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\documentclass[12pt, fullpage]{article}
\usepackage{graphicx}
\usepackage{colortbl}
\usepackage{longtable}
\usepackage{color}
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\author{Wei Cai}
\title{MD++ Reference Manual}
\date{\today}
\begin{document}
\maketitle
\section{Class organizer {\normalsize \rm (
4 commands and
2 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt quit} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  quit

Quit MD++.  Print total CPU time.
\FL\end{minipage}
\\ \hline
\colortwo {\tt setnolog} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  setnolog

This command tells MD++ not to open the A.log file in the directory
specified by {\tt dirname}.  Instead, the output is directed to the screen.
%
Use this command before assigning variable {\tt dirname}.
\FL\end{minipage}
\\ \hline
\colorone {\tt setoverwrite} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  setoverwrite

By default, MD++ will abort if the directory specified by
{\tt dirname} already exists, to avoid overwriting previous
simulation data.  Use this command before assigning {\tt dirname} if
you want to remove this protection and allow overwriting the data in
the existing directory.
\FL\end{minipage}
\\ \hline
\colortwo {\tt sleep} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  sleep

Put MD++ to sleep for the number of seconds specified in {\tt sleepseconds}.
\FL\end{minipage}
\\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt dirname} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ variable
%  dirname

Type: string.
%
Default: none.
%
MD++ immediately opens a directory specified by this variable and
enters (i.e. {\tt cd} into) this directory.  This becomes the working
directory for all future operations and the place for all output
files.
%
Output to screen is redirected to the A.log file in this directory
if {\tt setnolog} is not set beforehand.
\FL\end{minipage}
\\ \hline
\colortwo {\tt sleepseconds} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ variable
%  sleepsconds

Type: integer.
%
Default: 600.
%
Number of seconds used by command {\tt sleep}.  
\FL\end{minipage}
\\ \hline
\end{longtable}
\section{Class md {\normalsize \rm (
124 commands and
177 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt addtorque} & {no description file} \\ \hline
\colortwo {\tt allocchain} & {no description file} \\ \hline
\colorone {\tt alloccolors} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  alloccolors

Allocate colors for the X-window display.
%
Use after {\tt openwin} and before {\tt plot}.
%
Variables {\tt atomcolor}, {\tt backgroundcolor}, {\tt bondcolor},
{\tt color00}, $\cdots$, {\tt color10} may be set before calling
this command.
\FL\end{minipage}
\\ \hline
\colortwo {\tt alloccolorsX} & {no description file} \\ \hline
\colorone {\tt annealpath} & {no description file} \\ \hline
\colortwo {\tt applystrain} & {no description file} \\ \hline
\colorone {\tt atomeye} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  atomeye

Call Atomeye to visualize atomic structure.
%
Atomeye is an external visualization tool developed by Dr. Ju Li.
%http://164.107.79.177/Archive/Graphics/A/
%
Requires variables {\tt atomeyepath} and {\tt atomeyeexe} to be set
before calling this command.
%
MD++ saves the atomic configuration into file atomeye.cfg
in the current directory before calling Atomeye.
\FL\end{minipage}
\\ \hline
\colortwo {\tt calcentralsymmetry} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  calcentralsymmetry

Computes central symmetry deviation (CSD) parameter for each
atom and store them in {\tt TOPOL} array.
%
Requires {\tt NCS}  to be set
(number of nearest neighbors in CSD calculation).
%
Also see {\tt GnuPlotHistogram}.
\FL\end{minipage}
\\ \hline
\colorone {\tt calHessian} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  calHessian

Compute Hessian matrix by numerical differentiation.
%
The step size in ($\AA$) for numerical differentiation
is specified by {\tt timestep}.
%
Result saved in {\tt hessian.out} in the current directory.
%
If {\tt input[0]=0}, then the entire Hessian matrix is computed.
%
If {\tt input[0]$\neq$0}, then {\tt input[0]=n} specifies the number
of atoms whose corresponding (3) columns in the Hessian matrix will
be computed.  The atom indices are specified in {\tt input[1]},
$\cdots$, {\tt input[n]}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt calmisfit} & {no description file} \\ \hline
\colorone {\tt calphonondisp} & {no description file} \\ \hline
\colortwo {\tt changeH\_keepR} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  changeH_keepR

Requires {\tt input = [ i j $\alpha$ ]} to be set beforehand.
%
Change the supercell $\textbf{H}$ while keeping the real
coordinates of the atoms $\textbf{r}^{i}$ constant.  The scaled
coordinates $\textbf{s}^{i}$ change because
$\textbf{r}^{i}=\textbf{H}\cdot\textbf{s}^{i}$.
%
The matrix $\textbf{H}$ consists of three column vectors
$[\textbf{c}_1|\textbf{c}_2|\textbf{c}_3]$, and will be changed by
$\textbf{c}_i = \textbf{c}_i + \alpha\, \textbf{c}_j$.
%
Same as {\tt redefinepbc}.
\FL\end{minipage}
\\ \hline
\colorone {\tt changeH\_keepS} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  changeH_keepS

