PARADISCYL:Test-Run

Manual 02 for ParaDiS Cylinder Codes

How to run test simulations

This document describes the extension of the ParaDiS program that implements the cylindrical free surface boundary condition. This extension is based on Weinberger and Cai, J. Mech. Phys. Solids, 55, 2027 (2007)(PDF). The code is written by Chris Weinberger and Wei Cai and is not included in the standard distribution of ParaDiS. Keonwook Kang wrote the first draft of this document, which was later revised by Chris Weinberger and Wei Cai. Questions on this document should be addressed to Chris Weinberger. Please read the manual of ParaDiS before reading this document.

Run a Test Case

The command line to run the ParaDiS Cylinder code is the same as that of the original ParaDiS code. See ParaDiS manual for details. The command line format is:

paradiscyl [-r <numCycles>] [-d dataFile] <controlFile>

where:

	<ctrlFile>		Specifies the name of the ParaDiS control parameter file
	-d <dataFile>		Specifies the base name of the file(s) containing the nodal data for the run. If this file name is not supplied, the code looks for a data file named the same as the control file with the file name suffix (if any) replaced with ".data"
	-r  <numCycles>		Causes the code to execute a series of <numCycles> cycles during which no force calculations or dislocation movement will occur. These cycles will be used strictly for load-balancing purposes and will be done before the normal cycles. This can be useful when a simulation is started with a uniform domain decomposition and needs time to converge on an optimal decomposition as would occur when restarting a simulation on a different number of cpus

Run the following control file, which simulates a dislocation loop inside a cylinder. You will need two input files: one is control file (concentric_loop_test.ctrl) and the other is data file (concentric_loop_test.data). Both files are shown below. See here for details about input files.

$ bin/paradiscyl runs/concentric_loop_test.ctrl

This run requires the following two input files.

concentric_loop_test.ctrl concentric_loop_test.data

If your run is successful, you should see a pop-up window as shown below.

• 

  Fig.1 ParaDiS Cylinder Codes Test Run. A dislocation loop in a cylinder

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X Window Control

Default X Window control parameters are given in the file inputs/paradis.xdefaults. You can change window size, line width, rotation of angles, etc by modifying this file.

The 3D View in the X Window can be manipulated by both mouse and keyboard. For example, press r (default) and then move mouse to rotate the object, press s and then move mouse to scale the object. A complete list of hot keys are given below.

YWindow: yview:
Mouse drag to rotate
Hot Keys:
F1        : display this message
Up        : rotate up
Down      : rotate down
Left      : rotate left
Right     : rotate right
PgUp      : rotate counterclockwise
PgDn      : rotate clockwise
Home      : back to initial viewpoint
Space     : stop rotate
p         : toggle pause
t         : translation
s         : scaling
d         : move projection infinity point
r         : rotation
f         : toggle pbc enableness
m         : toggle drawframe
g         : pbc glide
x         : pbc shift in x
y         : pbc shift in y
z         : pbc shift in z
w         : print window specification
F9        : output gif
F10       : output postscript

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Tcl script to generate input data

The input data file concentric_loop_test.data is generated by the tcl script create_loop_data.tcl in the ParaDiS/tools directory, which can run by typing

$ tools/create_loop_data.tcl

You can easily modify this tcl script to change the resulting input dislocation structure, such as the radius of the dislocation loop.

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Problems and solutions

Cannot open shared library libgsl

Sometimes the code may compile successfully but throws the following error message when you try to run it.

./bin/paradiscyl: error while loading shared libraries: libgsl.so.0: cannot open
shared object file: No such file or directory

This means you need to specify the path to the GSL libraries, which are dynamically linked to the executable. For example, if your GSL library files are located in /usr/local/lib, then you can add the following line in your ~/.bash_profile file

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/

and then type

source ~/.bash_profile

Error in opening input file

When ParaDiS can not locate input files, it shows the following error message.

Fatal: ReadControlFile: Error 2 opening file XXXX

Check whether you gave the correct path for your input file.

Underflow error

In the old version of Cylinder code, you may get an underflow error message. This can be avoided by downloading the latest version or by inserting the following line into cylinder/gridstress.c

gsl_set_error_handler_off();

You also need to include the following header file at the beginning of gridstress.c.

#include <gsl/gsl_errno.h>

Notes