forked from lijiext/lammps
630 lines
19 KiB
HTML
Executable File
630 lines
19 KiB
HTML
Executable File
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
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<HTML>
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<HEAD>
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<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
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</HEAD>
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<BODY>
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<H2>
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Crib File</H2>
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<P>
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<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
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<P>
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This file contains one-line descriptions of the key variables and
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parameters used in LAMMPS. The variables are listed by their data type:</P>
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<UL>
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<LI>
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<A HREF="#_cch3_930764945">Parameters</A>
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<LI>
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<A HREF="#_cch3_930764951">Arrays (real</A>)
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<LI>
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<A HREF="#_cch3_930764957">Arrays (integer)</A>
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<LI>
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<A HREF="#_cch3_930764964">Variables (real)</A>
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<LI>
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<A HREF="#_cch3_930764969">Variables (integer)</A>
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<LI>
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<A HREF="#_cch3_930764974">Variables (character)</A>
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</UL>
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<P>
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Note: this file is somewhat out-of-date for LAMMPS 99.</P>
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<HR>
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<H3>
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<A NAME="_cch3_930764945">Parameters: </A></H3>
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<UL>
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<LI>
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maxown = max # of local owned atoms
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<LI>
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maxother = max # of local nearby atoms
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<LI>
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maxtotal = max # of total atoms in simulation
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<LI>
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maxtype = max # of atom types
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<LI>
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maxbond = max # of bonds to compute on one procesor
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<LI>
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maxangle = max # of angles to compute on one processor
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<LI>
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maxdihed = max # of dihedrals to compute on one processor
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<LI>
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maximpro = max # of impropers to compute on one processor
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<LI>
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maxbondper = max # of bonds of one atom
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<LI>
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maxangleper = max # of angles of one atom
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<LI>
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maxdihedper = max # of dihedrals of one atom
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<LI>
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maximproper = max # of impropers of one atom
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<LI>
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maxbondtype = max # of bond types
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<LI>
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maxangletype = max # of angle types
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<LI>
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maxdihedtype = max # of dihedral types
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<LI>
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maximprotype = max # of improper types
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<LI>
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maxexch = max # of atoms in exchange buffer
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<LI>
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maxsend = max # of atoms to send to all neighbors in all swaps
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<LI>
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maxsendone = max # of atoms to send in one swap
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<LI>
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maxswap = max # of swaps to do at each timestep
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<LI>
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maxneigh = max # of neighbors per owned atom
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<LI>
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maxsneigh = max # of special neighbors of one atom
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<LI>
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maxbin = max # of local neighbor bins
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<LI>
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maxfix = max # of defined constraints + 1
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<LI>
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maxdiag = max # of diagnostic routines
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<LI>
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maxgrid = max size of PPPM grid with ghosts on one processor
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<LI>
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maxfft = max size of PPPM FFT grid on one processor
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<LI>
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maxperatom = max # of data items stored/comm/output per atom
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<LI>
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maxatom = maxown + maxother = total # of own and nearby atoms
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<LI>
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maxexchtot = maxexch * (maxperatom + maxsneigh + 3*maxbondper +
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4*maxangleper + 5*maxdihedper + 5*maximproper) = total data volume for
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all exchanged atoms
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<LI>
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maxrestot = maxown * (maxperatom - 3 + 3*maxbondper + 4*maxangleper +
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5*maxdihedper + 5*maximproper)+1 = total data volume for all buffered
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restart atoms
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<LI>
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maxsendspec = 2 * maxsneigh * maxown total data volume for sending
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special requests
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<LI>
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maxrecvspec = maxsneigh + 1 total data volume for receiving a list of
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specials
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930764951">Arrays (real): </A></H3>
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<UL>
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<LI>
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anglecoeff(2,maxangletype) = angle coeffs for each angle type