Same as {\tt changeH\_keepR} except that the scaled
coordinates of the atoms $\textbf{s}^{i}$ remain constant.
The real coordinates $\textbf{r}^{i}$ change because
$\textbf{r}^{i}=\textbf{H}\cdot\textbf{s}^{i}$.
%
Same as {\tt shiftbox}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt constrainedrelax} & {no description file} \\ \hline
\colorone {\tt convertCNtoCFG} & {no description file} \\ \hline
\colortwo {\tt convertXDATCAR} & {no description file} \\ \hline
\colorone {\tt cutpastecn} & {no description file} \\ \hline
\colortwo {\tt cutpath} & {no description file} \\ \hline
\colorone {\tt cutslice} & {no description file} \\ \hline
\colortwo {\tt eval} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  eval

Call the potential function and compute total potential
energy, force, kinetic energy, temperature and Virial stress
for the current configuration.  The total potential energy
and stress are printed to the screen or to the A.log file
(depending on whether or not {\tt setnolog} is set).
\FL\end{minipage}
\\ \hline
\colorone {\tt extendbox} & {no description file} \\ \hline
\colortwo {\tt findcore} & {no description file} \\ \hline
\colorone {\tt fixallatoms} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  fixallatoms

Mark all atoms with {\tt fixed[i] = 1}, $i=0,\cdots,{\tt NP}-1$.
\FL\end{minipage}
\\ \hline
\colortwo {\tt fixatoms\_by\_ID} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  fixatoms_by_ID

Requires {\tt input = [ n $i_1 \cdots i_n$ ]} beforehand.
%
Mark all atoms $i = i_1, \cdots, i_n$ with {\tt fixed[i] = 1}.
\FL\end{minipage}
\\ \hline
\colorone {\tt fixatoms\_by\_pos\_topol} & {no description file} \\ \hline
\colortwo {\tt fixatoms\_by\_position} & {no description file} \\ \hline
\colorone {\tt fortranrelax} & {no description file} \\ \hline
\colortwo {\tt freeallatoms} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  freeallatoms

Mark all atoms with {\tt fixed[i] = 0}, $i=0,\cdots,{\tt NP}-1$.
\FL\end{minipage}
\\ \hline
\colorone {\tt GnuPlotHistogram} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  GnuPlotHistogram

Call gnuplot to plot the histogram of atom energy
i.e. {\tt EPOT\_IND}.
%
If {\tt plot\_color\_axis = 2} then the histogram of
{\tt TOPOL} is plotted instead.  {\tt TOPOL} stores the
computes the central symmetry deviation (CSD) parameters
computed by {\tt calcentralsymmetry}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt initRchain} & {no description file} \\ \hline
\colorone {\tt initvelocity} & {no description file} \\ \hline
\colortwo {\tt makecn} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  makecn

Same as {\tt makecrystal}.
\FL\end{minipage}
\\ \hline
\colorone {\tt makecrystal} & {no description file} \\ \hline
\colortwo {\tt makecut} & {no description file} \\ \hline
\colorone {\tt makecylinder} & {no description file} \\ \hline
\colortwo {\tt makedipole} & {no description file} \\ \hline
\colorone {\tt makedislcylinder} & {no description file} \\ \hline
\colortwo {\tt makedislocation} & {no description file} \\ \hline
\colorone {\tt makedisloop} & {no description file} \\ \hline
\colortwo {\tt makegb} & {no description file} \\ \hline
\colorone {\tt makegrainboundary} & {no description file} \\ \hline
\colortwo {\tt maketorquehandle} & {no description file} \\ \hline
\colorone {\tt makewave} & {no description file} \\ \hline
\colortwo {\tt markremovefixedatoms} & {no description file} \\ \hline
\colorone {\tt moveatom} & {no description file} \\ \hline
\colortwo {\tt movefixedatoms} & {no description file} \\ \hline
\colorone {\tt movegroup} & {no description file} \\ \hline
\colortwo {\tt multieval} & {no description file} \\ \hline
\colorone {\tt multiplyvelocity} & {no description file} \\ \hline
\colortwo {\tt nebrelax} & {no description file} \\ \hline
\colorone {\tt openintercnfile} & {no description file} \\ \hline
\colortwo {\tt openpropfile} & {no description file} \\ \hline
\colorone {\tt openwin} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  openwin

