ParaDiS Manual Updated - Revision history

Jieyin: /* How to set up data-file */

2011-01-13T02:16:10Z

How to set up data-file

← Older revision		Revision as of 02:16, 13 January 2011
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	</pre>		</pre>

	You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from Matlab if there exists too many nodes in your simulation box.		You need to set your own data file parameters, usually including minCoordinates, maxCoordinates, nodeCount, domainDecomposition and nodalData. The nodalData is a long array of data. You may want to create it from '''Matlab''' if there exists too many nodes in your simulation box.

	===How to set up ctrl-file===		===How to set up ctrl-file===

Jieyin at 02:15, 13 January 2011

2011-01-13T02:15:50Z

← Older revision		Revision as of 02:15, 13 January 2011
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	By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.		By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.

	===How to create input files with Matlab===

	==How to record properties==		==How to record properties==

Jieyin: /* How to set up ctrl-file */

2011-01-13T02:14:18Z

How to set up ctrl-file

← Older revision		Revision as of 02:14, 13 January 2011
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	</pre>		</pre>

	Lines relevant to saving properties and visulization are discussed in later part of this manual.		By setting <tt>savencn = 1</tt>, saving is enabled at a frequency of <tt>savecnfreq</tt>. Lines relevant to saving properties and visulization are discussed in later part of this manual.

	===How to create input files with Matlab===		===How to create input files with Matlab===

Jieyin: /* How to set up ctrl-file */

2011-01-13T02:12:54Z

How to set up ctrl-file

← Older revision		Revision as of 02:12, 13 January 2011
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	The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)		The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)

			The setting for mobility law is important, which should be consistent with the system you simulate. Cross-slip is enabled only when <tt>enableCrossSlip = 1</tt>. You need to adjust some of the geometric parameters to fit your problem.

	3 Third is the loading conditions		3 Third is the loading conditions
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	loadType = 1		loadType = 1
	edotdir = [ 0.0 0.0 1.0 ]		edotdir = [ 0.0 0.0 1.0 ]
	eRate = ~~100000~~.0		eRate = 100.0
	</pre>		</pre>

			<tt>loadType</tt> defines the type of load on the system. Usually we set it as 0 (creep, i.e. constant external stress) or 1 (constant strain rate). For detailed explanations for value 2, 3 and 4, please refer to the variable table. When <tt>loadType = 0</tt>, you need to set <tt>appliedStress</tt>(zero vector for relaxation). When <tt>loadType = 1</tt>, you need to define strain rate direction <tt>edotdir</tt> and strain rate <tt>eRate</tt>.

	4 And the last part is settings on saving,		4 And the last part is settings on saving,
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	saveprop = 1		saveprop = 1
	savepropfreq = 1		savepropfreq = 1
	#winDefaultsFile = "inputs/paradis.~~xdefaults2~~"		#winDefaultsFile = "inputs/paradis.xdefaults"
	</pre>		</pre>

			Lines relevant to saving properties and visulization are discussed in later part of this manual.
	Some visualization options

	===How to create input files with Matlab===		===How to create input files with Matlab===

Jieyin: /* How to set up ctrl-file */

2011-01-13T02:00:34Z

How to set up ctrl-file

← Older revision		Revision as of 02:00, 13 January 2011
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	elasticinteraction = 1		elasticinteraction = 1
	</pre>		</pre>

			Variable <tt>xBoundType</tt> defines the type of problem space boundaries in the X dimension. Valid values are 0, 1 and 2 respectively for periodic, free surface, and reflecting.

			The value of <tt>burgMag</tt> is the unit of length for all length variables in ParaDiS simulation, such as nodal positions and Burgers vectors (in data file, those data should be expressed in terms of the same <tt>burgMag</tt>)


	3 Third is the loading conditions		3 Third is the loading conditions

Jieyin: /* How to set up ctrl-file */

2011-01-13T01:56:29Z

How to set up ctrl-file

← Older revision		Revision as of 01:56, 13 January 2011
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	yBoundType = 0		yBoundType = 0
	zBoundType = 0		zBoundType = 0


	#Fundamental length unit		#Fundamental length unit
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	#Core cut-off radius		#Core cut-off radius
	rc = 2.886751		rc = 2.886751


	#Core energy		#Core energy
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	#Turn on elastic interaction		#Turn on elastic interaction
	elasticinteraction = 1		elasticinteraction = 1

	</pre>		</pre>

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	edotdir = [ 0.0 0.0 1.0 ]		edotdir = [ 0.0 0.0 1.0 ]
	eRate = 100000.0		eRate = 100000.0

	</pre>		</pre>

Jieyin: /* How to set up ctrl-file */

2011-01-13T01:55:51Z

How to set up ctrl-file

← Older revision		Revision as of 01:55, 13 January 2011
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	===How to set up ctrl-file===		===How to set up ctrl-file===

			The structure of the ctrl file is explained by parts.