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<LI>
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bondcoeff(5,maxbondtype) = bond coeffs for each bond type
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<LI>
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boundhi(maxswap) = hi slab boundary on atom positions for each swap
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send
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<LI>
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boundlo(maxswap) = lo slab boundary on atom positions for each swap
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send
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<LI>
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buf1(maxexchtot) = comm buffer for sending exchange atoms
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<LI>
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buf2(2*maxexchtot) = comm buffer for 2 recv of exchange atoms
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<LI>
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buf3(3*maxsendone) = comm buffer for sending one set of swap atom
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positions
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<LI>
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buf4(8*maxown) = comm buffer for output
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<LI>
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buf5(maxrestot) = comm buffer for restart atoms
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<LI>
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buf6(maxsendone) = comm buffer for sending one set of swap charges
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<LI>
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cutforcesq(maxtype,maxtype) = force cutoff squared for atom pair
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(LJ/Coul)
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<LI>
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cutljsq(maxtype,maxtype) = LJ cutoff squared for atom pairs
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<LI>
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cutljinner(maxtype,maxtype) = inner LJ cutoff for switched LJ
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<LI>
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cutljinnersq(maxtype,maxtype) = inner LJ cutoff squared for switched LJ
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<LI>
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cutneighsq(maxtype,maxtype) = neigh cutoff squared for atom pair
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(LJ/Coul + skin)
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<LI>
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diagparams(6,maxdiag) = parameters to pass into a diagnostic routine
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<LI>
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dihedcoeff(3,maxdihedtype) = dihedral coeffs for each dihedral type
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<LI>
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f(3,maxown) = forces on own atoms
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<LI>
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fixcoeff(8,maxfix) = constraint coeffs for each constraint
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<LI>
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fixstore(5*maxfix) = accumulated quantities for each constraint
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<LI>
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improcoeff(2,maximprotype) = improper coeffs for each improper type
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<LI>
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lj12345(maxtype,maxtype) = pre-computed LJ coeffs for use in energy and
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force
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<LI>
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ljsw01234(maxtype,maxtype) = pre-computed switched LJ coeffs for eng
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and force
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<LI>
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mass(maxtype) = mass of each atom type
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<LI>
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noncoeff1234(maxtype,maxtype) = nonbond coeffs input for atom pairs
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<LI>
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offset(maxtype,maxtype) = LJ potential offsets at cutoff for energy
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calc
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<LI>
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q(maxatom) = charge of own and nearby atoms (electron units)
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<LI>
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v(3,maxown) = velocity of owned atoms
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<LI>
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x(3,maxatom) = positions of own and nearby atoms
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<LI>
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xhold(3,maxown) = positions of own atoms at last reneighboring
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930764957">Arrays (integer): </A></H3>
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<UL>
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<LI>
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angleatom123(maxangleper,maxown) = angle atoms for angles of owned
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atoms
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<LI>
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anglelist(4,maxangle) = atoms and type of each angle to compute locally
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<LI>
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angletype(maxangleper,maxown) = angle type for angles of owned atoms
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<LI>
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bin(maxatom) = linked list pointers from one atom to next in bin
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<LI>
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binpnt(maxbin) = pointer to 1st atom in each bin
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<LI>
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bondatom12(maxbondper,maxown) = bond atoms for bonds of owned atoms
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<LI>
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bondlist(3,maxbond) = atoms and type of each bond to compute locally
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<LI>
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bondtype(maxbondper,maxown) = bond type for bonds of owned atoms
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<LI>
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bondtypeflag(maxbondtype) = flag for whether bond coeffs are set
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<LI>
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diagfileflag(maxdiag) = whether a file has been specified for a diag
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routine
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<LI>
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diagfreq(maxdiag) = call a diagnostic routine every this many steps
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<LI>
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diagnparams(maxdiag) = # of parameters specified for a diagnostic
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routine
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<LI>
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diagstyle(maxdiag) = whether a diagnostic has been set 0/1
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<LI>
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dihedatom1234(maxdihedper,maxown) = dihed atoms for diheds of owned
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atoms
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<LI>
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dihedlist(5,maxdihed) = atoms and type of each dihedral to compute
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locally
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<LI>