Open X-window to display current atom position in 3D.
%
Click and drag in the X-window to rotate.  Press F1 for help.
%
Usually used as \\
{\tt openwin alloccolors rotate saverot eval plot}
\FL\end{minipage}
\\ \hline
\colortwo {\tt pbcshiftatom} & {no description file} \\ \hline
\colorone {\tt plot} & {no description file} \\ \hline
\colortwo {\tt printatoms\_in\_sphere} & {no description file} \\ \hline
\colorone {\tt printnnlist} & {no description file} \\ \hline
\colortwo {\tt randomposition} & {no description file} \\ \hline
\colorone {\tt readcn} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  read_cn

Requires {\tt incnfile = $file$} to be set.  Read atomic
positions, velocities and other information from $file$ to
the current configuration.
\FL\end{minipage}
\\ \hline
\colortwo {\tt readHessian} & {no description file} \\ \hline
\colorone {\tt readLAMMPS} & {no description file} \\ \hline
\colortwo {\tt readMDCASK} & {no description file} \\ \hline
\colorone {\tt readMDCASKJAIME} & {no description file} \\ \hline
\colortwo {\tt readPOSCAR} & {no description file} \\ \hline
\colorone {\tt readRASMOLXYZ} & {no description file} \\ \hline
\colortwo {\tt readRchain} & {no description file} \\ \hline
\colorone {\tt redefinepbc} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  redefinepbc

Same as {\tt changeH\_keepR}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt refreshnnlist} & {no description file} \\ \hline
\colorone {\tt relabelatom} & {no description file} \\ \hline
\colortwo {\tt relax} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  relax

Conjugate gradient relaxation.
%
Variables {\tt conj\_fevalmax}, {\tt conj\_fixbox}, {\tt
conj\_fixboxvec}, {\tt conj\_ftol} should be set before calling
this command.
\FL\end{minipage}
\\ \hline
\colorone {\tt removeellipsoid} & {no description file} \\ \hline
\colortwo {\tt removefixedatoms} & {no description file} \\ \hline
\colorone {\tt removeoverlapatoms} & {no description file} \\ \hline
\colortwo {\tt removerectbox} & {no description file} \\ \hline
\colorone {\tt reorientH} & {no description file} \\ \hline
\colortwo {\tt replacefreeatom} & {no description file} \\ \hline
\colorone {\tt restoreH} & {no description file} \\ \hline
\colortwo {\tt reversefixedatoms} & {no description file} \\ \hline
\colorone {\tt reversergb} & {no description file} \\ \hline
\colortwo {\tt reversespecies} & {no description file} \\ \hline
\colorone {\tt rotate} & {no description file} \\ \hline
\colortwo {\tt run} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  run

Molecular dynamics simulation.
%
Variables {\tt totalsteps}, {\tt integrator\_type}, {\tt saveprop},
{\tt savecn}, etc. should be set before calling this command.
\FL\end{minipage}
\\ \hline
\colorone {\tt runcommand} & {no description file} \\ \hline
\colortwo {\tt runMC} & {no description file} \\ \hline
\colorone {\tt runMCSWITCH} & {no description file} \\ \hline
\colortwo {\tt runTAMC} & {no description file} \\ \hline
\colorone {\tt saveH} & {no description file} \\ \hline
\colortwo {\tt saverot} & {no description file} \\ \hline
\colorone {\tt scaleH} & {no description file} \\ \hline
\colortwo {\tt scaleVel} & {no description file} \\ \hline
\colorone {\tt setconfig1} & {no description file} \\ \hline
\colortwo {\tt setconfig2} & {no description file} \\ \hline
\colorone {\tt setfilecounter} & {no description file} \\ \hline
\colortwo {\tt setfixedatomsgroup} & {no description file} \\ \hline
\colorone {\tt setfixedatomsspecies} & {no description file} \\ \hline
\colortwo {\tt setgroupcomvel} & {no description file} \\ \hline
\colorone {\tt setH} & {no description file} \\ \hline
\colortwo {\tt shiftbox} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  shiftbox

Same as {\tt changeH\_keepS}.
\FL\end{minipage}
\\ \hline
\colorone {\tt splicecn} & {no description file} \\ \hline
\colortwo {\tt srand} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  srand

Randomize random number generator using {\tt randseed},
which must be set before calling this command.  This affects
future calls to {\tt drand48()}.   Notice that
by default MD++ uses {\tt drand48()} (which is not affected
by this command), and only if it is not available from the compiler
does MD++ use {\tt rand()}.
\FL\end{minipage}
\\ \hline
\colorone {\tt srand48} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  srand48

Randomize random number generator using {\tt randseed},
which must be set before calling this command.  This affects
future calls to {\tt drand48()}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt srand48bytime} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  srand48bytime

