Comprehensive Nuclear Materials MD Case Studies - Revision history

Yanmingw: /* Zero Temperature Properties */

2011-06-29T06:56:57Z

Zero Temperature Properties

← Older revision		Revision as of 06:56, 29 June 2011
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	cd ${MDPP}		cd ${MDPP}
	bin/fs_gpp scripts/work/cnm_chap/ta_perfect_crystal.tcl 0		bin/fs_gpp scripts/work/cnm_chap/ta_perfect_crystal.tcl 1

	The data are saved in the files <tt>C11_C12.dat</tt>, <tt>C44.dat</tt> in the <tt>${MDPP}/runs/ta-perf</tt> folder. To analyze the result, use the following commands.		The data are saved in the files <tt>C11_C12.dat</tt>, <tt>C44.dat</tt> in the <tt>${MDPP}/runs/ta-perf</tt> folder. To analyze the result, use the following commands.

Caiwei: /* Mobility at Finite Temperature */

2011-03-14T14:43:05Z

Mobility at Finite Temperature

← Older revision		Revision as of 14:43, 14 March 2011
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	bin/fs_gpp scripts/work/cnm_chap/ta_edge_dislocation.tcl 2		bin/fs_gpp scripts/work/cnm_chap/ta_edge_dislocation.tcl 2

	This takes about 40 ~~minutes~~ to finish. After this, we are ready to simulate dislocation motion at finite stress, using the following command, e.g.,		This takes about 2 hours to finish. After this, we are ready to simulate dislocation motion at finite stress, using the following command, e.g.,

	cd ${MDPP}		cd ${MDPP}

Caiwei at 07:12, 14 March 2011

2011-03-14T07:12:10Z

← Older revision		Revision as of 07:12, 14 March 2011
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	</DIV>		</DIV>

	This tutorial describes how to reproduce the case studies on crystals and dislocations described in ''Comprehensive Nuclear Materials'', Chapter 128 Molecular Dynamics. We provide the MD++ script files and describe how to use them in detail.		This tutorial describes how to reproduce the case studies on crystals and dislocations described in ''Comprehensive Nuclear Materials'', [[media:cnm_chap128_draft.pdf \| Chapter 128 Molecular Dynamics]]. We provide the MD++ script files and describe how to use them in detail.

	<HR>		<HR>

Caiwei at 06:54, 14 March 2011

2011-03-14T06:54:06Z

← Older revision		Revision as of 06:54, 14 March 2011
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	bin/fs_gpp scripts/work/cnm_chap/ta_edge_dislocation.tcl 2		bin/fs_gpp scripts/work/cnm_chap/ta_edge_dislocation.tcl 2

		⚫	This takes about 40 minutes to finish. After this, we are ready to simulate dislocation motion at finite stress, using the following command, e.g.,
	This takes about ?? minutes to complete.

⚫	After this, we are ready to simulate dislocation motion at finite stress, using the following command, e.g.,

	cd ${MDPP}		cd ${MDPP}
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	find_disl_vel		find_disl_vel

	Modify the <tt>filepath</tt> line to analyze data from MD simulation under different stresses.		Modify the <tt>filepath</tt> line to analyze data from MD simulation under different stresses. This reproduces Fig.9 of the chapter.

Caiwei at 06:48, 14 March 2011

2011-03-14T06:48:46Z

← Older revision		Revision as of 06:48, 14 March 2011
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	This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.		This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.

	Here is a [[~~image~~:md++.pbs.mc2.ta-edge.txt \| PBS script]] for submitting MD simulations jobs under different stresses to a parallel cluster (<tt>mc2.stanford.edu</tt>).		Here is a [[media:md++.pbs.mc2.ta-edge.txt \| PBS script]] for submitting MD simulations jobs under different stresses to a parallel cluster (<tt>mc2.stanford.edu</tt>).

	The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[media:Find_disl_vel.m.txt \| find_disl_vel.m]] file in Octave or Matlab. Use the following commands.		The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[media:Find_disl_vel.m.txt \| find_disl_vel.m]] file in Octave or Matlab. Use the following commands.

Caiwei at 06:46, 14 March 2011

2011-03-14T06:46:53Z

← Older revision		Revision as of 06:46, 14 March 2011
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	This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.		This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.

			Here is a [[image:md++.pbs.mc2.ta-edge.txt \| PBS script]] for submitting MD simulations jobs under different stresses to a parallel cluster (<tt>mc2.stanford.edu</tt>).
⚫	The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[media:Find_disl_vel.m.txt \| find_disl_vel.m]] file (in Octave or Matlab~~) from the <tt>${MDPP}/Tools/matlab</tt> folder~~. Use the following commands.

