Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/99/crib.html
96a73d51cd98lammm-master-deprecated

Last Change
Raw File

crib.html
View Options

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
</HEAD>
<BODY>
<H2>
Crib File</H2>
<P>
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation.</P>
<P>
This file contains one-line descriptions of the key variables and
parameters used in LAMMPS. The variables are listed by their data type:</P>
<UL>
<LI>
<A HREF="#_cch3_930764945">Parameters</A>
<LI>
<A HREF="#_cch3_930764951">Arrays (real</A>)
<LI>
<A HREF="#_cch3_930764957">Arrays (integer)</A>
<LI>
<A HREF="#_cch3_930764964">Variables (real)</A>
<LI>
<A HREF="#_cch3_930764969">Variables (integer)</A>
<LI>
<A HREF="#_cch3_930764974">Variables (character)</A>
</UL>
<P>
Note: this file is somewhat out-of-date for LAMMPS 99.</P>
<HR>
<H3>
<A NAME="_cch3_930764945">Parameters: </A></H3>
<UL>
<LI>
maxown = max # of local owned atoms
<LI>
maxother = max # of local nearby atoms
<LI>
maxtotal = max # of total atoms in simulation
<LI>
maxtype = max # of atom types
<LI>
maxbond = max # of bonds to compute on one procesor
<LI>
maxangle = max # of angles to compute on one processor
<LI>
maxdihed = max # of dihedrals to compute on one processor
<LI>
maximpro = max # of impropers to compute on one processor
<LI>
maxbondper = max # of bonds of one atom
<LI>
maxangleper = max # of angles of one atom
<LI>
maxdihedper = max # of dihedrals of one atom
<LI>
maximproper = max # of impropers of one atom
<LI>
maxbondtype = max # of bond types
<LI>
maxangletype = max # of angle types
<LI>
maxdihedtype = max # of dihedral types
<LI>
maximprotype = max # of improper types
<LI>
maxexch = max # of atoms in exchange buffer
<LI>
maxsend = max # of atoms to send to all neighbors in all swaps
<LI>
maxsendone = max # of atoms to send in one swap
<LI>
maxswap = max # of swaps to do at each timestep
<LI>
maxneigh = max # of neighbors per owned atom
<LI>
maxsneigh = max # of special neighbors of one atom
<LI>
maxbin = max # of local neighbor bins
<LI>
maxfix = max # of defined constraints + 1
<LI>
maxdiag = max # of diagnostic routines
<LI>
maxgrid = max size of PPPM grid with ghosts on one processor
<LI>
maxfft = max size of PPPM FFT grid on one processor
<LI>
maxperatom = max # of data items stored/comm/output per atom
<LI>
maxatom = maxown + maxother = total # of own and nearby atoms
<LI>
maxexchtot = maxexch * (maxperatom + maxsneigh + 3*maxbondper +
4*maxangleper + 5*maxdihedper + 5*maximproper) = total data volume for
all exchanged atoms
<LI>
maxrestot = maxown * (maxperatom - 3 + 3*maxbondper + 4*maxangleper +
5*maxdihedper + 5*maximproper)+1 = total data volume for all buffered
restart atoms
<LI>
maxsendspec = 2 * maxsneigh * maxown total data volume for sending
special requests
<LI>
maxrecvspec = maxsneigh + 1 total data volume for receiving a list of
specials
</UL>
<HR>
<H3>
<A NAME="_cch3_930764951">Arrays (real): </A></H3>
<UL>
<LI>
anglecoeff(2,maxangletype) = angle coeffs for each angle type
<LI>
bondcoeff(5,maxbondtype) = bond coeffs for each bond type
<LI>
boundhi(maxswap) = hi slab boundary on atom positions for each swap
send
<LI>
boundlo(maxswap) = lo slab boundary on atom positions for each swap
send
<LI>
buf1(maxexchtot) = comm buffer for sending exchange atoms
<LI>
buf2(2*maxexchtot) = comm buffer for 2 recv of exchange atoms
<LI>
buf3(3*maxsendone) = comm buffer for sending one set of swap atom
positions
<LI>
buf4(8*maxown) = comm buffer for output
<LI>
buf5(maxrestot) = comm buffer for restart atoms