Randomize random number generator using current CPU time
as the seed.  This affects future calls to {\tt drand48()}.
\FL\end{minipage}
\\ \hline
\colorone {\tt srandbytime} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  srand48bytime

Randomize random number generator using current CPU time
as the seed.  This affects future calls to {\tt rand()}.  Notice that
by default MD++ uses {\tt drand48()} (which is not affected
by this command), and only if it is not available from the compiler
does MD++ use {\tt rand()}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt statedistance} & {no description file} \\ \hline
\colorone {\tt step} & {no description file} \\ \hline
\colortwo {\tt switchconfig} & {no description file} \\ \hline
\colorone {\tt testcolor} & {no description file} \\ \hline
\colortwo {\tt testpotential} & {no description file} \\ \hline
\colorone {\tt wintogglepause} & {no description file} \\ \hline
\colortwo {\tt writeatomeyecfg} & {no description file} \\ \hline
\colorone {\tt writeatomtv} & {no description file} \\ \hline
\colortwo {\tt writecn} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  writecn

Requires {\tt finalcnfile = $file$} to be set before calling
this command.  Write atomic positions of the current configurationto $file$.
%
If {\tt write\_all = 1} is also set,
the atomic velocities and other information are written in $file$ as well.
\FL\end{minipage}
\\ \hline
\colorone {\tt writeENERGY} & {no description file} \\ \hline
\colortwo {\tt writeFORCE} & {no description file} \\ \hline
\colorone {\tt writeintercn} & {no description file} \\ \hline
\colortwo {\tt writeLAMMPS} & {no description file} \\ \hline
\colorone {\tt writeMDCASK} & {no description file} \\ \hline
\colortwo {\tt writeMDCASKXYZ} & {no description file} \\ \hline
\colorone {\tt writePINYMD} & {no description file} \\ \hline
\colortwo {\tt writePOSCAR} & {no description file} \\ \hline
\colorone {\tt writePOSITION} & {no description file} \\ \hline
\colortwo {\tt writepovray} & {no description file} \\ \hline
\colorone {\tt writeRASMOLXYZ} & {no description file} \\ \hline
\colortwo {\tt writeRchain} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt allocmultiple} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ variable
%  allocmultiple

