Use Au-Si MEAM Potential in LAMMPS - Revision history

Adrianos: /* Seunghwa's Instructions on How to Use MEAM Au-Si Potential */

2015-09-08T05:09:08Z

Seunghwa's Instructions on How to Use MEAM Au-Si Potential

← Older revision		Revision as of 05:09, 8 September 2015
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	==~~Seunghwa's~~ Instructions on How to Use MEAM Au-Si Potential==		==Instructions on How to Use MEAM Au-Si Potential==

			First download the potential from the following link:
	Adriano: please past the content here.

			https://docs.google.com/open?id=0B1TUP8O860rBVnBITjdIby1mbDQ
	<references/>

			which is this file meamRyu_LAMMPS_overwrite.tar

			Then make a new lammps directory because it overwrites a few
			MEAM Fortran files.

			copy "meamRyu_LAMMPS_overwrite.tar" to LAMMPS/directory

			and unzip the file.

			Them compile meam file with

			make meam-lammps build=R SYS=intel

			For validation, do following test.

			cd runs/meamRyu/ and run the .in file for two different configurations

			for
			testcase 1, -1.88746969e+04 for PotEng from lammps.out file

			for
			testcase 2, -1.93012101e+04 for PotEng from lammps.out file

			If you get those two values, you got the JPCM09 potential correctly.

Yanmingw: /* MD++ test cases */

2015-09-08T02:53:57Z

MD++ test cases

← Older revision		Revision as of 02:53, 8 September 2015
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	===MD++ test cases===		===MD++ test cases===
	Assuming you've got the latest MD++ package (e.g., revision 452 or later) from the '''svn''' server, you can download [[Media:Md++_meam_test_r452.tar \|MD++ test case]] that contains one input '''tcl'''~~scripts~~ and two configuration '''cn''' files, and unzip it under the MD++ home directory using the command		Assuming you've got the latest MD++ package (e.g., revision 452 or later) from the '''svn''' server, you can download [[Media:Md++_meam_test_r452.tar \|MD++ test case]] that contains one input '''tcl''' script and two configuration '''cn''' files, and unzip it under the MD++ home directory using the command
	cd ~/Codes/MD++.svn/		cd ~/Codes/MD++.svn/
	tar -xvf Md++_meam_test_r452.tar		tar -xvf Md++_meam_test_r452.tar

Caiwei: /* MD++ test case */

2015-09-08T02:49:08Z

MD++ test case

← Older revision		Revision as of 02:49, 8 September 2015
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	Supposing you've known how to run MD++ code from [http://micro.stanford.edu/wiki/MD%2B%2B_Manuals our manuals] and downloaded the MD++ package from our SVN server, you can do the following test case.		Supposing you've known how to run MD++ code from [http://micro.stanford.edu/wiki/MD%2B%2B_Manuals our manuals] and downloaded the MD++ package from our SVN server, you can do the following test case.

	~~Downlaod~~ [[media:md++_meam_testcase.tar.gz \|md++_meam_testcase.tar.gz]], which contains a input '''tcl''' script, three configuration '''cn''' files and a help text file.		Download [[media:md++_meam_testcase.tar.gz \|md++_meam_testcase.tar.gz]], which contains a input '''tcl''' script, three configuration '''cn''' files and a help text file.

	Unzip this '''gz''' file under the certain folder using the command		Unzip this '''gz''' file under the certain folder using the command
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	make meam-lammps build=R SYS=mc2		make meam-lammps build=R SYS=mc2

	Run the simulation within the MD++ home folder. ~~for~~ example,		Run the simulation within the MD++ home folder. For example,

	bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase1		bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase1

	This will read the atoms' configuration from AuSiTestCase1.cn, visualize the atoms and calculate the potential and forces of the system. Meanwhile, it provides one '''.lammps''' file for '''LAMMPS''' and one '''.cfg''' file for '''Atomeye'''. The potential energy in this case should be ~~-18874.6969309944. You can compare this value with the number from LAMMPS later.~~		This will read the atoms' configuration from AuSiTestCase1.cn, visualize the atoms and calculate the potential and forces of the system. Meanwhile, it provides one '''.lammps''' file for '''LAMMPS''' and one '''.cfg''' file for '''Atomeye'''. The potential energy in this case should be

			EPOT = -18874.6969309944

			You can compare this value with the number from LAMMPS later.

			Run the second test case,

			bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2

			You should get this potential energy

			EPOT=-19301.21011320015

			You can compare this value with the number from LAMMPS later.

