PARADISCYL:How-To-Install

Manual 01 for ParaDiS Cylinder Codes

How to install

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. It is owned by Chris 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. Please read the manual of ParaDiS before reading this document.

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Prerequisite

For serial mode, GNU scientific libraries (libgsl and libgslcblas) and DFT library (libfftw3) are sufficient to run ParaDiS in general linux PC. You will additionally need intel compilers to compile with icc instead of gcc. You can download free evaluation verion of intel compilers from Intel Software Network Site.

libgsl and libgslcblas

GNU Scientific library can be downloaded at http://www.gnu.org/software/gsl/. Install gsl library by the following procedures.

# mv ./gsl-1.9.tar.gz /usr/local/src/
# cd /usr/local/src
# tar -zxvf gsl-1.9.tar.gz
# cd gsl-1.9
# ./configure
# make
# make install

The libraries will be installed at /usr/local/lib/.

libfftw3

C subroutine library for computing the discrete Fourier transform (DFT). Download from FFTW home page. To install the library, run the following commands.

# mv ./fftw-3.1.2.tar.gz /usr/local/src/
# cd /usr/local/src
# tar -zxvf fftw-3.1.2.tar.gz
# cd fftw-3.1.2
# ./configure
# make 
# make install

libfftw3.a and libfftw3.la will be installed at /usr/local/lib/.

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Download

Download the latest ParaDiS codes from micro repository site using subversion checkout command.

 $ mkdir ParaDiS
 $ svn co https://micro.stanford.edu/svn/ParaDiS ./ParaDiS

Note that this version of ParaDiS has branched out from the public ParaDiS codes v.2.2 downloadable from the official site. You see there are extra subdirectories such as aniso, cylinder, halfspace, matlab, thinfilm and fem in this version of ParaDiS codes. Each subdirectory contains additional source codes for its own purpose. For example, source codes in cylinder directory enable to run ParaDiS simulation of dislocations inside cylindrical geometry taking account of the image stress and Yoffe stress.

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MAKE

Move into cylinder subdirectory.

$ cd ParaDiS/cylinder

There is a make description file, makefile, at the top of which, it includes ../makefile.sys and ../makefile.setup from the upper directory.

makefile.sys defines system-dependent compilers and compiling options for different systems such as linux, aix, etc. The pre-defined system types and their descriptions are listed in the head of makefile.sys file.

In makefile.setup file, you can select various 'make' settings and switches, some of which are explained below.

SYS

select system type. ex. SYS = linux

MODE

set serial or parallel mode. ex. MODE = SERIAL

XLIB_MODE

enable or disable xwindow plotting capability. ex. XLIB_MODE = ON

OPT

define optimization level. ex. OPT = -O3

In makefile, there is important macro DEFS. The cylinder codes behave differently depending on how DEFS is defined.

DEFS += -D_CYL

Needs to be included for cylinder codes.

DEFS += -D_NOBEMSTRESS

No boundary image stress will be considered.

DEFS += -D_NOYOFFESTRESS

No Yoffe stress will be considered.

DEFS += -D_NULLCYLSTRESS

Ignore all image stress. (BEM, Yoffe, Virtual seg.(??))

DEFS += -D_NOVIRTUALSEG

No force contribution from virtual segments.(??)

DEFS += -D_CYLMETHOD1

If defined, grid stress is used for image stress calculation. If not, Green stress is used.

DEFS += -D_WRITENODEFORCE

Will write nodal force data in force.out file. Each line of the file contains nodal position x, y, z and nodal force f_x, f_y and f_z.

DEFS += -D_PRINTCYLSTRESS

Will write nodal force in force.out and stress in stress.out files. Each line of stress.out contains grid position r, θ, z and stress components σ₁₁, σ₂₂, σ₃₃, σ₂₃, σ₃₁, σ₁₂. (??)

Depending on your need, you can selectively define DEFS macro.

You can make the executible file, paradiscyl by simply typing

$ make

and you will see paradiscyl in the directory ../bin/.

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Notes