Type: integer.  If {\tt allocmultiple = $n$} is set before {\tt
readcn} or {\tt makecrystal}, then the memory for {\tt NP} $\times\ n$
atoms is allocated, where {\tt NP} is the actual number of atoms.
%
Useful for {\tt extendbox}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt annealspec} & {no description file} \\ \hline
\colorone {\tt applyshear} & {no description file} \\ \hline
\colortwo {\tt atomcolor} & {no description file} \\ \hline
\colorone {\tt atomeyeexe} & {no description file} \\ \hline
\colortwo {\tt atomeyepath} & {no description file} \\ \hline
\colorone {\tt atomeyerepeat} & {no description file} \\ \hline
\colortwo {\tt atommass} & {no description file} \\ \hline
\colorone {\tt atomradius} & {no description file} \\ \hline
\colortwo {\tt atomTcpl} & {no description file} \\ \hline
\colorone {\tt autowritegiffreq} & {no description file} \\ \hline
\colortwo {\tt backgroundcolor} & {no description file} \\ \hline
\colorone {\tt bondcolor} & {no description file} \\ \hline
\colortwo {\tt bondlength} & {no description file} \\ \hline
\colorone {\tt bondradius} & {no description file} \\ \hline
\colortwo {\tt boxdamp} & {no description file} \\ \hline
\colorone {\tt boxTcpl} & {no description file} \\ \hline
\colortwo {\tt chainlength} & {no description file} \\ \hline
\colorone {\tt command} & {no description file} \\ \hline
\colortwo {\tt conj\_dfpred} & {no description file} \\ \hline
\colorone {\tt conj\_fevalmax} & {no description file} \\ \hline
\colortwo {\tt conj\_fixatoms} & {no description file} \\ \hline
\colorone {\tt conj\_fixbox} & {no description file} \\ \hline
\colortwo {\tt conj\_fixboxvec} & {no description file} \\ \hline
\colorone {\tt conj\_fixdir} & {no description file} \\ \hline
\colortwo {\tt conj\_fixshape} & {no description file} \\ \hline
\colorone {\tt conj\_ftol} & {no description file} \\ \hline
\colortwo {\tt conj\_g2res} & {no description file} \\ \hline
\colorone {\tt conj\_itmax} & {no description file} \\ \hline
\colortwo {\tt constrainatoms} & {no description file} \\ \hline
\colorone {\tt constrainS} & {no description file} \\ \hline
\colortwo {\tt crystalstructure} & {no description file} \\ \hline
\colorone {\tt curstep} & {no description file} \\ \hline
\colortwo {\tt dEdlambda} & {no description file} \\ \hline
\colorone {\tt dH} & {no description file} \\ \hline
\colortwo {\tt DOUBLE\_T} & {no description file} \\ \hline
\colorone {\tt Ecoh} & {no description file} \\ \hline
\colortwo {\tt ecspring} & {no description file} \\ \hline
\colorone {\tt energycolorbar} & {no description file} \\ \hline
\colortwo {\tt ensemble\_type} & {no description file} \\ \hline
\colorone {\tt EPBOX} & {no description file} \\ \hline
\colortwo {\tt EPOT} & {no description file} \\ \hline
\colorone {\tt EPOT0} & {no description file} \\ \hline
\colortwo {\tt EPOT\_IND} & {no description file} \\ \hline
\colorone {\tt equilsteps} & {no description file} \\ \hline
\colortwo {\tt ESTRAIN} & {no description file} \\ \hline
\colorone {\tt extforce} & {no description file} \\ \hline
\colortwo {\tt F} & {no description file} \\ \hline
\colorone {\tt F0} & {no description file} \\ \hline
\colortwo {\tt Fext} & {no description file} \\ \hline
\colorone {\tt filecounter} & {no description file} \\ \hline
\colortwo {\tt finalcnfile} & {no description file} \\ \hline
\colorone {\tt fixatomcolor} & {no description file} \\ \hline
\colortwo {\tt fixbox} & {no description file} \\ \hline
\colorone {\tt fixboxvec} & {no description file} \\ \hline
\colortwo {\tt fixed} & {no description file} \\ \hline
\colorone {\tt fixedatomenergypartition} & {no description file} \\ \hline
\colortwo {\tt forcemul} & {no description file} \\ \hline
\colorone {\tt fortranexe} & {no description file} \\ \hline
\colortwo {\tt fortranpath} & {no description file} \\ \hline
\colorone {\tt GH} & {no description file} \\ \hline
\colortwo {\tt group} & {no description file} \\ \hline
\colorone {\tt H} & {no description file} \\ \hline
\colortwo {\tt H0} & {no description file} \\ \hline
\colorone {\tt H\_11} & {no description file} \\ \hline
\colortwo {\tt H\_12} & {no description file} \\ \hline
\colorone {\tt H\_13} & {no description file} \\ \hline
\colortwo {\tt H\_21} & {no description file} \\ \hline
\colorone {\tt H\_22} & {no description file} \\ \hline
\colortwo {\tt H\_23} & {no description file} \\ \hline
\colorone {\tt H\_31} & {no description file} \\ \hline
\colortwo {\tt H\_32} & {no description file} \\ \hline
\colorone {\tt H\_33} & {no description file} \\ \hline
\colortwo {\tt HELM} & {no description file} \\ \hline
\colorone {\tt HELMP} & {no description file} \\ \hline
\colortwo {\tt highlightcolor} & {no description file} \\ \hline
\colorone {\tt hprecond} & {no description file} \\ \hline
\colortwo {\tt image} & {no description file} \\ \hline
\colorone {\tt incnfile} & {no description file} \\ \hline
\colortwo {\tt input} & {no description file} \\ \hline
\colorone {\tt integrator\_type} & {no description file} \\ \hline
\colortwo {\tt intercnfile} & {no description file} \\ \hline
\colorone {\tt KATOM} & {no description file} \\ \hline
\colortwo {\tt KBOX} & {no description file} \\ \hline
\colorone {\tt lambda0} & {no description file} \\ \hline
\colortwo {\tt lambda1} & {no description file} \\ \hline
\colorone {\tt latticeconst} & {no description file} \\ \hline
\colortwo {\tt latticesize} & {no description file} \\ \hline
\colorone {\tt latticestructure} & {no description file} \\ \hline
