finalcnfile\label{var:finalcnfile}
incnfile\label{var:incnfile}
intercnfile\label{var:intercnfile}

outpropfile\label{var:outpropfile}
perfcnfile\label{var:perfcnfile}
phonondispfile\label{var:phonondispfile}

savecnfreq\label{var:savecnfreq}
savecn\label{var:savecn}
savepropfreq\label{var:savepropfreq}
saveprop\label{var:saveprop}

potfile\label{var:potfile}

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

myname\label{var:myname}

atomcolor\label{var:atomcolor}
atomradius\label{var:atomradius}

autowritegiffreq\label{var:autowritegiffreq}
backgroundcolor\label{var:backgroundcolor}
bondlength\label{var:bondlength}
bondradius\label{var:bondradius}

energycolorbar\label{var:energycolorbar}

fixatomcolor\label{var:fixatomcolor}
fixedatomenergypartition\label{var:fixedatomenergypartition}

hideatomenergy\label{var:hideatomenergy}
hidetopology\label{var:hidetopology}
highlightcolor\label{var:highlightcolor}
highlightenergy\label{var:highlightenergy}

plotfreq\label{var:plotfreq}
plot\_highlight\label{var:plot\_highlight}
plot\_restrict\label{var:plot\_restrict}
plot\_select\label{var:plot\_select}
plot\_xmax\label{var:plot\_xmax}
plot\_xmin\label{var:plot\_xmin}
plot\_ymax\label{var:plot\_ymax}
plot\_ymin\label{var:plot\_ymin}
plot\_zmax\label{var:plot\_zmax}
plot\_zmin\label{var:plot\_zmin}

potavgfreq\label{var:potavgfreq}
rotateangles\label{var:rotateangles}
showavgpot\label{var:showavgpot}

win\_height\label{var:win\_height}
win\_width\label{var:win\_width}
\subsection{Structure Manipulation}

applyshear\label{var:applyshear}
cutpastecnspec\label{var:cutpastecnspec}

hrescale\label{var:hrescale}
latticeconst\label{var:latticeconst}
latticestructure\label{var:latticestructure}
makecnspec\label{var:makecnspec}

mkcutspec\label{var:mkcutspec}
mkdipole\label{var:mkdipole}
mkgbspec\label{var:mkgbspec}
moveatomspec\label{var:moveatomspec}

pickfixedatomspec\label{var:pickfixedatomspec}

removerc\label{var:removerc}
shiftspec\label{var:shiftspec}
shrinkboxspec\label{var:shrinkboxspec}
splicecnspec\label{var:splicecnspec}
strainspec\label{var:strainspec}

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


\subsection{Conjugate Gradient Relaxation}

conj\_dfpred\label{var:conj\_dfpred}
conj\_fevalmax\label{var:conj\_fevalmax}
conj\_fixbox\label{var:conj\_fixbox}
conj\_fixshape\label{var:conj\_fixshape}
conj\_ftol\label{var:conj\_ftol}
conj\_itmax\label{var:conj\_itmax}

stress\label{var:stress}
strrotspec\label{var:strrotspec}

\subsection{External Fortran Calls}

command\label{var:command}
fortranexe\label{var:fortranexe}
fortranpath\label{var:fortranpath}

MDCASKpot\label{var:MDCASKpot}


\subsection{Molecular Dynamics Simulation}

atommass\label{var:atommass}
atomTcpl\label{var:atomTcpl}

calphonondispspec\label{var:calphonondispspec}

equilsteps\label{var:equilsteps}

DOUBLE\_T\label{var:DOUBLE\_T}

scalevelocity\label{var:scalevelocity}
shearrate\label{var:shearrate}

timestep\label{var:timestep}
T\_OBJ\label{var:T\_OBJ}
totalsteps\label{var:totalsteps}
usenosehoover\label{var:usenosehoover}
vt2\label{var:vt2}


