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

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

sleepseconds\label\label{com:sleepseconds\label}{var:sleepseconds}

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

setnolog\label{com:setnolog}
setoverwrite\label{com:setoverwrite}

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

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

makecn\label{com:makecn}

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

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

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

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

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

potfile\label\label{com:potfile\label}{var:potfile}

writeall\label\label{com:writeall\label}{var:writeall}
writevelocity\label\label{com:writevelocity\label}{var:writevelocity}

openintercnfile\label{com:openintercnfile}
openpropfile\label{com:openpropfile}
readcn\label{com:readcn}
readMDCASK\label{com:readMDCASK}
readPOSCAR\label{com:readPOSCAR}
redefinepbc\label{com:redefinepbc}
writecn\label{com:writecn}
writeintercn\label{com:writeintercn}
writeMDCASK\label{com:writeMDCASK}
writePOSCAR\label{com:writePOSCAR}

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

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

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

energycolorbar\label\label{com:energycolorbar\label}{var:energycolorbar}

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

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

plotfreq\label\label{com:plotfreq\label}{var:plotfreq}
plot\_highlight\label\label{com:plot\_highlight\label}{var:plot_highlight}
plot\_restrict\label\label{com:plot\_restrict\label}{var:plot_restrict}
plot\_select\label\label{com:plot\_select\label}{var:plot_select}
plot\_xmax\label\label{com:plot\_xmax\label}{var:plot_xmax}
plot\_xmin\label\label{com:plot\_xmin\label}{var:plot_xmin}
plot\_ymax\label\label{com:plot\_ymax\label}{var:plot_ymax}
plot\_ymin\label\label{com:plot\_ymin\label}{var:plot_ymin}
plot\_zmax\label\label{com:plot\_zmax\label}{var:plot_zmax}
plot\_zmin\label\label{com:plot\_zmin\label}{var:plot_zmin}

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

win\_height\label\label{com:win\_height\label}{var:win_height}
win\_width\label\label{com:win\_width\label}{var:win_width}


alloccolors\label{com:alloccolors}
alloccolorsX\label{com:alloccolorsX}
openwin\label{com:openwin}
plot\label{com:plot}
reversergb\label{com:reversergb}
rotate\label{com:rotate}
saverot\label{com:saverot}
testcolor\label{com:testcolor}
wintogglepause\label{com:wintogglepause}

\subsection{Structure Manipulation}

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

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

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

pickfixedatomspec\label\label{com:pickfixedatomspec\label}{var:pickfixedatomspec}

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

mkdipole\label\label{com:mkdipole\label}{var:mkdipole}

applystrain\label{com:applystrain}
cutpastecn\label{com:cutpastecn}
cutslice\label{com:cutslice}
extendbox\label{com:extendbox}
makecut\label{com:makecut}
makedipole\label{com:makedipole}
makegb\label{com:makegb}
moveatom\label{com:moveatom}
pickfixedatoms\label{com:pickfixedatoms}
removeextraatoms\label{com:removeextraatoms}
removepickedatoms\label{com:removepickedatoms}
replacenonfixatom\label{com:replacenonfixatom}
restoreH\label{com:restoreH}
scaleH\label{com:scaleH}
shiftbox\label{com:shiftbox}
shiftpbc\label{com:shiftpbc}
splicecn\label{com:splicecn}

\subsection{Conjugate Gradient Relaxation}

conj\_dfpred\label\label{com:conj\_dfpred\label}{var:conj_dfpred}
conj\_fevalmax\label\label{com:conj\_fevalmax\label}{var:conj_fevalmax}
conj\_fixbox\label\label{com:conj\_fixbox\label}{var:conj_fixbox}
conj\_fixshape\label\label{com:conj\_fixshape\label}{var:conj_fixshape}
conj\_ftol\label\label{com:conj\_ftol\label}{var:conj_ftol}
conj\_itmax\label\label{com:conj\_itmax\label}{var:conj_itmax}

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

eval\label{com:eval}
multieval\label{com:multieval}
relax\label{com:relax}

\subsection{External Fortran Calls}

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

MDCASKpot\label\label{com:MDCASKpot\label}{var:MDCASKpot}

fortranrelax\label{com:fortranrelax}
runcommand\label{com:runcommand}

\subsection{Molecular Dynamics Simulation}

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

calphonondispspec\label\label{com:calphonondispspec\label}{var:calphonondispspec}

equilsteps\label\label{com:equilsteps\label}{var:equilsteps}

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

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

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

calphonondisp\label{com:calphonondisp}
initvelocity\label{com:initvelocity}
run\label{com:run}
step\label{com:step}


\subsection{Parallel Execution}

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

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