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dihedtype(maxdihedper,maxown) = dihed type for diheds of owned atoms
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<LI>
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fix(maxown) = constraint assignments for each owned atom
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<LI>
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fixflag(3,maxfix) = 0/1 flags for various fix styles
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<LI>
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fixptr(maxfix) = how many values are accumulated for each constraint
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<LI>
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fixstyle(maxfix) = style of each constraint
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<LI>
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ibuf1(maxsendone) = comm buffer for sending one set of swap atom tags
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<LI>
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ibuf2(maxsendone) = comm buffer for sending one set of swap atom types
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<LI>
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ibuf3(maxspec) = comm buffer for sending special requests
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<LI>
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ibuf4(maxspec) = comm buffer for receiving special lists
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<LI>
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improatom1234(maximproper,maxown) = impro atoms for impros of owned
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atoms
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<LI>
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improlist(5,maximpro) = atoms and type of each improper to compute
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locally
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<LI>
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improtype(maximproper,maxown) = impro type for impros of owned atoms
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<LI>
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list(maxown) = linked list of local atoms (last one -> maxown+1)
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<LI>
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localptr(0:maxtotal) = ptr from global atom to local array (0 if don't
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have)
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<LI>
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molecule(maxown) = molecule id # each owned atom is in
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<LI>
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nlist(maxown*maxneigh+maxneigh) = neighbor lists of own atoms
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<LI>
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nliststart(maxown) = pointer to where neighbor list for this atom
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starts
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<LI>
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nliststop(maxown) = pointer to where neighbor list for this atom stops
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<LI>
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nontypeflag(maxtype,maxtype) = flag for whether nonbond coeffs are set
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<LI>
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nrlist(maxswap+1) = prt to where received other atoms start for each
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swap
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<LI>
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nslist(maxswap+1) = pointer to where swap list starts for each swap
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<LI>
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numangle(maxown) = # of angles of each owned atom
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<LI>
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numbond(maxown) = # of 1st neighbors bonded to each owned atom
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<LI>
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num2bond(maxown) = # of 2nd neighbors for each owned atom
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<LI>
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num3bond(maxown) = # of 3rd neighbors for each owned atom
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<LI>
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numdihed(maxown) = # of dihedrals of each owned atom
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<LI>
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numimpro(maxown) = # of impropers of each owned atom
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<LI>
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rpart(maxswap) = node # of who to recv from for each swap
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<LI>
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slist(maxsend) = send list of atoms to send out in all swaps
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<LI>
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spart(maxswap) = node # of who to send to for each swap
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<LI>
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specbond(maxsneigh,maxown) = special bond neighbors of each owned atom
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<LI>
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tag(maxatom) = global id # of own and nearby atoms
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<LI>
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true(maxown) = which periodic box atom is truly in for all 3 dims
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<LI>
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type(maxatom) = type # of own and nearby atoms
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<LI>
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typecheck(maxtype) = consistency check for all existing atom types
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<LI>
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typechecktmp(maxtype) = summing array for atom type consistency check
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<LI>
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velflag(maxown) = whether velocity for each atom has been created
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930764964">Variables (real): </A></H3>
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<UL>
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<LI>
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binsize[xyz] = size of global neighbor bins in each dimension
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<LI>
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boltz = Boltzmann factor
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<LI>
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border(2,3) = lo/hi boundaries of my sub-box in each dimension
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<LI>
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coulpre = Coulombic force prefactor
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<LI>
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createregion(6) = bounding box for atoms to create temperature for
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<LI>
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createvec(3) = initial velocity for create temp atoms
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<LI>
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cutcoul = input force cutoff for Coulombic interactions
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<LI>
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cutcoulsq = Coul cutoff squared for all atom pairs
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<LI>
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cutforce = max force cutoff for all atom pairs (LJ/Coul)
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<LI>
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cutlj = input global (default) LJ cutoff for all atom pairs
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<LI>
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cutljinterior = global inner LJ cutoff for switched LJ
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<LI>
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cutneigh = max neighbor cutoff for all atom pairs (LJ/Coul + skin)