		⚫	The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[media:Find_disl_vel.m.txt \| find_disl_vel.m]] file in Octave or Matlab. Use the following commands.
⚫	cd ${MDPP}/~~Tools~~/~~matlab~~

		⚫	cd ${MDPP}/runs/ta-edge-0
	wget http://micro.stanford.edu/mediawiki/images/d/d6/Find_disl_vel.m.txt -O find_disl_vel.m		wget http://micro.stanford.edu/mediawiki/images/d/d6/Find_disl_vel.m.txt -O find_disl_vel.m
	octave		octave
	filepath = '../../runs/ta-edge-100';		filepath = '../../runs/ta-edge-100';
	find_disl_vel		find_disl_vel

			Modify the <tt>filepath</tt> line to analyze data from MD simulation under different stresses.

Caiwei at 06:37, 14 March 2011

2011-03-14T06:37:55Z

← Older revision		Revision as of 06:37, 14 March 2011
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	This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.		This set the shear stress to be <math>\sigma_{xy} = 100</math> MPa. The simulation data are stored in the <tt>${MDPP}/runs/ta-edge-100</tt> folder. The <tt>auto####.cfg</tt> files are the simulation snapshots that can be visualized by Atomeye. The <tt>inter####.cn</tt> files are the restart files containing all atomic positions and velocities.

	The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[~~image~~:Find_disl_vel.m.txt]] ~~<tt>~~find_disl_vel.m~~</tt>~~ file (in Octave or Matlab) in the <tt>${MDPP}/Tools/matlab</tt> folder. Use the following commands.		The dislocation core position as a function of time and the average dislocation velocity can be obtained by running the [[media:Find_disl_vel.m.txt \| find_disl_vel.m]] file (in Octave or Matlab) from the <tt>${MDPP}/Tools/matlab</tt> folder. Use the following commands.

	cd ${MDPP}/Tools/matlab		cd ${MDPP}/Tools/matlab

Caiwei at 06:31, 14 March 2011

2011-03-14T06:31:03Z

← Older revision		Revision as of 06:31, 14 March 2011
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	cd ${MDPP}/Tools/matlab		cd ${MDPP}/Tools/matlab
			wget http://micro.stanford.edu/mediawiki/images/d/d6/Find_disl_vel.m.txt -O find_disl_vel.m
	wget ???
	octave		octave
	filepath = '../../runs/ta-edge-100';		filepath = '../../runs/ta-edge-100';

Caiwei at 06:28, 14 March 2011

2011-03-14T06:28:33Z

@@ Line 150: / Line 150: @@
  bin/fs_gpp scripts/work/cnm_chap/ta_edge_dislocation.tcl 1
-The dislocation core atoms will be displayed in an X-window as the crystal is relaxed under increasing amount of shear stresses.  The potential energies of the relaxed structures are saved in the <tt>EPOT.dat</tt> file.  When the Peierls stress is exceeded, the dislocation moves over large distances during the relaxation and the potential energy decreases abruptly.  The relaxation also takes a much longer time to terminate compared with the case when the applied stress is below the Peierls stress.  All these can be used as indications for having reached the Peierls stress.   Dislocation motion can also be directly observed in the X-window.  The Peierls stress predicted by this simulation is 28 MPa.  The atomic configurations of relaxed structures at different applied stresses can be examined using Atomeye by the following commands, e.g.,
+The dislocation core atoms will be displayed in an X-window as the crystal is relaxed under increasing amount of shear stresses.  The potential energies of the relaxed structures are saved in the <tt>EPOT.dat</tt> file.  When the Peierls stress is exceeded, the dislocation moves over large distances during the relaxation and the potential energy decreases abruptly.  The relaxation also takes a much longer time to terminate compared with the case when the applied stress is below the Peierls stress.  All these can be used as indications for having reached the Peierls stress.   Dislocation motion can also be directly observed in the X-window.   The atomic configurations of relaxed structures at different applied stresses can be examined using Atomeye by the following commands, e.g.,
  cd ${MDPP}/runs/ta-edge-0
@@ Line 156: / Line 156: @@
 This plots the relaxed configuration under <math>\sigma_{xy} = 20</math> MPa.
 ===Mobility at Finite Temperature===

Caiwei at 05:50, 14 March 2011

2011-03-14T05:50:41Z

@@ Line 26: / Line 26: @@
 Both files contain a comment section in the beginning that describes in detail the various options to reproduce various steps of the case studies.  In this tutorial, we describe how to run these scripts and what kind of results you should expect.
 ==Compile executable file==
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 ==Perfect Crystal==
 ===Zero Temperature Properties===
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 Octave should plot the stress as a function of strain and print out the fitted value of the elastic constants: <math>C_{11} = 266.00</math> GPa, <math>C_{12} = 161.20</math> GPa, <math>C_{44} = 82.41</math> GPa.  (This reproduces Fig.6 of the chapter.)
 ===Finite Temperature Properties===
@@ Line 113: / Line 107: @@
 Figure 1 plots instantaneous temperature (in K) as a function of time (in ps) and figure 2 plots the instantaneous pressure (in GPa) as a function of time (reproducing Fig.7a of the chapter).
 To perform a series of MD simulations in the NVT ensemble and adjust the box sizes iteratively to relax the stress (Fig.7b of the chapter),  run the following command.
@@ Line 137: / Line 129: @@
 ===Peierls Stress at Zero Temperature===
 ===Mobility at Finite Temperature===