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

I have the following subdirectory within $ParaDiS 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 .cn and .data 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).

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 ../../Runs directory, which is specified by the matlab variable paradis_input_dir. This variable is specified in the input_binary_junction.m file.

In your Unix (or cygwin) terminal, go to the $ParaDiS directory. Suppose you have compiled the source code and have the dd3d executable. You can run the input files created by DDLab using the following command.

./dd3d Runs/matlab_input.cn

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