: /* Exporting networks */

2016-10-15T00:14:14Z

Exporting networks

← Older revision		Revision as of 00:14, 15 October 2016
Line 110:		Line 110:
	</pre>		</pre>

	where array <tt>weights</tt> contains the list of weight associated with each link such that <tt>~~numel~~(weights) = size(links,1)</tt>.		where array <tt>weights</tt> contains the list of weight associated with each link such that <tt>size(weights,1) = size(links,1)</tt>.

Nbertin: /* Introduction and examples */

2016-10-15T00:12:17Z

Introduction and examples

← Older revision		Revision as of 00:12, 15 October 2016
Line 97:		Line 97:

	== Exporting networks ==		== Exporting networks ==
			Networks can be exported in standard graph formats <tt>GML</tt> and <tt>GEXF</tt> for visualization / analysis with other network tools with the following functions:

			<pre>
			export_gml('filename.gml',rn,links);
			export_gexf('filename.gexf',rn,links);
			</pre>

			Properties can be associated with nodes or links. For instance, the weight of the links can be exported by specifying property <tt>'EdgeWeights'</tt>:

			<pre>
			export_gml('filename.gml',rn,links,'EdgeWeights',weights);
			</pre>

			where array <tt>weights</tt> contains the list of weight associated with each link such that <tt>numel(weights) = size(links,1)</tt>.

Nbertin at 02:30, 14 October 2016

2016-10-14T02:30:13Z

← Older revision		Revision as of 02:30, 14 October 2016
Line 1:		Line 1:
	NetworCh manuals: ~~Reference~~		NetworCh manuals: Getting started
	= Introduction and examples =		= Introduction and examples =

Nbertin: /* Introduction and examples */

2016-10-14T02:27:09Z

Introduction and examples

@@ Line 21: / Line 21: @@
 === Network visualization ===
-A network can plotted with function <tt>plot_structure</tt>:
+A network can be plotted with function <tt>plot_structure</tt>:
 <pre>
@@ Line 27: / Line 27: @@
 </pre>
-Note that function <tt>plot_structure</tt> uses the spatial coordinates <tt>rn(:,1:3)</tt> to position nodes and does not relie and graph drawing algorithm to generate a planar layout of the network.
+Note that function <tt>plot_structure</tt> uses the spatial coordinates <tt>rn(:,1:3)</tt> to position nodes and does not rely and graph drawing algorithm to generate a planar layout of the network.
-In many situations, the nodes of the network are contained in a rectangular box (e.g. the simulation box in DD or MD simulations). In NetworCh, the such volume is defined with array <tt>bounds</tt>. Array <tt>bounds</tt> specifies the bounds of the volume in the following manner: <tt>bounds = [xmin,xmax;ymin,ymax;zmin,zmax]</tt>. For example, if we assume that our structure is contained in a cubic simulation box of edge size <tt>L</tt> centered in the origin <tt>(0,0,0)</tt>, it can be visualised using:
+In many situations, the nodes of the network are contained in a rectangular box (e.g. the simulation box in DD or MD simulations). In NetworCh, such a volume is defined with array <tt>bounds</tt>. Array <tt>bounds</tt> specifies the bounds of the volume in the following manner: <tt>bounds = [xmin,xmax;ymin,ymax;zmin,zmax]</tt>. For example, if we assume that our structure is contained in a cubic simulation box of edge size <tt>L</tt> centered in the origin <tt>(0,0,0)</tt>, it can be visualized using:
 <pre>
@@ Line 36: / Line 36: @@
 </pre>
-By default, periodic boundary conditions will be applied for the visualization when argument <tt>bounds</tt> is specified in function <tt>plot_structure</tt>, such that nodes whose position lie outside the volume defined by <tt>bounds</tt> will be folded back to the volume.
+By default, periodic boundary conditions will be applied for the visualization when argument <tt>bounds</tt> is specified in function <tt>plot_structure</tt>, such that nodes whose position lies outside the volume defined by <tt>bounds</tt> will be folded back to the volume.
 == Importing/Creating networks ==
@@ Line 52: / Line 52: @@
 === DD structures ===
 === MD structures ===
 == Exporting networks ==

Nbertin: Created page with "NetworCh manuals: Reference = Introduction and examples = == NetworCh basics == === Network representation === A network is a collection of vertices (nodes) joined by edges..."

2016-10-13T02:49:32Z

Created page with "NetworCh manuals: Reference = Introduction and examples = == NetworCh basics == === Network representation === A network is a collection of vertices (nodes) joined by edges..."

New page

NetworCh manuals: Reference
= Introduction and examples =

== NetworCh basics ==

=== Network representation ===
A network is a collection of vertices (nodes) joined by edges (links). In NetworCh, each network/structure is represented by a list of nodes position <tt>rn</tt> and a list of links <tt>links</tt>. The first three columns of <tt>rn</tt> are reserved for the <tt>(x,y,z)</tt> spatial coordinates of each node. The two first columns of <tt>links</tt> must contain the id of nodes connected by the edges.

For example, a simple network consisting of two nodes A = <tt>(xa,ya,za)</tt> and B = <tt>(xb,yb,zb)</tt> joined by a single segment can be initialized as:

<pre>
% Nodes
rn = zeros(2,3);
rn(1,1:3) = [xa,ya,za];
rn(2,1:3) = [xb,yb,zb];

% Links
links = zeros(1,2);
links(1,1:2) = [1,2];
</pre>

=== Network visualization ===
A network can plotted with function <tt>plot_structure</tt>:

<pre>
plot_structure(rn,links);
</pre>

Note that function <tt>plot_structure</tt> uses the spatial coordinates <tt>rn(:,1:3)</tt> to position nodes and does not relie and graph drawing algorithm to generate a planar layout of the network.

In many situations, the nodes of the network are contained in a rectangular box (e.g. the simulation box in DD or MD simulations). In NetworCh, the such volume is defined with array <tt>bounds</tt>. Array <tt>bounds</tt> specifies the bounds of the volume in the following manner: <tt>bounds = [xmin,xmax;ymin,ymax;zmin,zmax]</tt>. For example, if we assume that our structure is contained in a cubic simulation box of edge size <tt>L</tt> centered in the origin <tt>(0,0,0)</tt>, it can be visualised using:

<pre>
bounds = L/2*[-1,1;-1,1;-1,1];
plot_structure(rn,links,bounds);
</pre>

By default, periodic boundary conditions will be applied for the visualization when argument <tt>bounds</tt> is specified in function <tt>plot_structure</tt>, such that nodes whose position lie outside the volume defined by <tt>bounds</tt> will be folded back to the volume.

== Importing/Creating networks ==

NetworCh can generate or import networks from different sources.

=== Test structures ===
Several simple test structures are provided within the library to test its functions. Test structures are generated by using the <tt>test_structure</tt> function:

<pre>
[rn,links,bounds] = test_structure(id);
</pre>

where <tt>id</tt> is the index of the test structure to generate.

=== DD structures ===

=== MD structures ===

=== Newtorks generation ===

== Exporting networks ==