<LI>
buf6(maxsendone) = comm buffer for sending one set of swap charges
<LI>
cutforcesq(maxtype,maxtype) = force cutoff squared for atom pair
(LJ/Coul)
<LI>
cutljsq(maxtype,maxtype) = LJ cutoff squared for atom pairs
<LI>
cutljinner(maxtype,maxtype) = inner LJ cutoff for switched LJ
<LI>
cutljinnersq(maxtype,maxtype) = inner LJ cutoff squared for switched LJ
<LI>
cutneighsq(maxtype,maxtype) = neigh cutoff squared for atom pair
(LJ/Coul + skin)
<LI>
diagparams(6,maxdiag) = parameters to pass into a diagnostic routine
<LI>
dihedcoeff(3,maxdihedtype) = dihedral coeffs for each dihedral type
<LI>
f(3,maxown) = forces on own atoms
<LI>
fixcoeff(8,maxfix) = constraint coeffs for each constraint
<LI>
fixstore(5*maxfix) = accumulated quantities for each constraint
<LI>
improcoeff(2,maximprotype) = improper coeffs for each improper type
<LI>
lj12345(maxtype,maxtype) = pre-computed LJ coeffs for use in energy and
force
<LI>
ljsw01234(maxtype,maxtype) = pre-computed switched LJ coeffs for eng
and force
<LI>
mass(maxtype) = mass of each atom type
<LI>
noncoeff1234(maxtype,maxtype) = nonbond coeffs input for atom pairs
<LI>
offset(maxtype,maxtype) = LJ potential offsets at cutoff for energy
calc
<LI>
q(maxatom) = charge of own and nearby atoms (electron units)
<LI>
v(3,maxown) = velocity of owned atoms
<LI>
x(3,maxatom) = positions of own and nearby atoms
<LI>
xhold(3,maxown) = positions of own atoms at last reneighboring
</UL>
<HR>
<H3>
<A NAME="_cch3_930764957">Arrays (integer): </A></H3>
<UL>
<LI>
angleatom123(maxangleper,maxown) = angle atoms for angles of owned
atoms
<LI>
anglelist(4,maxangle) = atoms and type of each angle to compute locally
<LI>
angletype(maxangleper,maxown) = angle type for angles of owned atoms
<LI>
bin(maxatom) = linked list pointers from one atom to next in bin
<LI>
binpnt(maxbin) = pointer to 1st atom in each bin
<LI>
bondatom12(maxbondper,maxown) = bond atoms for bonds of owned atoms
<LI>
bondlist(3,maxbond) = atoms and type of each bond to compute locally
<LI>
bondtype(maxbondper,maxown) = bond type for bonds of owned atoms
<LI>
bondtypeflag(maxbondtype) = flag for whether bond coeffs are set
<LI>
diagfileflag(maxdiag) = whether a file has been specified for a diag
routine
<LI>
diagfreq(maxdiag) = call a diagnostic routine every this many steps
<LI>
diagnparams(maxdiag) = # of parameters specified for a diagnostic
routine
<LI>
diagstyle(maxdiag) = whether a diagnostic has been set 0/1
<LI>
dihedatom1234(maxdihedper,maxown) = dihed atoms for diheds of owned
atoms
<LI>
dihedlist(5,maxdihed) = atoms and type of each dihedral to compute
locally
<LI>
dihedtype(maxdihedper,maxown) = dihed type for diheds of owned atoms
<LI>
fix(maxown) = constraint assignments for each owned atom
<LI>
fixflag(3,maxfix) = 0/1 flags for various fix styles
<LI>
fixptr(maxfix) = how many values are accumulated for each constraint
<LI>
fixstyle(maxfix) = style of each constraint
<LI>
ibuf1(maxsendone) = comm buffer for sending one set of swap atom tags
<LI>
ibuf2(maxsendone) = comm buffer for sending one set of swap atom types
<LI>
ibuf3(maxspec) = comm buffer for sending special requests
<LI>
ibuf4(maxspec) = comm buffer for receiving special lists
<LI>
improatom1234(maximproper,maxown) = impro atoms for impros of owned
atoms
<LI>
improlist(5,maximpro) = atoms and type of each improper to compute
locally
<LI>
improtype(maximproper,maxown) = impro type for impros of owned atoms
<LI>
list(maxown) = linked list of local atoms (last one -&gt; maxown+1)
<LI>