\colortwo {\tt makecnspec} & {no description file} \\ \hline
\colorone {\tt MC\_accept\_ratio} & {no description file} \\ \hline
\colortwo {\tt MC\_dr} & {no description file} \\ \hline
\colorone {\tt mcatom} & {no description file} \\ \hline
\colortwo {\tt MDCASKpot} & {no description file} \\ \hline
\colorone {\tt mkcylinderspec} & {no description file} \\ \hline
\colortwo {\tt mkdipole} & {no description file} \\ \hline
\colorone {\tt mkdislspec} & {no description file} \\ \hline
\colortwo {\tt myname} & {no description file} \\ \hline
\colorone {\tt NCS} & {no description file} \\ \hline
\colortwo {\tt nebspec} & {no description file} \\ \hline
\colorone {\tt NIC} & {no description file} \\ \hline
\colortwo {\tt NNM} & {no description file} \\ \hline
\colorone {\tt NP} & {no description file} \\ \hline
\colortwo {\tt nspecies} & {no description file} \\ \hline
\colorone {\tt OMEGA} & {no description file} \\ \hline
\colortwo {\tt outpropfile} & {no description file} \\ \hline
\colorone {\tt output} & {no description file} \\ \hline
\colortwo {\tt output\_fmt} & {no description file} \\ \hline
\colorone {\tt plot\_atom\_info} & {no description file} \\ \hline
\colortwo {\tt plot\_color\_axis} & {no description file} \\ \hline
\colorone {\tt plot\_color\_bar} & {no description file} \\ \hline
\colortwo {\tt plot\_color\_windows} & {no description file} \\ \hline
\colorone {\tt plot\_limits} & {no description file} \\ \hline
\colortwo {\tt plot\_map\_pbc} & {no description file} \\ \hline
\colorone {\tt plotfreq} & {no description file} \\ \hline
\colortwo {\tt potfile} & {no description file} \\ \hline
\colorone {\tt PRESSURE} & {no description file} \\ \hline
\colortwo {\tt pressureadd} & {no description file} \\ \hline
\colorone {\tt printfreq} & {no description file} \\ \hline
\colortwo {\tt PSTRESS} & {no description file} \\ \hline
\colorone {\tt R} & {no description file} \\ \hline
\colortwo {\tt R0} & {no description file} \\ \hline
\colorone {\tt randseed} & {no description file} \\ \hline
\colortwo {\tt refpotential} & {no description file} \\ \hline
\colorone {\tt RLIST} & {no description file} \\ \hline
\colortwo {\tt rotateangles} & {no description file} \\ \hline
\colorone {\tt savecn} & {no description file} \\ \hline
\colortwo {\tt savecnfreq} & {no description file} \\ \hline
\colorone {\tt SAVEMEMORY} & {no description file} \\ \hline
\colortwo {\tt saveprop} & {no description file} \\ \hline
\colorone {\tt savepropfreq} & {no description file} \\ \hline
\colortwo {\tt shearrate} & {no description file} \\ \hline
\colorone {\tt SIGMA} & {no description file} \\ \hline
\colortwo {\tt species} & {no description file} \\ \hline
\colorone {\tt SR} & {no description file} \\ \hline
\colortwo {\tt storedr} & {no description file} \\ \hline
\colorone {\tt stress} & {no description file} \\ \hline
\colortwo {\tt stressmul} & {no description file} \\ \hline
\colorone {\tt switchfreq} & {no description file} \\ \hline
\colortwo {\tt switchfunc} & {no description file} \\ \hline
\colorone {\tt switchoffatoms} & {no description file} \\ \hline
\colortwo {\tt T\_OBJ} & {no description file} \\ \hline
\colorone {\tt timestep} & {no description file} \\ \hline
\colortwo {\tt Tinst} & {no description file} \\ \hline
\colorone {\tt TOPOL} & {no description file} \\ \hline
\colortwo {\tt torquespec} & {no description file} \\ \hline
\colorone {\tt totalsteps} & {no description file} \\ \hline
\colortwo {\tt TSTRESS} & {no description file} \\ \hline
\colorone {\tt TSTRESS\_xx} & {no description file} \\ \hline
\colortwo {\tt TSTRESS\_xy} & {no description file} \\ \hline
\colorone {\tt TSTRESS\_xz} & {no description file} \\ \hline
\colortwo {\tt TSTRESS\_yx} & {no description file} \\ \hline
\colorone {\tt TSTRESS\_yy} & {no description file} \\ \hline
\colortwo {\tt TSTRESS\_yz} & {no description file} \\ \hline
\colorone {\tt TSTRESS\_zx} & {no description file} \\ \hline
\colortwo {\tt TSTRESS\_zy} & {no description file} \\ \hline
\colorone {\tt TSTRESS\_zz} & {no description file} \\ \hline
\colortwo {\tt usenosehoover} & {no description file} \\ \hline
\colorone {\tt usescalevelocity} & {no description file} \\ \hline
\colortwo {\tt vacuumratio} & {no description file} \\ \hline
\colorone {\tt VH} & {no description file} \\ \hline
\colortwo {\tt VIRIAL} & {no description file} \\ \hline
\colorone {\tt VIRIAL\_IND} & {no description file} \\ \hline
\colortwo {\tt VR} & {no description file} \\ \hline
\colorone {\tt VSR} & {no description file} \\ \hline
\colortwo {\tt vt2} & {no description file} \\ \hline
\colorone {\tt wallmass} & {no description file} \\ \hline
\colortwo {\tt win\_height} & {no description file} \\ \hline
\colorone {\tt win\_width} & {no description file} \\ \hline
\colortwo {\tt writeall} & {no description file} \\ \hline
\colorone {\tt writevelocity} & {no description file} \\ \hline
\colortwo {\tt xprecond} & {no description file} \\ \hline
\colorone {\tt yprecond} & {no description file} \\ \hline
\colortwo {\tt zeta} & {no description file} \\ \hline
\colorone {\tt zetaa} & {no description file} \\ \hline
\colortwo {\tt zetav} & {no description file} \\ \hline
\colorone {\tt zprecond} & {no description file} \\ \hline
\end{longtable}
\section{Class mdparallel {\normalsize \rm (
9 commands and
15 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt alloc\_all} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  alloc_all

