From DDLab to ParaDiS - Revision history

Caiwei at 21:54, 19 December 2007

2007-12-19T21:54:50Z

← Older revision		Revision as of 21:54, 19 December 2007
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	which will show the formation of a junction (after the 200 simulation steps as specified by the input file).		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.		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.
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	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.		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:ddlab_junction.~~jpb~~\|thumb\|Junction formation in DDLab simulation]]

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

Caiwei: added pictures

2007-12-19T21:54:13Z

added pictures

← Older revision		Revision as of 21:54, 19 December 2007
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	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.		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:ddlab_junction.jpb\|thumb\|Junction formation in DDLab simulation]]

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

Caiwei at 21:51, 19 December 2007

2007-12-19T21:51:13Z

← Older revision		Revision as of 21:51, 19 December 2007
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	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.		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.~~jpg~~\|thumb\|~~200px~~]]		[[image:paradis_junction.gif\|thumb\|Junction formation in ParaDiS simulation]]

Caiwei at 21:50, 19 December 2007

2007-12-19T21:50:19Z

← Older revision		Revision as of 21:50, 19 December 2007
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	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.		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.jpg\|thumb\|200px]]

Caiwei at 21:47, 19 December 2007

2007-12-19T21:47:40Z

← Older revision		Revision as of 21:47, 19 December 2007
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	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.		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>$ParaDiS</tt> directory. Suppose you have compiled the source code and have the <tt>dd3d</tt> executable [M01_How_to_Obtain_and_Run_ParaDiS see here]. You can run the input files created by <tt>DDLab</tt> using the following command.		In your Unix (or cygwin) terminal, go to the <tt>$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		./dd3d Runs/matlab_input.cn

Caiwei at 21:42, 19 December 2007

2007-12-19T21:42:24Z

← Older revision		Revision as of 21:42, 19 December 2007
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	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.		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>$ParaDiS</tt> directory. Suppose you have compiled the source code and have the <tt>dd3d</tt> executable. You can run the input files created by <tt>DDLab</tt> using the following command.		In your Unix (or cygwin) terminal, go to the <tt>$ParaDiS</tt> directory. Suppose you have compiled the source code and have the <tt>dd3d</tt> executable [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		./dd3d Runs/matlab_input.cn

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

Caiwei: initial input

2007-12-19T21:36:22Z

initial input

New page

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).

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. 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.