Crib File

Return to top-level of LAMMPS documentation.

This file contains one-line descriptions of the key variables and parameters used in LAMMPS. The variables are listed by their data type:

• Parameters

• Arrays (real)

• Arrays (integer)

• Variables (real)

• Variables (integer)

• Variables (character)

Note: this file is somewhat out-of-date for LAMMPS 99.

Parameters:

• maxown = max # of local owned atoms

• maxother = max # of local nearby atoms

• maxtotal = max # of total atoms in simulation

• maxtype = max # of atom types

• maxbond = max # of bonds to compute on one processor

• maxangle = max # of angles to compute on one processor

• maxdihed = max # of dihedrals to compute on one processor

• maximpro = max # of impropers to compute on one processor

• maxbondper = max # of bonds of one atom

• maxangleper = max # of angles of one atom

• maxdihedper = max # of dihedrals of one atom

• maximproper = max # of impropers of one atom

• maxbondtype = max # of bond types

• maxangletype = max # of angle types

• maxdihedtype = max # of dihedral types

• maximprotype = max # of improper types

• maxexch = max # of atoms in exchange buffer

• maxsend = max # of atoms to send to all neighbors in all swaps

• maxsendone = max # of atoms to send in one swap

• maxswap = max # of swaps to do at each timestep

• maxneigh = max # of neighbors per owned atom

• maxsneigh = max # of special neighbors of one atom

• maxbin = max # of local neighbor bins

• maxfix = max # of defined constraints + 1

• maxdiag = max # of diagnostic routines

• maxgrid = max size of PPPM grid with ghosts on one processor

• maxfft = max size of PPPM FFT grid on one processor

• maxperatom = max # of data items stored/comm/output per atom

• maxatom = maxown + maxother = total # of own and nearby atoms

• maxexchtot = maxexch * (maxperatom + maxsneigh + 3*maxbondper + 4*maxangleper + 5*maxdihedper + 5*maximproper) = total data volume for all exchanged atoms

• maxrestot = maxown * (maxperatom - 3 + 3*maxbondper + 4*maxangleper + 5*maxdihedper + 5*maximproper)+1 = total data volume for all buffered restart atoms

• maxsendspec = 2 * maxsneigh * maxown total data volume for sending special requests

• maxrecvspec = maxsneigh + 1 total data volume for receiving a list of specials

Arrays (real):

• anglecoeff(2,maxangletype) = angle coeffs for each angle type

• bondcoeff(5,maxbondtype) = bond coeffs for each bond type

• boundhi(maxswap) = hi slab boundary on atom positions for each swap send

• boundlo(maxswap) = lo slab boundary on atom positions for each swap send

• buf1(maxexchtot) = comm buffer for sending exchange atoms

• buf2(2*maxexchtot) = comm buffer for 2 recv of exchange atoms

• buf3(3*maxsendone) = comm buffer for sending one set of swap atom positions

• buf4(8*maxown) = comm buffer for output

• buf5(maxrestot) = comm buffer for restart atoms

• buf6(maxsendone) = comm buffer for sending one set of swap charges

• cutforcesq(maxtype,maxtype) = force cutoff squared for atom pair (LJ/Coul)

• cutljsq(maxtype,maxtype) = LJ cutoff squared for atom pairs

• cutljinner(maxtype,maxtype) = inner LJ cutoff for switched LJ

• cutljinnersq(maxtype,maxtype) = inner LJ cutoff squared for switched LJ

• cutneighsq(maxtype,maxtype) = neigh cutoff squared for atom pair (LJ/Coul + skin)

• diagparams(6,maxdiag) = parameters to pass into a diagnostic routine

• dihedcoeff(3,maxdihedtype) = dihedral coeffs for each dihedral type

• f(3,maxown) = forces on own atoms

• fixcoeff(8,maxfix) = constraint coeffs for each constraint

• fixstore(5*maxfix) = accumulated quantities for each constraint

• improcoeff(2,maximprotype) = improper coeffs for each improper type

• lj12345(maxtype,maxtype) = pre-computed LJ coeffs for use in energy and force

• ljsw01234(maxtype,maxtype) = pre-computed switched LJ coeffs for eng and force

• mass(maxtype) = mass of each atom type

• noncoeff1234(maxtype,maxtype) = nonbond coeffs input for atom pairs

• offset(maxtype,maxtype) = LJ potential offsets at cutoff for energy calc

• q(maxatom) = charge of own and nearby atoms (electron units)

