Micro and Nano Mechanics Group - User contributions [en]

Cross-slip in ParaDiS

2010-11-10T18:24:36Z

Saubry: New page

=Explanation of BCC and FCC Cross-slip currently implemented in ParaDiS=

==Sylvie Aubry==
===Wednesday November 10 2010===

Thexe explanations are from Tom Arsenlis at LLNL who wrote the CrossSlipBCC.c routine.

Cross slip is treated as a topological operation because it modifies the connectivity data.

It does not introduce new nodes and change any topology, but it can potentially change the glide plane information in the connections.

This may affect mobility depending on the mobility used and ruin an implicit time integration step so it is done in between time steps.

The cross slip routine considers the cross slip of discretization nodes that are close to screw.

Closeness to screw is determined by a critical angle, and this value is currently 1 degree. Both of the segments connected to the node being considered must be within this critical angle as well as the virtual line connecting the its two neighbor segments.

If the segments connected to a node are considered close to screw then the node is considered for a possible cross slip operation.

A test is conducted to determine which glide direction of the screw in its three glide planes sees the greatest projection of force.

If the greatest projection is a glide plane different than the current glide plane a cross slip event is attempted. Currently there is no threshold or any preference to remain on the primary plane.

I say attempted because we may not be able to execute the event depending on the current geometry of three nodes in question.

We must consider several possibilities:

a) both segments are on same plane (classic case)

b) the segments are on two different planes with one plane being the intended cross slip plane (we call this a zipper)

c) the segments are on two different planes with neither plane being the cross slip plane. (most general case)

Along with these situations there are also other things that cross slip operation must take into account

1) The processor must own the segments whose data will be modified

2) The processor must own the nodes whose positions may be modified

3) The positions of the neighboring node may have to be modified slightly so that line up with the intersection of two glide planes

All of these checks are performed and if they all pass then the following operations are performed:

For case a) either one or both neighboring nodes are moved into perfect screw alignment, the segments are flipped to the cross slip plane and the cross slip node is slightly moved into the cross slip plane and a small areal nucleus is created

For case b) the node on the primary plane is moved into screw alignment with the cross slipping node, the segment is flipped into the cross slip plane and the node is moved into the cross slip plane

For case c) both neighboring nodes are moved into screw alignment with the cross slipping node and then the rest is the same as in case a.

Now recently we have modified the code to invesgate whether the cross slip event survives so a new force calculation is conducted to see if the cross slip nucleus continues to move outward into the cross slip plane or whether it tends to move back and cause a cross slip flicker. If a flicker is detected then the cross slip event is never inititated. I don’t believe that you have this version of the cross slip function.

ParaDiS Manuals

2010-11-10T18:19:14Z

Saubry:

<UL>

<LI> [[Overview of ParaDiS 2.2]]

<LI> [[Before You Start: Known Bugs in ParaDiS]]

<LI> [[M01 How to Obtain and Run ParaDiS]]

<LI> [[M02 Straight dislocations]]

<LI> [[M03 Frank-Read Source]]

<LI> [[M04 Binary Junction]]

<LI> [[Create Straight Dislocations for ParaDiS Input]]

<LI> [[Programming tips for ParaDiS]]

<LI> [[ParaDiS FAQs]]

<LI> [[ Cross-slip in ParaDiS]]

</UL>

ParaDiS Manuals

2010-11-10T18:18:56Z

Saubry:

ParaDiS Aniso Code Manuals

2010-01-28T19:38:16Z

Saubry: /* Anisotropic code in ParaDiS */

Anisotropic Elasticity
Sylvie Aubry Jan 28 2010.

The aniso module is similar to DDLab/aniso. For more information refer
to Jie Yin, David Barnett and Wei Cai's paper titled "Computing forces
on dislocation segments in anisotopic elasticity".

The aniso module contains only the files that are modified from the
source code. Mainly, the aniso structure has to be defined, the
Seg-Seg forces and the Self-Force for anisotropic elasticity are
computed.

Several flags are available:

D_ANISOTROPIC : turns on or off anisotropic elasticity.

You have the option of computing the Q, S, B matrices with or
without tables. If you want to use tables, then you have to turn on
the _USE_QSB_TABLES flag. Tables files have to be present in the
inputs directory. To create the tables, turn on the
_CREATE_QSB_TABLES flag (along with the _USE_QSB_TABLES flag). Tables
will be automatically created in the right directory. You can also
specify the name of the table files in the input file. The syntax is
as follows:

TableQ character Define the name of the file to read in tables.
Defaults is inputs/Qtable.dat

TableS character Define the name of the file to read in tables.
Defaults is inputs/Stable.dat
TableB character Define the name of the file to read in tables.
Defaults is inputs/Btable.dat

Two methods have been implemented for anisotropic elasticity. The
second one is by Steve Fitzgerald at Culham Centre for Fusion Energy
+44 (0)1235 466350. Turn on _ANISO_Steve to run his method.