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<LI>
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dielectric = dielectric constant
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<LI>
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dt = timestep
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<LI>
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dtfactor = timestep conversion factor from input to program units
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<LI>
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dthalf = timestep / 2
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<LI>
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efactor = energy conversion factor from Coulombic to Kcals
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<LI>
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e_angle = energy in angles
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<LI>
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e_bond = energy in bonds
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<LI>
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e_coul = energy in nonbond Coulombic
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<LI>
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e_dihedral = energy in dihedrals
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<LI>
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e_improper = energy in impropers
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<LI>
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e_total = total energy
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<LI>
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e_vdwl = energy in nonbond LJ
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<LI>
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fixregion(6) = bounding box for atoms to assign to a constraint
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<LI>
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skin = distance between force and neighbor cutoffs
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<LI>
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special(3) = weight factors for special neighbors
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<LI>
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triggersq = squared distance to trigger neighbor list rebuild
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<LI>
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two16 = 2 ^ (1/6) constant for use in FENE bond potentials
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<LI>
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t_create = requested initialization temp
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<LI>
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t_current = current temp returned from temp routine
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<LI>
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t_nph = default temp for constant NPH
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<LI>
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t_start = target temp at beginning of run
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<LI>
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t_stop = target temp at end of run
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<LI>
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t_window = control temp within this window
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<LI>
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time_angle = angle time
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<LI>
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time_bond = bond time
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<LI>
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time_comm = communication time
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<LI>
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time_current = current time
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<LI>
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time_dihedral = dihedral time
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<LI>
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time_exch = exchange time
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<LI>
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time_improper = improper time
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<LI>
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time_io = i/o time
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<LI>
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time_loop = time for integration loop
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<LI>
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time_neigh1 = neighboring time in nonbond
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<LI>
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time_neigh2 = neighboring time in bonds
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<LI>
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time_nonbond = nonbond force time
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<LI>
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time_other = other miscellaneous time
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<LI>
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time_total = total run time of entire simulation
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<LI>
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x[yz]mc = box size minus force cutoff for PBC checks
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<LI>
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x[yz]ms box size minus neighbor list cutoff for PBC checks
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<LI>
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x[yz]boundlo = lower global box boundary in each dimension
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<LI>
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x[yz]boundhi = upper global box boundary in each dimension
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<LI>
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x[yz]prd = global box size in each dimension
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930764969">Variables (integer): </A></H3>
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<UL>
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<LI>
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atompnt = pointer to 1st atom in my list
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<LI>
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bondstyle = style of bond computation
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<LI>
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boxflag = flag if box has been remapped (non-PBC)
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<LI>
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coulstyle = style of Coulomb interaction
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<LI>
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creategroup = kind of atom group to create temp for
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<LI>
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createstyle = style of temp creation
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<LI>
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createtypehi = upper range of atom types to create temp for
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<LI>
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createtypelo = lower range of atom types to create temp for
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<LI>
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dumpfileflag = has dump file been opened or not (1/0)
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<LI>
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dumpflag = dump atoms to file every this many steps (0 = never)
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<LI>
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dumpforcefileflag = has dump force file been opened or not (1/0)
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<LI>
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dumpforceflag = dump forces to file every this many steps (0 = never)
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<LI>
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dumpvelfileflag = has dump velocity file been opened or not (1/0)
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<LI>
