
\subsection{Log and Control}
\label{log}

%%extra variables
dirname\label{var:dirname} 

sleepseconds\label{var:sleepseconds}

%%extra commands
setoverwrite\label{com:setoverwrite}
setnolog\label{com:setnolog}
quit\label{com:quit}
sleep\label{com:sleep}

setnolog
setoverwrite

\subsection{Make Perfect Lattice}
\label{makecn}

allocmultiple\label{var:allocmultiple}
basisatoms\label{var:basisatoms} 

makecn

\subsection{File I/O}
\label{fileio}

%cat allvar2.tex | sed -e 's/\(^[^ \][a-zA-Z\_0-9]*\)/\1\\label\{var:\1}/'

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}

openintercnfile
openpropfile
readcn
readMDCASK
readPOSCAR
redefinepbc
writecn
writeintercn
writeMDCASK
writePOSCAR

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

atomcolor\label{var:atomcolor}
bondcolor\label{var:bondcolor}
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}


alloccolors
alloccolorsX
openwin
plot
reversergb
rotate
saverot
testcolor
wintogglepause

\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}
extendboxspec\label{var:extendboxspec}

mkdipole\label{var:mkdipole}

applystrain
cutpastecn
cutslice
extendbox
makecut
makedipole
makegb
moveatom
pickfixedatoms
removeextraatoms
removepickedatoms
replacenonfixatom
restoreH
scaleH
shiftbox
shiftpbc
splicecn

\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}

eval
multieval
relax

\subsection{External Fortran Calls}

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

MDCASKpot\label{var:MDCASKpot}

fortranrelax
runcommand

\subsection{Molecular Dynamics Simulation}

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

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}

calphonondisp
initvelocity
run
step


\subsection{Parallel Execution}

ncpu\label{var:ncpu}
shmsize\label{var:shmsize}

spawn\label{com:spawn}
collect\label{com:collect}
shmallocate\label{com:shmallocate}