A test case isalso included in the aniso module, it is called
aniso_fr_src.*. Forces from the Matlab code are also added for
comparison. The file is compare_aniso_matlab.txt.

Also several tests files are in the aniso module. They verify several
components of the implementation.

ParaDiS Aniso Code Manuals

2009-12-11T18:50:34Z

Saubry: /* Flow chart of the aniso code */

=Anisotropic code in ParaDiS=
==Sylvie Aubry==
====December 11 2009====

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
define C, eps
define mu and nu. User can choose between the Voigt or the Reuss averages.
calls the routine that defines Q, S, B. Uses file QSBMatrices.c
user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
defines the tables files.

'''NodeForce.c'''

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.

This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:48:37Z

Saubry: /* Aniso code in ParaDiS */

=Anisotropic code in ParaDiS=
==Sylvie Aubry==
====December 11 2009====

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
Also defines the tables files.

NodeForce.c

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:48:24Z

Saubry: /* =December 11 2009 */

=Aniso code in ParaDiS=
==Sylvie Aubry==
====December 11 2009====

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
Also defines the tables files.

NodeForce.c

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:48:10Z

Saubry: /* Sylvie Aubry Dec 11 2009 */

=Aniso code in ParaDiS=
==Sylvie Aubry==
====December 11 2009===

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
Also defines the tables files.

NodeForce.c

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:47:41Z

Saubry: /* DDAniso */

=Aniso code in ParaDiS=
==Sylvie Aubry Dec 11 2009==

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
Also defines the tables files.

NodeForce.c

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:47:25Z

Saubry: /* Flow chart of the aniso code */

=DDAniso=
===Sylvie Aubry (11/14/08) - Updated 12/11/09===

This code is being developed in collaboration with Steve Fitzgerald at
Culham Science Centre, Abingdon, UK.

=Aniso code in ParaDiS=
==Sylvie Aubry Dec 11 2009==

===How to use the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

===Flow chart of the aniso code===
'''ANI_Main'''

defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

'''ANI_Init'''

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

'''Param.c and Param.h'''

defines variables specific to aniso code: C12, C44, Cpr.
Also defines the tables files.

NodeForce.c

When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

'''LocalSegForces.c'''
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

'''Stress.c'''

ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:42:42Z

Saubry: /* Files in the aniso code */

=DDAniso=
===Sylvie Aubry (11/14/08) - Updated 12/11/09===

This code is being developed in collaboration with Steve Fitzgerald at
Culham Science Centre, Abingdon, UK.

=Aniso code in ParaDiS=
==Sylvie Aubry Dec 11 2009==

===Flow chart of the aniso code===

Before starting using the aniso code, the user decides if he/she wants to use the tables or not and if he/she wants to use the Voigt or the Reuss averages for mu and nu.

To use the tables, turn on DEFS += D_TABLES in the makefile.
To create the table files, set QSBMETHOD = 1 in tabulate.c.
To read the table, make sure they are located in the inputs directory.

To set the mu and nu variables, set #define VOIGT and #define REUSS variables in ANI_Util.c

ANI_Main
defines the directory where files Qtable.dat, Stable.dat and Rtable.dat will be created or read.
define the aniso0 structure
calls ANI_Init in ANI_Utils.

ANI_Init

initialize the aniso0 structure.
. define C, eps

. define mu and nu. User can choose between the Voigt or the Reuss averages.

. calls the routine that defines Q, S, B. Uses file QSBMatrices.c

. user can choose to read in tables (QSBMETHOD = 1) in tabulate.c or not.

Param.c & Param.h
. defines variables specific to aniso code: C12, C44, Cpr

NodeForce.c
When the ANISOTROPIC flag is on, use anisotropic SelfForce.
The SeflForce routine calls QSBMatrices.c routines to get the QSB matrices.

LocalSegForces.c
When the ANISOTROPIC flag is on, use anisotropic SegSegForces.
This routine calls ComputeANIForces located in Stress.c.

Stress.c
ComputeANIForces.c calls the ANI_WillisSteeds function also located in Stress.c.
ANI_WillisSteeds decide whether to use the regular definition or the collinear one.

That's it!

ParaDiS Aniso Code Manuals

2009-12-11T18:15:14Z

Saubry: /* Sylvie Aubry (11/14/08) - Updated 12/11/09 */

=DDAniso=
===Sylvie Aubry (11/14/08) - Updated 12/11/09===

This code is being developed in collaboration with Steve Fitzgerald at
Culham Science Centre, Abingdon, UK.

= Files in the aniso code =

The aniso code is a part of ParaDiSv2.2.

ANI_Main.c is a copy of Main.c. On top of regular ParaDiS routines, it includes calls to specific anisotropic routines such as

ANI_Util.c
This file contains ANI_Init, where specific anisotropic variables are defined such as C12, C44, C[i,j,k,l], Q, S, B.

tabulate.c
This file either create Q S B tables or read from files called Qtable.dat, Stable.dat and Btable.dat. To create the tables files, turn the variable
QSBMETHOD by setting it to 1, to read from existing tables files, set the variable to 0.