localptr(0:maxtotal) = ptr from global atom to local array (0 if don't
have)
<LI>
molecule(maxown) = molecule id # each owned atom is in
<LI>
nlist(maxown*maxneigh+maxneigh) = neighbor lists of own atoms
<LI>
nliststart(maxown) = pointer to where neighbor list for this atom
starts
<LI>
nliststop(maxown) = pointer to where neighbor list for this atom stops
<LI>
nontypeflag(maxtype,maxtype) = flag for whether nonbond coeffs are set
<LI>
nrlist(maxswap+1) = prt to where received other atoms start for each
swap
<LI>
nslist(maxswap+1) = pointer to where swap list starts for each swap
<LI>
numangle(maxown) = # of angles of each owned atom
<LI>
numbond(maxown) = # of 1st neighbors bonded to each owned atom
<LI>
num2bond(maxown) = # of 2nd neighbors for each owned atom
<LI>
num3bond(maxown) = # of 3rd neighbors for each owned atom
<LI>
numdihed(maxown) = # of dihedrals of each owned atom
<LI>
numimpro(maxown) = # of impropers of each owned atom
<LI>
rpart(maxswap) = node # of who to recv from for each swap
<LI>
slist(maxsend) = send list of atoms to send out in all swaps
<LI>
spart(maxswap) = node # of who to send to for each swap
<LI>
specbond(maxsneigh,maxown) = special bond neighbors of each owned atom
<LI>
tag(maxatom) = global id # of own and nearby atoms
<LI>
true(maxown) = which periodic box atom is truly in for all 3 dims
<LI>
type(maxatom) = type # of own and nearby atoms
<LI>
typecheck(maxtype) = consistency check for all existing atom types
<LI>
typechecktmp(maxtype) = summing array for atom type consistency check
<LI>
velflag(maxown) = whether velocity for each atom has been created
</UL>
<HR>
<H3>
<A NAME="_cch3_930764964">Variables (real): </A></H3>
<UL>
<LI>
binsize[xyz] = size of global neighbor bins in each dimension
<LI>
boltz = Boltzmann factor
<LI>
border(2,3) = lo/hi boundaries of my sub-box in each dimension
<LI>
coulpre = Coulombic force prefactor
<LI>
createregion(6) = bounding box for atoms to create temperature for
<LI>
createvec(3) = initial velocity for create temp atoms
<LI>
cutcoul = input force cutoff for Coulombic interactions
<LI>
cutcoulsq = Coul cutoff squared for all atom pairs
<LI>
cutforce = max force cutoff for all atom pairs (LJ/Coul)
<LI>
cutlj = input global (default) LJ cutoff for all atom pairs
<LI>
cutljinterior = global inner LJ cutoff for switched LJ
<LI>
cutneigh = max neighbor cutoff for all atom pairs (LJ/Coul + skin)
<LI>
dielectric = dielectric constant
<LI>
dt = timestep
<LI>
dtfactor = timestep conversion factor from input to program units
<LI>
dthalf = timestep / 2
<LI>
efactor = energy conversion factor from Coulombic to Kcals
<LI>
e_angle = energy in angles
<LI>
e_bond = energy in bonds
<LI>
e_coul = energy in nonbond Coulombic
<LI>
e_dihedral = energy in dihedrals
<LI>
e_improper = energy in impropers
<LI>
e_total = total energy
<LI>
e_vdwl = energy in nonbond LJ
<LI>
fixregion(6) = bounding box for atoms to assign to a constraint
<LI>
skin = distance between force and neighbor cutoffs
<LI>
special(3) = weight factors for special neighbors
<LI>
triggersq = squared distance to trigger neighbor list rebuild
<LI>
two16 = 2 ^ (1/6) constant for use in FENE bond potentials
<LI>
t_create = requested initialization temp
<LI>
t_current = current temp returned from temp routine
<LI>
t_nph = default temp for constant NPH
<LI>
t_start = target temp at beginning of run
<LI>
t_stop = target temp at end of run
<LI>
t_window = control temp within this window
<LI>
time_angle = angle time
<LI>
time_bond = bond time
<LI>
time_comm = communication time
<LI>
time_current = current time
<LI>