	===LAMMPS test case===		===LAMMPS test case===

Caiwei: /* Test case:Comparsion with MD++ */

2015-09-08T01:46:42Z

Test case:Comparsion with MD++

← Older revision		Revision as of 01:46, 8 September 2015
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	When the simulation is finished, in the same folder, you can check the potential information in the '''lammps.out''' file and the forces information in the '''dump.md'''file. Specifically, if you read the configuration from '''AuSiTestCase1.lammpsdata''', you would expect the potential and forces results are exactly the same as those come from MD++ simulation, like the potential should be -1.88746969e+04.		When the simulation is finished, in the same folder, you can check the potential information in the '''lammps.out''' file and the forces information in the '''dump.md'''file. Specifically, if you read the configuration from '''AuSiTestCase1.lammpsdata''', you would expect the potential and forces results are exactly the same as those come from MD++ simulation, like the potential should be -1.88746969e+04.


			==Seunghwa's Instructions on How to Use MEAM Au-Si Potential==

			Adriano: please past the content here.

	<references/>		<references/>

Yanmingw: /* Test cases */

2014-07-24T06:29:52Z

Test cases

← Older revision		Revision as of 06:29, 24 July 2014
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	bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2		bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2

	The two runs will create two folders named as '''AuSiTestCase1''' and '''AuSiTestCase2''' in the '''Codes/MD++.svn/runs'''folder. In inside each folder, you can find one '''energy.txt''' file that stores the total potential energy value and one '''force.txt''' file that lists the forces act on each atom. You can download this Matlab code [[Media:Matlab_meam_check.tar \|Energy and force check]] to test if your results are correct. When you unzip the tar file, you will have a folder named '''TEST''' that contains one Matlab script '''data_compare.m''' and several standard test case results for comparison. You need to put your'''force.txt''' and '''force.txt''' in the same folder, then the Matlab code will tell you if you pass the tests.		The two runs will create two folders named as '''AuSiTestCase1''' and '''AuSiTestCase2''' in the '''Codes/MD++.svn/runs'''folder. In inside each folder, you can find one '''energy.txt''' file that stores the total potential energy value and one '''force.txt''' file that lists the forces act on each atom. You can download this Matlab code [[Media:Matlab_meam_check.tar \|Energy and force check]] to test if your results are correct. When you unzip the tar file, you will have a folder named '''TEST''' that contains one Matlab script '''data_compare.m''' and several standard test case results for comparison. You need to put your '''force.txt''' and '''force.txt''' in the same folder, then the Matlab code will tell you if you pass the tests.

	===LAMMPS test cases===		===LAMMPS test cases===

	~~You~~ can ~~download~~ [[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]] and ~~unzip~~ it within the LAMMPS home folder.		Assuming you've followed the previous instruction and compiled the LAMMPS executable successfully, you can start the test cases by downloading [[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]] and unzipping it within the LAMMPS home folder.
	cd ~/Codes/LAMMPS.svn/		cd ~/Codes/LAMMPS.svn/
	tar -xvf Lammps_meam_test_r24.tar		tar -xvf Lammps_meam_test_r24.tar

			For mc2 test cases, you need to enter the folder created for each test case and submit your simulation request via a '''PBS''' script by typing
	[[Media:Matlab_meam_check.tar \|Energy and force check]]

			Test case 1:
			cd ~/Codes/LAMMPS.svn/runs/AuSiTestCase1/
			qsub golammps.pbs

			Test case 2:
			cd ~/Codes/LAMMPS.svn/runs/AuSiTestCase2/
			qsub golammps.pbs

			If you prefer to work on WCR, you can avoid touching the '''PBS''' scripts. Instead you can type

			Test case 1:
			cd ~/Codes/LAMMPS.svn/runs/AuSiTestCase1/
			../../src/lmp_wcr -in in.md

			Test case 2:
			cd ~/Codes/LAMMPS.svn/runs/AuSiTestCase2/
			../../src/lmp_wcr -in in.md

			When the simulation is finished, in the same folder, it will create a '''log.md''' file contains potential energy value and a '''dump.md''' file contains force information. To check these results with the provided Matlab code, you need to copy these two files into the '''TEST''' folder generated by unzipping [[Media:Matlab_meam_check.tar \|Energy and force check]]. The Matlab code will tell you if you pass the tests via the messages displayed on screen.

