finalcnfile
incnfile
intercnfile

outpropfile
perfcnfile
phonondispfile

savecnfreq
savecn
savepropfreq
saveprop

potfile

writeall
writevelocity
\subsection{X-window Display}
\label{xwin}

myname

atomcolor
atomradius

autowritegiffreq
backgroundcolor
bondlength
bondradius

energycolorbar

fixatomcolor
fixedatomenergypartition

hideatomenergy
hidetopology
highlightcolor
highlightenergy

plotfreq
plot\_highlight
plot\_restrict
plot\_select
plot\_xmax
plot\_xmin
plot\_ymax
plot\_ymin
plot\_zmax
plot\_zmin

potavgfreq
rotateangles
showavgpot

win\_height
win\_width
\subsection{Structure Manipulation}

applyshear
cutpastecnspec

hrescale
latticeconst
latticestructure
makecnspec

mkcutspec
mkdipole
mkgbspec
moveatomspec

pickfixedatomspec

removerc
shiftspec
shrinkboxspec
splicecnspec
strainspec

\subsection{Creating Dislocation Dipole}
\label{mkdipole}


\subsection{Conjugate Gradient Relaxation}

conj\_dfpred
conj\_fevalmax
conj\_fixbox
conj\_fixshape
conj\_ftol
conj\_itmax

stress
strrotspec

\subsection{External Fortran Calls}

command
fortranexe
fortranpath

MDCASKpot


\subsection{Molecular Dynamics Simulation}

atommass
atomTcpl

calphonondispspec

equilsteps

DOUBLE\_T

scalevelocity
shearrate

timestep
T\_OBJ
totalsteps
usenosehoover
vt2