time_dihedral = dihedral time
<LI>
time_exch = exchange time
<LI>
time_improper = improper time
<LI>
time_io = i/o time
<LI>
time_loop = time for integration loop
<LI>
time_neigh1 = neighboring time in nonbond
<LI>
time_neigh2 = neighboring time in bonds
<LI>
time_nonbond = nonbond force time
<LI>
time_other = other miscellaneous time
<LI>
time_total = total run time of entire simulation
<LI>
x[yz]mc = box size minus force cutoff for PBC checks
<LI>
x[yz]ms box size minus neighbor list cutoff for PBC checks
<LI>
x[yz]boundlo = lower global box boundary in each dimension
<LI>
x[yz]boundhi = upper global box boundary in each dimension
<LI>
x[yz]prd = global box size in each dimension
</UL>
<HR>
<H3>
<A NAME="_cch3_930764969">Variables (integer): </A></H3>
<UL>
<LI>
atompnt = pointer to 1st atom in my list
<LI>
bondstyle = style of bond computation
<LI>
boxflag = flag if box has been remapped (non-PBC)
<LI>
coulstyle = style of Coulomb interaction
<LI>
creategroup = kind of atom group to create temp for
<LI>
createstyle = style of temp creation
<LI>
createtypehi = upper range of atom types to create temp for
<LI>
createtypelo = lower range of atom types to create temp for
<LI>
dumpfileflag = has dump file been opened or not (1/0)
<LI>
dumpflag = dump atoms to file every this many steps (0 = never)
<LI>
dumpforcefileflag = has dump force file been opened or not (1/0)
<LI>
dumpforceflag = dump forces to file every this many steps (0 = never)
<LI>
dumpvelfileflag = has dump velocity file been opened or not (1/0)
<LI>
dumpvelflag = dump vels to file every this many steps (0 = never)
<LI>
fixatom = assign atom/molecule with this tag to a constraint
<LI>
fixgroup = kind of atom group to assign to a constraint
<LI>
fixnum = total # of accumulated values for all constraints
<LI>
fixtype = assign group of atoms of this type to a constraint
<LI>
fixwhich = which constraint a atom group is to be assigned to
<LI>
freepnt = pointer to 1st free space in list (last one -&gt; 0)
<LI>
idimension = dimension of problem (2-d or 3-d)
<LI>
iseed = RNG seed for generating initial velocities
<LI>
itime = current timestep loop counter in integrator
<LI>
iversion = version number of restart files (for backward compat)
<LI>
max_angle = most angles I ever have to compute
<LI>
max_angleper = most angles ever attached to any atom
<LI>
max_bond = most bonds I ever have to compute
<LI>
max_bondper = most bonds ever attached to any atom
<LI>
max_dihed = most diheds I ever have to compute
<LI>
max_dihedper = most diheds ever attached to any atom
<LI>
max_exch = most atoms ever leaving my box (in one dimension)
<LI>
max_impro = most impros I ever have to compute
<LI>
max_improper = most impros ever attached to any atom
<LI>
max_nlocal = most atoms I ever owned
<LI>
max_neigh = most neighbors ever stored in neighbor list
<LI>
max_nother = most nearby atoms I ever stored
<LI>
max_slist = biggest size swap list ever reached
<LI>
max_swap = most atoms ever sent in one swap
<LI>
mbin[xyz] = # of bins in my box with nearby atoms included
<LI>
mbin[xyz]lo = global bin indices (offset) at corner of extended box
<LI>
me(3) = which box I am (0 - pgrid-1) in each dimension
<LI>
mixflag = whether mixing style has been set or not
<LI>
mixstyle = style of mixing for nonbond coeffs (arith,geom,sixth)
<LI>
mpart(2,3)= node # of neighbor processor in each dimension
<LI>
nanglelocal = local # of angless to compute
<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
<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>
c4science · Help