• v(3,maxown) = velocity of owned atoms

• x(3,maxatom) = positions of own and nearby atoms

• xhold(3,maxown) = positions of own atoms at last reneighboring

Arrays (integer):

• angleatom123(maxangleper,maxown) = angle atoms for angles of owned atoms

• anglelist(4,maxangle) = atoms and type of each angle to compute locally

• angletype(maxangleper,maxown) = angle type for angles of owned atoms

• bin(maxatom) = linked list pointers from one atom to next in bin

• binpnt(maxbin) = pointer to 1st atom in each bin

• bondatom12(maxbondper,maxown) = bond atoms for bonds of owned atoms

• bondlist(3,maxbond) = atoms and type of each bond to compute locally

• bondtype(maxbondper,maxown) = bond type for bonds of owned atoms

• bondtypeflag(maxbondtype) = flag for whether bond coeffs are set

• diagfileflag(maxdiag) = whether a file has been specified for a diag routine

• diagfreq(maxdiag) = call a diagnostic routine every this many steps

• diagnparams(maxdiag) = # of parameters specified for a diagnostic routine

• diagstyle(maxdiag) = whether a diagnostic has been set 0/1

• dihedatom1234(maxdihedper,maxown) = dihed atoms for diheds of owned atoms

• dihedlist(5,maxdihed) = atoms and type of each dihedral to compute locally

• dihedtype(maxdihedper,maxown) = dihed type for diheds of owned atoms

• fix(maxown) = constraint assignments for each owned atom

• fixflag(3,maxfix) = 0/1 flags for various fix styles

• fixptr(maxfix) = how many values are accumulated for each constraint

• fixstyle(maxfix) = style of each constraint

• ibuf1(maxsendone) = comm buffer for sending one set of swap atom tags

• ibuf2(maxsendone) = comm buffer for sending one set of swap atom types

• ibuf3(maxspec) = comm buffer for sending special requests

• ibuf4(maxspec) = comm buffer for receiving special lists

• improatom1234(maximproper,maxown) = impro atoms for impros of owned atoms

• improlist(5,maximpro) = atoms and type of each improper to compute locally

• improtype(maximproper,maxown) = impro type for impros of owned atoms

• list(maxown) = linked list of local atoms (last one -> maxown+1)

• localptr(0:maxtotal) = ptr from global atom to local array (0 if don't have)

• molecule(maxown) = molecule id # each owned atom is in

• nlist(maxown*maxneigh+maxneigh) = neighbor lists of own atoms

• nliststart(maxown) = pointer to where neighbor list for this atom starts

• nliststop(maxown) = pointer to where neighbor list for this atom stops

• nontypeflag(maxtype,maxtype) = flag for whether nonbond coeffs are set

• nrlist(maxswap+1) = prt to where received other atoms start for each swap

• nslist(maxswap+1) = pointer to where swap list starts for each swap

• numangle(maxown) = # of angles of each owned atom

• numbond(maxown) = # of 1st neighbors bonded to each owned atom

• num2bond(maxown) = # of 2nd neighbors for each owned atom

• num3bond(maxown) = # of 3rd neighbors for each owned atom

• numdihed(maxown) = # of dihedrals of each owned atom

• numimpro(maxown) = # of impropers of each owned atom

• rpart(maxswap) = node # of who to recv from for each swap

• slist(maxsend) = send list of atoms to send out in all swaps

• spart(maxswap) = node # of who to send to for each swap

• specbond(maxsneigh,maxown) = special bond neighbors of each owned atom

• tag(maxatom) = global id # of own and nearby atoms

• true(maxown) = which periodic box atom is truly in for all 3 dims

• type(maxatom) = type # of own and nearby atoms

• typecheck(maxtype) = consistency check for all existing atom types

• typechecktmp(maxtype) = summing array for atom type consistency check

• velflag(maxown) = whether velocity for each atom has been created

Variables (real):