Every processor (master and slave) allocate memory
(such as {\tt SR}, {\tt F} arrays) according to the number
of atoms {\tt NP}.
%
Needed before {\tt eval\_parallel}.
%
Effective only when MD++ is compiled for parallel runs,
e.g. with {\tt SYS = mpicc} or {\tt SYS = mpigpp}.
\FL\end{minipage}
\\ \hline
\colortwo {\tt Broadcast\_Atoms} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  Broadcast_Atoms

CPU 0 (master) broadcast all atom positions to other CPUs (slaves).
%
Needed before {\tt eval\_parallel}.
%
Effective only when MD++ is compiled for parallel runs,
e.g. with {\tt SYS = mpicc} or {\tt SYS = mpigpp}.
\FL\end{minipage}
\\ \hline
\colorone {\tt eval\_parallel} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  eval_parallel

CPU 0 (Master) calls {\tt eval} with the help of all other CPUs (slaves).
%
Requires {\tt Broadcast\_Atoms} to be called beforehand.
\FL\end{minipage}
\\ \hline
\colortwo {\tt Mark\_Local\_Atoms} & {no description file} \\ \hline
\colorone {\tt Master\_to\_Slave} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  Master_to_Slave

Requires {\tt command = $cmd$ } to be set beforehand.
%
CPU 0 (master) request other CPUs (slaves) to execute $cmd$,
which can be any MD++ command or variable assignment.
\FL\end{minipage}
\\ \hline
\colortwo {\tt Partition\_Domains} & {no description file} \\ \hline
\colorone {\tt quit\_all} & 
\begin{minipage}[c]{.65\textwidth}\FL
%%%%%%%%%%%%%%%  -*-Tex-*-  %%%%%%%%%%%%%%%%%%
% short description of MD++ command
%  quit_all