NodeForce.c which is called in ParadisStep.c. It implements the anisotropic version of the self-force.

Other files modifying the current ParaDiD version are:
LocalSegForces.c
Forces and
<math>\sigma \cdot b </math>
are computed using anisotropic routines and not regular ParaDiS ones.

This file calls ANI_Stress which in turns calls the Willis-Steed stress calculations and also SelfForceSPF, which are specific anisotropic self-forces.

Param.c that contains all variables specific to the anisotropic code.

ParaDiS Aniso Code Manuals

2009-12-11T18:14:54Z

Saubry: /* Sylvie Aubry (11/14/08) */

=DDAniso=
===Sylvie Aubry (11/14/08) - Updated 12/11/09===

This code is being developed in collaboration with Steve Fitzgerald at
Culham Science Centre, Abingdon, UK.

The aniso code is a part of ParaDiSv2.2.

ANI_Main.c is a copy of Main.c. On top of regular ParaDiS routines, it includes calls to specific anisotropic routines such as

ANI_Util.c
This file contains ANI_Init, where specific anisotropic variables are defined such as C12, C44, C[i,j,k,l], Q, S, B.

tabulate.c
This file either create Q S B tables or read from files called Qtable.dat, Stable.dat and Btable.dat. To create the tables files, turn the variable
QSBMETHOD by setting it to 1, to read from existing tables files, set the variable to 0.

NodeForce.c which is called in ParadisStep.c. It implements the anisotropic version of the self-force.

Other files modifying the current ParaDiD version are:
LocalSegForces.c
Forces and
<math>\sigma \cdot b </math>
are computed using anisotropic routines and not regular ParaDiS ones.

This file calls ANI_Stress which in turns calls the Willis-Steed stress calculations and also SelfForceSPF, which are specific anisotropic self-forces.

Param.c that contains all variables specific to the anisotropic code.

ParaDiS Aniso Code Manuals

2009-12-11T18:12:25Z

Saubry: /* Sylvie Aubry (11/14/08) */

=DDAniso=
===Sylvie Aubry (11/14/08)===

This code is being developed in collaboration with Steve Fitzgerald at
Culham Science Centre, Abingdon, UK.

The aniso code is a part of ParaDiSv2.2.

ANI_Main.c is a copy of Main.c. On top of regular ParaDiS routines, it includes calls to specific anisotropic routines such as

ANI_Util.c
This file contains ANI_Init, where specific anisotropic variables are defined such as C12, C44, C[i,j,k,l], Q, S, B.

tabulate.c
This file either create Q S B tables or read from files called Qtable.dat, Stable.dat and Btable.dat. To create the tables files, turn the variable
QSBMETHOD by setting it to 1, to read from existing tables files, set the variable to 0.

NodeForce.c which is called in ParadisStep.c

Forces and
<math>\sigma \cdot b </math>
are computed using anisotropic routines and not regular ParaDiS ones.

This file calls ANI_Stress which in turns calls the Willis-Steed stress calculations and also SelfForceSPF, which are specific anisotropic self-forces.

Other files modifying the current ParaDiD version are:
LocalSegForces.c

SegSelfForce.c

Param.c

Before You Start: Known Bugs in ParaDiS

2009-11-23T18:53:26Z

Saubry: Add a new "bug"

== Bug 1 ==

If you download the standard distribution of ParaDiS <tt>pub-dd3d.v2.0.tar.gz</tt>, you will not be able to compile and run it in SERIAL mode. The fix to this problem is described below.

You need to download these three files (available on [http://paradis.stanford.edu/downloads ParaDiS download site]):

makefile.sys
makefile.setup
ReadConfig.c

This will allow you to use <tt>SYS = i386</tt> or <tt>SYS = cygwin</tt> and <tt>MODE = SERIAL</tt> in <tt>makefile.setup</tt>.

The <tt>SYS = i386</tt> option requires intel compiler <tt>icc</tt>. If you do not have this compiler, you can modify the <tt>makefile.sys</tt> file to use a different compiler.

We are working to enable the <tt>SYS = mac</tt> option. Please come back soon.

If your computer does not allow opening of X-window, then you need to set <tt>enable_window = 0</tt> in your <tt>win.script</tt> file. This is also necessary if you submit your job to a queue in a cluster, because you won't be able to open an interactive window there.

== Bug 2 ==
As the numbers of
cells and numbers of processors are changed, ownership or nodes/segments can
alter which may result in segments changing the cells into which they
are accounted... and hence alter results. So for a small test case, forces may be perfectly correct in serial but slightly off in parallel using cells (option FULL_N2Forces turned off).

On a large simulation the
results should be insignificant, but on small simulations with very few
dislocations, differences are more noticable.