			1 First is the basic setup information for the simulation,

			<pre>
			#Directory to write output files
			dirname = "outputs/filename"

			#Input files for PBC image stresses
			Rijmfile = "inputs/Rijm.cube.out"
			RijmPBCfile = "inputs/RijmPBC.cube.out"

			#Total simulation steps
			maxstep = 100

			#The total number of CPUs should be numXdoms * numYdoms * numZdoms
			numXdoms = 1
			numYdoms = 1
			numZdoms = 1

			#Cells for dislocation grouping (cannot be less than 3)
			numXcells = 3
			numYcells = 3
			numZcells = 3

			#Fast multipole method specs.
			fmEnabled = 0 #disable fast multipole
			fmMPOrder = 2
			fmTaylorOrder = 4
			fmCorrectionTbl = "Inputs/fm-ctab.m2.t4.dat"
			</pre>

			You can set the directory name where you want to store the output. You can also set the total number of simulation steps <tt>maxstep</tt>. As for numXdoms, numYdoms and numZdoms, note that the product should be the total number of CPUs. This setting is crucial for parallel jobs. When all of them as set as 2, the total number of CUPs is 8. This should be consistant with the pbs file setting, which will be discussed in the end of this manual. If you want to enable fast multipole method (FMM), you need to set <tt>fmEnabled = 1</tt> and assign the path for the corresponding table.

			2 Next is some settings on geometry, material parameters etc

			<pre>

			timestepIntegrator = "trapezoid"

			#Boundary conditions
			xBoundType = 0
			yBoundType = 0
			zBoundType = 0


			#Fundamental length unit
			burgMag = 2.556120e-010

			#Elastic constants
			shearModulus = 40000000000.000000
			pois = 0.369000

			#Mobility law function
			mobilityLaw = "FCC_0"
			enforceGlidePlanes = 1
			enableCrossSlip = -1
			MobScrew = 1.000000e+005
			MobEdge = 1.000000e+005
			MobClimb = 1.000000e-002

			#Discretization
			maxSeg = 200.000000
			minSeg = 10.000000

			#Maximum nodal displacement at each time step
			rmax = 100

			#Error tolerance in determining time step
			rTol = 0.721688

			#Maximum time step
			maxDT = 1

			#Core cut-off radius
			rc = 2.886751


			#Core energy
			Ecore = 0.000000e+000

			#Turn on elastic interaction
			elasticinteraction = 1

			</pre>

			3 Third is the loading conditions

			<pre>
			#Applied stress in Pa (xx,yy,zz,yz,zx,xy)
			appliedStress = [ 0 0 0 0 0 0 ]

			#Constant Strain rate
			loadType = 1
			edotdir = [ 0.0 0.0 1.0 ]
			eRate = 100000.0

			</pre>

			4 And the last part is settings on saving,

			<pre>
			#Save files
			savecn = 1
			savecnfreq = 100

			#Save Properties
			saveprop = 1
			savepropfreq = 1
			#winDefaultsFile = "inputs/paradis.xdefaults2"
			</pre>

			Some visualization options

	===How to create input files with Matlab===		===How to create input files with Matlab===

Jieyin at 01:42, 13 January 2011

2011-01-13T01:42:12Z

← Older revision		Revision as of 01:42, 13 January 2011
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	~~Under construction~~ by Jie Yin		Written by Jie Yin

	Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. ~~This guide includes following how-tos:~~		Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips.

	While reading this document, don't forget to check out paradis.stanford.edu for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.		While reading this document, don't forget to check out [[paradis.stanford.edu]] for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.

	==How to obtain the latest ParaDiS codes==		==How to obtain the latest ParaDiS codes==

Jieyin: /* How to obtain the latest ParaDiS codes */

2011-01-13T01:40:47Z

How to obtain the latest ParaDiS codes

← Older revision		Revision as of 01:40, 13 January 2011
Line 2:		Line 2:

	Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:		Here is a practical guide to ParaDiS corresponding to the latest version. It is especially useful for beginners with latest command templates and programming tips. This guide includes following how-tos:

			While reading this document, don't forget to check out paradis.stanford.edu for a complete and searchable table of parameters in ParaDiS code (some parameter names are not up-to-date). Detailed descriptions can be found in the official documentation ParaDiSInfo.txt.

	==How to obtain the latest ParaDiS codes==		==How to obtain the latest ParaDiS codes==

Jieyin: /* How to set up data-file */

2011-01-13T01:38:19Z

How to set up data-file

← Older revision		Revision as of 01:38, 13 January 2011
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	nodalData =		nodalData =
	0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7		0,0 3.52197261266669e+003 -2.10366848600532e+003 8.35974608889734e+002 2 7
	0,1 -0.707107 0.707107 0		0,1 -0.707107 0.707107 0 1 1 1
	1 1 1		0,15 0.707107 -0.707107 0 -0.408248 -0.408248 0.816497
			...
	0,15 0.707107 -0.707107 0
	-0.408248 -0.408248 0.816497
	</pre>		</pre>