Shortest paths PBC calculation - Revision history

Nbertin at 20:20, 31 January 2018

2018-01-31T20:20:56Z

← Older revision		Revision as of 20:20, 31 January 2018
Line 1:		Line 1:
			<P ALIGN="CENTER">NetworCh manuals</P>
⚫	= Shortest paths calculation in periodic CGSD simulation =
			<P ALIGN="CENTER"><FONT SIZE="+2" color="darkred"><STRONG>
		⚫	Shortest paths calculation in periodic CGSD simulation</STRONG></font></P>
			<DIV>
			<P ALIGN="CENTER"><STRONG>Nicolas Bertin</STRONG></P>
			</DIV>
			<DIV>
			<P ALIGN="CENTER">October 2016</P>
			</DIV>

			<HR>

	== Introduction ==		== Introduction ==

Nbertin: /* Shortest paths calculation in periodic CGSD simulation */

2016-10-18T02:21:55Z

Shortest paths calculation in periodic CGSD simulation

← Older revision		Revision as of 02:21, 18 October 2016
Line 5:		Line 5:

	== Loading and replicating the structure ==		== Loading and replicating the structure ==
			The chain structure corresponding to a CGSD simulation is outputted in two files: a beads position file (e.g. <tt><simulationName>.cn</tt>) which contains the id and the spatial coordinates of every beads in the simulation, and a bond file (e.g. <tt><simulationName>.bnd</tt>) which contains the connectivity information between the beads. The structure can be loaded in Matlab using function <tt>read_cgsd</tt> by specifying the name of the simulation cn and bnd files (without their extension). For instance, files <tt>0_percent_strain_x500.cn</tt> and <tt>0_percent_strain_x500.bnd</tt> can be loaded with:

	<pre>		<pre>
Line 10:		Line 11:
	filename = '0_percent_strain_x500';		filename = '0_percent_strain_x500';
	[cn,bnds,vol] = read_cgsd(filename);		[cn,bnds,vol] = read_cgsd(filename);
			</pre>

			By default, a cross-link is represented by a cross-link bond of zero length between two beads. To simplify the structure and reduce the computation time, one can merge the cross-linked beads into a single bead by using the <tt>merge_cross_links</tt> function:
	cn(:,end+1) = [1:size(cn,1)]';

			<pre>
	% Merge cross-linked nodes		% Merge cross-linked nodes
	[cn,bnds] = merge_cross_links(cn,bnds);		[cn,bnds] = merge_cross_links(cn,bnds);
	</pre>		</pre>

			The physical length of each bond can be calculated using function <tt>all_segments_length</tt>:

	<pre>		<pre>
	% Calculate bonds physical lengths		% Calculate bonds physical lengths
	~~bnds(:,end+1)~~ = all_segments_length(cn,bnds,vol);		bonds_length = all_segments_length(cn,bnds,vol);
			</pre>

			Since we are interseted in calculated the shortest path from a bead to its periodic image, we need to replicate our structure by periodicity. For instance, if we wish to calculate the shortest path between a bead and its replica along the y-direction, we can use function <tt>replicate_volume</tt> as follows:

			<pre>
	ndir = 2; % replicate in the y-direction		ndir = 2; % replicate in the y-direction
	[cn1,bnds1,vol1] = replicate_volume(cn,bnds,vol,ndir);		[cn1,bnds1,vol1] = replicate_volume(cn,bnds,vol,ndir);
			</pre>

			where beads position array <tt>cn1</tt> will contain both the position of the beads in the primary volume <tt>vol</tt> in <tt>cn1(1:size(cn,1),:)</tt> and their replica in the y-direction in <tt>cn1(size(cn,1)+1:end,:)</tt> such that <tt>size(cn1,1) = 2*size(cn,1)</tt>.


			<pre>
		⚫	bonds_weight = bnds1(:,4); %use chain length as bond weight

			% or
⚫	~~bond_weight~~ = bnds1(:,4); %use chain length as bond weight
⚫	~~bond_weight~~ = bnds1(:,end); %use physical distance as bond weight

		⚫	bonds_weight = bnds1(:,end); %use physical distance as bond weight
	plot_structure(cn1,bnds1,vol1,'r');
	</pre>		</pre>

Line 45:		Line 60:
	conn1 = generate_connectivity(size(cn1,1),bnds1);		conn1 = generate_connectivity(size(cn1,1),bnds1);

	A1 = adjacency(cn1,bnds1,~~bond_weight~~);		A1 = adjacency(cn1,bnds1,bonds_weight);
	[~,comp1] = find_components(conn1);		[~,comp1] = find_components(conn1);

Nbertin: /* Shortest paths calculation in periodic CGSD simulation */

2016-10-17T20:29:51Z

Shortest paths calculation in periodic CGSD simulation

@@ Line 39: / Line 39: @@
 <pre>
 n = size(cn,1);
 </pre>

Nbertin: Created page with "= Shortest paths calculation in periodic CGSD simulation = == Introduction == This example shows how to compute the shortest path between a bead in a CGSD simulation and its ..."

2016-10-16T23:14:15Z

Created page with "= Shortest paths calculation in periodic CGSD simulation = == Introduction == This example shows how to compute the shortest path between a bead in a CGSD simulation and its ..."

New page

= Shortest paths calculation in periodic CGSD simulation =

== Introduction ==
This example shows how to compute the shortest path between a bead in a CGSD simulation and its periodic image using the NetworCh library. The scripts and data files corresponding to this tutorial can be found in directory <tt><NetworChDir>/tests/shortest_path_pbc/</tt>.

== Loading and replicating the structure ==

<pre>
% Load CGSD structure
filename = '0_percent_strain_x500';
[cn,bnds,vol] = read_cgsd(filename);

cn(:,end+1) = [1:size(cn,1)]';

% Merge cross-linked nodes
[cn,bnds] = merge_cross_links(cn,bnds);
</pre>

<pre>
% Calculate bonds physical lengths
bnds(:,end+1) = all_segments_length(cn,bnds,vol);

ndir = 2; % replicate in the y-direction
[cn1,bnds1,vol1] = replicate_volume(cn,bnds,vol,ndir);

bond_weight = bnds1(:,4); %use chain length as bond weight
bond_weight = bnds1(:,end); %use physical distance as bond weight

plot_structure(cn1,bnds1,vol1,'r');
</pre>

== Computing the shortest path between a bead and its periodic replica ==

== Computing the periodic image shortest path distribution ==

<pre>
n = size(cn,1);
</pre>

== Final script ==