Equivalent of {\tt quit} in parallel.
\FL\end{minipage}
\\ \hline
\colortwo {\tt run\_parallel} & {no description file} \\ \hline
\colorone {\tt Slave\_to\_Master\_Atoms} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt domainID} & {no description file} \\ \hline
\colortwo {\tt myDomain} & {no description file} \\ \hline
\colorone {\tt myIX} & {no description file} \\ \hline
\colortwo {\tt myIY} & {no description file} \\ \hline
\colorone {\tt myIZ} & {no description file} \\ \hline
\colortwo {\tt myXmax} & {no description file} \\ \hline
\colorone {\tt myXmin} & {no description file} \\ \hline
\colortwo {\tt myYmax} & {no description file} \\ \hline
\colorone {\tt myYmin} & {no description file} \\ \hline
\colortwo {\tt myZmax} & {no description file} \\ \hline
\colorone {\tt myZmin} & {no description file} \\ \hline
\colortwo {\tt numDomains} & {no description file} \\ \hline
\colorone {\tt nXdoms} & {no description file} \\ \hline
\colortwo {\tt nYdoms} & {no description file} \\ \hline
\colorone {\tt nZdoms} & {no description file} \\ \hline
\end{longtable}
\section{Class fs {\normalsize \rm (
1 commands and
10 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt readpot} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt A} & {no description file} \\ \hline
\colortwo {\tt alpha} & {no description file} \\ \hline
\colorone {\tt B} & {no description file} \\ \hline
\colortwo {\tt b0} & {no description file} \\ \hline
\colorone {\tt beta} & {no description file} \\ \hline
\colortwo {\tt c} & {no description file} \\ \hline
\colorone {\tt c0} & {no description file} \\ \hline
\colortwo {\tt c1} & {no description file} \\ \hline
\colorone {\tt c2} & {no description file} \\ \hline
\colortwo {\tt d} & {no description file} \\ \hline
\end{longtable}
\section{Class lj2 {\normalsize \rm (
1 commands and
6 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt initLJ} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt C6\_00} & {no description file} \\ \hline
\colortwo {\tt C6\_01} & {no description file} \\ \hline
\colorone {\tt C6\_11} & {no description file} \\ \hline
\colortwo {\tt C12\_00} & {no description file} \\ \hline
\colorone {\tt C12\_01} & {no description file} \\ \hline
\colortwo {\tt C12\_11} & {no description file} \\ \hline
\end{longtable}
\section{Class eam {\normalsize \rm (
2 commands and
3 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt readeam} & {no description file} \\ \hline
\colortwo {\tt readMEAM} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt eamfiletype} & {no description file} \\ \hline
\colortwo {\tt eamgrid} & {no description file} \\ \hline
\colorone {\tt pottype} & {no description file} \\ \hline
\end{longtable}
\section{Class meam {\normalsize \rm (
3 commands and
18 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt Broadcast\_MEAM\_Param} & {no description file} \\ \hline
\colortwo {\tt printpairpot} & {no description file} \\ \hline
\colorone {\tt readMEAM} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt a8b} & {no description file} \\ \hline
\colortwo {\tt ag} & {no description file} \\ \hline
\colorone {\tt atpe2b} & {no description file} \\ \hline
\colortwo {\tt atpe3b} & {no description file} \\ \hline
\colorone {\tt b8c} & {no description file} \\ \hline
\colortwo {\tt c8a} & {no description file} \\ \hline
\colorone {\tt cg8c} & {no description file} \\ \hline
\colortwo {\tt d8d} & {no description file} \\ \hline
\colorone {\tt dang1} & {no description file} \\ \hline
\colortwo {\tt dang2} & {no description file} \\ \hline
\colorone {\tt embf} & {no description file} \\ \hline
\colortwo {\tt enable\_square\_rscrn} & {no description file} \\ \hline
\colorone {\tt enable\_zbl\_fdimer} & {no description file} \\ \hline
\colortwo {\tt rhotot} & {no description file} \\ \hline
\colorone {\tt rhsq} & {no description file} \\ \hline
\colortwo {\tt tav} & {no description file} \\ \hline
\colorone {\tt xzbl} & {no description file} \\ \hline
\colortwo {\tt xzbl0} & {no description file} \\ \hline
\end{longtable}
\section{Class meam-baskes {\normalsize \rm (
2 commands and
11 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt printpairpot} & {no description file} \\ \hline
\colortwo {\tt readMEAM} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt cmin0} & {no description file} \\ \hline
\colortwo {\tt ename0} & {no description file} \\ \hline
\colorone {\tt ename1} & {no description file} \\ \hline
\colortwo {\tt ename2} & {no description file} \\ \hline
\colorone {\tt kode0} & {no description file} \\ \hline
\colortwo {\tt kode1} & {no description file} \\ \hline
\colorone {\tt kode2} & {no description file} \\ \hline
\colortwo {\tt meafile} & {no description file} \\ \hline
\colorone {\tt meamfile} & {no description file} \\ \hline
\colortwo {\tt ntypes} & {no description file} \\ \hline
\colorone {\tt rcut} & {no description file} \\ \hline
\end{longtable}
\section{Class meam-lammps {\normalsize \rm (
3 commands and
19 variables )}}


\FL {\large \bf Commands}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt Broadcast\_MEAM\_Param} & {no description file} \\ \hline
\colortwo {\tt printpairpot} & {no description file} \\ \hline
\colorone {\tt readMEAM} & {no description file} \\ \hline
\end{longtable}
\FL {\large \bf Variables}


\begin{longtable}{|l|l|}
\hline
\colorone {\tt arho1} & {no description file} \\ \hline
\colortwo {\tt arho2} & {no description file} \\ \hline
\colorone {\tt arho2b} & {no description file} \\ \hline
\colortwo {\tt arho3} & {no description file} \\ \hline
\colorone {\tt arho3b} & {no description file} \\ \hline
\colortwo {\tt dgamma1} & {no description file} \\ \hline
\colorone {\tt dgamma2} & {no description file} \\ \hline
\colortwo {\tt dgamma3} & {no description file} \\ \hline
\colorone {\tt frhop} & {no description file} \\ \hline
\colortwo {\tt gamma} & {no description file} \\ \hline
\colorone {\tt meafile} & {no description file} \\ \hline
\colortwo {\tt meamfile} & {no description file} \\ \hline
\colorone {\tt rcut} & {no description file} \\ \hline
\colortwo {\tt rho} & {no description file} \\ \hline
\colorone {\tt rho0} & {no description file} \\ \hline
\colortwo {\tt rho1} & {no description file} \\ \hline
\colorone {\tt rho2} & {no description file} \\ \hline
\colortwo {\tt rho3} & {no description file} \\ \hline
\colorone {\tt t\_ave} & {no description file} \\ \hline
\end{longtable}
\bibliography{a}
\bibliographystyle{unsrt}
\end{document}