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dumpvelflag = dump vels to file every this many steps (0 = never)
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<LI>
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fixatom = assign atom/molecule with this tag to a constraint
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<LI>
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fixgroup = kind of atom group to assign to a constraint
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<LI>
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fixnum = total # of accumulated values for all constraints
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<LI>
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fixtype = assign group of atoms of this type to a constraint
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<LI>
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fixwhich = which constraint a atom group is to be assigned to
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<LI>
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freepnt = pointer to 1st free space in list (last one -> 0)
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<LI>
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idimension = dimension of problem (2-d or 3-d)
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<LI>
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iseed = RNG seed for generating initial velocities
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<LI>
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itime = current timestep loop counter in integrator
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<LI>
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iversion = version number of restart files (for backward compat)
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<LI>
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max_angle = most angles I ever have to compute
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<LI>
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max_angleper = most angles ever attached to any atom
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<LI>
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max_bond = most bonds I ever have to compute
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<LI>
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max_bondper = most bonds ever attached to any atom
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<LI>
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max_dihed = most diheds I ever have to compute
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<LI>
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max_dihedper = most diheds ever attached to any atom
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<LI>
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max_exch = most atoms ever leaving my box (in one dimension)
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<LI>
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max_impro = most impros I ever have to compute
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<LI>
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max_improper = most impros ever attached to any atom
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<LI>
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max_nlocal = most atoms I ever owned
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<LI>
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max_neigh = most neighbors ever stored in neighbor list
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<LI>
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max_nother = most nearby atoms I ever stored
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<LI>
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max_slist = biggest size swap list ever reached
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<LI>
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max_swap = most atoms ever sent in one swap
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<LI>
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mbin[xyz] = # of bins in my box with nearby atoms included
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<LI>
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mbin[xyz]lo = global bin indices (offset) at corner of extended box
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<LI>
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me(3) = which box I am (0 - pgrid-1) in each dimension
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<LI>
|
|
mixflag = whether mixing style has been set or not
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|
<LI>
|
|
mixstyle = style of mixing for nonbond coeffs (arith,geom,sixth)
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|
<LI>
|
|
mpart(2,3)= node # of neighbor processor in each dimension
|
|
<LI>
|
|
nanglelocal = local # of angless to compute
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|
<LI>
|
|
nangles = total # of angles
|
|
<LI>
|
|
nangletypes = total # of angle types
|
|
<LI>
|
|
natoms = total # of atoms
|
|
<LI>
|
|
nbin[xyz] # of global neighbor bins in each dimension
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|
<LI>
|
|
nbondlocal = local # of bonds to compute
|
|
<LI>
|
|
nbonds = total # of bonds
|
|
<LI>
|
|
nbondtypes = total # of bond types
|
|
<LI>
|
|
ndanger = # of neighbor rebuilds triggered by 1st check
|
|
<LI>
|
|
ndiags = # of user-specified diagnostic routines
|
|
<LI>
|
|
ndihedlocal = local # of dihedrals to compute
|
|
<LI>
|
|
ndihedrals = total # of diheds
|
|
<LI>
|
|
ndihedtypes = total # of dihedral types
|
|
<LI>
|
|
need(3) how many processors I need neighbors from in each dim
|
|
<LI>
|
|
neighago = how many timesteps ago neighboring was done
|
|
<LI>
|
|
neighdelay = delay neighbor list build for this many steps
|
|
<LI>
|
|
neighfreq = build neighbor list every this many steps
|
|
<LI>
|
|
neighstyle = neighboring by (0) N^2 or (1) binning method
|
|
<LI>
|
|
neightop = last used position in neighbor list (nlist)
|
|
<LI>
|
|
neightrigger = always (0) do neighbor list or trigger (1) on atom move
|
|
<LI>
|
|
newton = flag for kind of Newton's 3rd law used (0,1,2,3)
|
|
<LI>
|
|
newton_bond = Newton's 3rd is not used (0) or (1) used for bonds
|
|
<LI>
|
|
newton_nonbond = Newton's 3rd is not used (0) or (1) used for nonbonds
|
|
<LI>
|
|
nfixes = # of constraints
|
|
<LI>
|
|
nimprolocal = local # of impropers to compute
|
|
<LI>
|
|
nimpropers = total # of impros
|
|
<LI>
|
|
nimprotypes = total # of improper types
|
|
<LI>
|
|
nlocal = # of atoms I currently own
|
|
<LI>
|
|
nother = # of nearby atoms I currently store
|
|
<LI>
|
|
node = my node #
|
|
<LI>
|
|
nonstyle = style on nonbond computation
|
|
<LI>
|
|
nprocs = total # of processors
|
|
<LI>
|
|
nsteps = # of timesteps to simulate
|
|
<LI>
|
|
nswap = # of swaps at each timestep
|
|
<LI>
|
|
ntimestep = current global timestep
|
|
<LI>
|
|
ntypes = total # of atom types
|
|
<LI>
|
|
numneigh = number of times reneighboring is done
|
|
<LI>
|
|
offsetflag = whether to include energy offset in LJ energy calc
|
|
<LI>
|
|
peratom = # of values/atom not including bond info
|
|
<LI>
|
|
perflagx[yz] = flag for periodic (0) or non-periodic (1) BC
|
|
<LI>
|
|
pgrid(3) = # of processors in each dimension
|
|
<LI>
|
|
readflag = whether atom input file has been read or not (1/0)
|
|
<LI>
|
|
restartfileflag = which restart file to open next (0/1)
|
|
<LI>
|
|
restartflag = write restart file every this many steps (0=never)
|
|
<LI>
|
|
t_every = rescale/replace temp every this many steps
|
|
<LI>
|
|
tempflag = constant temperature style flag
|
|
<LI>
|
|
thermoflag = print thermo info every this many steps (0 = never)
|
|
<LI>
|
|
thermostyle = style of thermo output (0 = full, 1 = reduced)
|
|
<LI>
|
|
trueflag = whether to dump remapped or true atom positions
|
|
<LI>
|
|
units = flag for real vs reduced LJ units
|
|
</UL>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_930764974">Variables (character): </A></H3>
|
|
<UL>
|
|
<LI>
|
|
datafile = file to read atom and connectivity info from
|
|
<LI>
|
|
diagfile(maxdiag) = files to print user-specified diagnostics to
|
|
<LI>
|
|
diagname(maxdiag) = name of a user-specified diagnostic routine
|
|
<LI>
|
|
dumpfile = file to dump atom info to
|
|
<LI>
|
|
dumpforcefile = file to dump force info to
|
|
<LI>
|
|
dumpvelfile = file to dump velocity info to
|
|
<LI>
|
|
restart_in = file to read restart info from
|
|
<LI>
|
|
restart_out[12] = files to write restart info to
|
|
</UL>
|
|
<P>
|
|
</P>
|
|
</BODY>
|
|
</HTML>
|