	==Test case:Comparsion with MD++ ==		==Test case:Comparsion with MD++ ==

Yanmingw: /* LAMMPS test cases= */

2014-07-24T06:10:24Z

LAMMPS test cases=

← Older revision		Revision as of 06:10, 24 July 2014
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	The two runs will create two folders named as '''AuSiTestCase1''' and '''AuSiTestCase2''' in the '''Codes/MD++.svn/runs'''folder. In inside each folder, you can find one '''energy.txt''' file that stores the total potential energy value and one '''force.txt''' file that lists the forces act on each atom. You can download this Matlab code [[Media:Matlab_meam_check.tar \|Energy and force check]] to test if your results are correct. When you unzip the tar file, you will have a folder named '''TEST''' that contains one Matlab script '''data_compare.m''' and several standard test case results for comparison. You need to put your'''force.txt''' and '''force.txt''' in the same folder, then the Matlab code will tell you if you pass the tests.		The two runs will create two folders named as '''AuSiTestCase1''' and '''AuSiTestCase2''' in the '''Codes/MD++.svn/runs'''folder. In inside each folder, you can find one '''energy.txt''' file that stores the total potential energy value and one '''force.txt''' file that lists the forces act on each atom. You can download this Matlab code [[Media:Matlab_meam_check.tar \|Energy and force check]] to test if your results are correct. When you unzip the tar file, you will have a folder named '''TEST''' that contains one Matlab script '''data_compare.m''' and several standard test case results for comparison. You need to put your'''force.txt''' and '''force.txt''' in the same folder, then the Matlab code will tell you if you pass the tests.

	==LAMMPS test cases===		===LAMMPS test cases===

	[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]		You can download [[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]] and unzip it within the LAMMPS home folder.
			cd ~/Codes/LAMMPS.svn/
			tar -xvf Lammps_meam_test_r24.tar

	[[Media:Matlab_meam_check.tar \|Energy and force check]]		[[Media:Matlab_meam_check.tar \|Energy and force check]]

Yanmingw: /* MD++ test cases */

2014-07-24T06:06:17Z

MD++ test cases

← Older revision		Revision as of 06:06, 24 July 2014
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	Run the below command within the MD++ home folder to start the test cases.		Run the below command within the MD++ home folder to start the test cases.

	Test case 1:		Test case 1:
	bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase1		bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase1
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	bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2		bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2

			The two runs will create two folders named as '''AuSiTestCase1''' and '''AuSiTestCase2''' in the '''Codes/MD++.svn/runs'''folder. In inside each folder, you can find one '''energy.txt''' file that stores the total potential energy value and one '''force.txt''' file that lists the forces act on each atom. You can download this Matlab code [[Media:Matlab_meam_check.tar \|Energy and force check]] to test if your results are correct. When you unzip the tar file, you will have a folder named '''TEST''' that contains one Matlab script '''data_compare.m''' and several standard test case results for comparison. You need to put your'''force.txt''' and '''force.txt''' in the same folder, then the Matlab code will tell you if you pass the tests.

			==LAMMPS test cases===

	[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]		[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]

Yanmingw: /* Test cases */

2014-07-24T05:53:50Z

Test cases

← Older revision		Revision as of 05:53, 24 July 2014
Line 65:		Line 65:

	==Test cases==		==Test cases==

			===MD++ test cases===
			Assuming you've got the latest MD++ package (e.g., revision 452 or later) from the '''svn''' server, you can download [[Media:Md++_meam_test_r452.tar \|MD++ test case]] that contains one input '''tcl'''scripts and two configuration '''cn''' files, and unzip it under the MD++ home directory using the command
			cd ~/Codes/MD++.svn/
		⚫	tar -xvf Md++_meam_test_r452.tar

			The compilation of MEAM on cluster (for example mc2) can be done with the following command,
			make meam-lammps build=R SYS=mc2

			Run the below command within the MD++ home folder to start the test cases.
			Test case 1:
			bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase1
			Test case 2:
			bin/meam-lammps_mc2 scripts/work/si_au/si_au_compare.tcl AuSiTestCase2


⚫	~~[[Media:~~Md++_meam_test_r452.tar ~~\|MD++ test case]]~~

	[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]		[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]

Yanmingw: /* Test cases */

2014-07-24T05:42:55Z

Test cases

← Older revision		Revision as of 05:42, 24 July 2014
Line 65:		Line 65:

	==Test cases==		==Test cases==


	[[Media:Md++_meam_test_r452.tar \|MD++ test case]]		[[Media:Md++_meam_test_r452.tar \|MD++ test case]]
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	[[Media:Matlab_meam_check.tar \|Energy and force check]]		[[Media:Matlab_meam_check.tar \|Energy and force check]]



	==Test case:Comparsion with MD++ ==		==Test case:Comparsion with MD++ ==

Yanmingw at 05:42, 24 July 2014

2014-07-24T05:42:39Z

← Older revision		Revision as of 05:42, 24 July 2014
Line 66:		Line 66:
	==Test cases==		==Test cases==

			[[Media:Md++_meam_test_r452.tar \|MD++ test case]]

			[[Media:Lammps_meam_test_r24.tar \|LAMMPS test case]]

			[[Media:Matlab_meam_check.tar \|Energy and force check]]