View source for From DDLab to ParaDiS

To simplify the discussion, let us use <tt>$ParaDiS</tt> to represent the directory where you ParaDiS code is installed.  For example, on my computer, <tt>$ParaDiS</tt> is <tt>~/Codes/ParaDiS</tt>.

I have the following subdirectory within <tt>$ParaDiS</tt> that holds my DDLab files.

 $ParaDiS/Matlab/dd3d

In this test case, I will illustrate how to convert DDLab control parameters and dislocation structures into <tt>.cn</tt> and <tt>.data</tt> files that can be recognized by ParaDiS.  It assumes that the DDLab is installed in a subdirectory of ParaDiS as described above.

In Matlab, first go to your DDLab directory.  Then set up the initial structure for a binary junction by 

 cd Inputs; input_binary_junction; cd ..

You can run this test case in Matlab by simply typing

 dd3d

which will show the formation of a junction (after the 200 simulation steps as specified by the input file).

[[image:ddlab_junction.jpg|thumb|Junction formation in DDLab simulation]]

Suppose we now want to run the same simulation in ParaDiS.  We need to re-run the input file and then ask Matlab to write the data into ParaDiS format.  This can be done by the following command.

 cd Inputs; input_binary_junction; cd ..
 write_paradis_input

The computer will print out the following information.

 ParaDiS input file ../../Runs/matlab_input.cn created.
 ParaDiS node data file ../../Runs/matlab_input.data created.

The two files are created in the <tt>../../Runs</tt> directory, which is specified by the matlab variable <tt>paradis_input_dir</tt>.  This variable is specified in the <tt>input_binary_junction.m</tt> file.

In your Unix (or cygwin) terminal, go to the <tt>$ParaDiS</tt> directory.  Suppose you have compiled the source code and have the <tt>dd3d</tt> executable [http://micro.stanford.edu/wiki/M01_How_to_Obtain_and_Run_ParaDiS see here].  You can run the input files created by <tt>DDLab</tt> using the following command.

 ./dd3d Runs/matlab_input.cn

You should see the formation of junction in the X-window of ParaDiS.

You are certainly able to modify (or rename) the input files created by DDLab before running ParaDiS.  The <tt>.cn</tt> file and the <tt>.data</tt> file must have the same name.



[[image:paradis_junction.gif|thumb|Junction formation in ParaDiS simulation]]