• binsize[xyz] = size of global neighbor bins in each dimension

• boltz = Boltzmann factor

• border(2,3) = lo/hi boundaries of my sub-box in each dimension

• coulpre = Coulombic force prefactor

• createregion(6) = bounding box for atoms to create temperature for

• createvec(3) = initial velocity for create temp atoms

• cutcoul = input force cutoff for Coulombic interactions

• cutcoulsq = Coul cutoff squared for all atom pairs

• cutforce = max force cutoff for all atom pairs (LJ/Coul)

• cutlj = input global (default) LJ cutoff for all atom pairs

• cutljinterior = global inner LJ cutoff for switched LJ

• cutneigh = max neighbor cutoff for all atom pairs (LJ/Coul + skin)

• dielectric = dielectric constant

• dt = timestep

• dtfactor = timestep conversion factor from input to program units

• dthalf = timestep / 2

• efactor = energy conversion factor from Coulombic to Kcals

• e_angle = energy in angles

• e_bond = energy in bonds

• e_coul = energy in nonbond Coulombic

• e_dihedral = energy in dihedrals

• e_improper = energy in impropers

• e_total = total energy

• e_vdwl = energy in nonbond LJ

• fixregion(6) = bounding box for atoms to assign to a constraint

• skin = distance between force and neighbor cutoffs

• special(3) = weight factors for special neighbors

• triggersq = squared distance to trigger neighbor list rebuild

• two16 = 2 ^ (1/6) constant for use in FENE bond potentials

• t_create = requested initialization temp

• t_current = current temp returned from temp routine

• t_nph = default temp for constant NPH

• t_start = target temp at beginning of run

• t_stop = target temp at end of run

• t_window = control temp within this window

• time_angle = angle time

• time_bond = bond time

• time_comm = communication time

• time_current = current time

• time_dihedral = dihedral time

• time_exch = exchange time

• time_improper = improper time

• time_io = i/o time

• time_loop = time for integration loop

• time_neigh1 = neighboring time in nonbond

• time_neigh2 = neighboring time in bonds

• time_nonbond = nonbond force time

• time_other = other miscellaneous time

• time_total = total run time of entire simulation

• x[yz]mc = box size minus force cutoff for PBC checks

• x[yz]ms box size minus neighbor list cutoff for PBC checks

• x[yz]boundlo = lower global box boundary in each dimension

• x[yz]boundhi = upper global box boundary in each dimension

• x[yz]prd = global box size in each dimension

Variables (integer):

• atompnt = pointer to 1st atom in my list

• bondstyle = style of bond computation

• boxflag = flag if box has been remapped (non-PBC)

• coulstyle = style of Coulomb interaction

• creategroup = kind of atom group to create temp for

• createstyle = style of temp creation

• createtypehi = upper range of atom types to create temp for

• createtypelo = lower range of atom types to create temp for

• dumpfileflag = has dump file been opened or not (1/0)

• dumpflag = dump atoms to file every this many steps (0 = never)

• dumpforcefileflag = has dump force file been opened or not (1/0)

• dumpforceflag = dump forces to file every this many steps (0 = never)

• dumpvelfileflag = has dump velocity file been opened or not (1/0)

• dumpvelflag = dump vels to file every this many steps (0 = never)

• fixatom = assign atom/molecule with this tag to a constraint

• fixgroup = kind of atom group to assign to a constraint

• fixnum = total # of accumulated values for all constraints

• fixtype = assign group of atoms of this type to a constraint

• fixwhich = which constraint a atom group is to be assigned to

• freepnt = pointer to 1st free space in list (last one -> 0)

• idimension = dimension of problem (2-d or 3-d)

• iseed = RNG seed for generating initial velocities

• itime = current timestep loop counter in integrator

• iversion = version number of restart files (for backward compat)

• max_angle = most angles I ever have to compute

• max_angleper = most angles ever attached to any atom

• max_bond = most bonds I ever have to compute

• max_bondper = most bonds ever attached to any atom

• max_dihed = most diheds I ever have to compute

• max_dihedper = most diheds ever attached to any atom

• max_exch = most atoms ever leaving my box (in one dimension)

• max_impro = most impros I ever have to compute

• max_improper = most impros ever attached to any atom

• max_nlocal = most atoms I ever owned

• max_neigh = most neighbors ever stored in neighbor list

• max_nother = most nearby atoms I ever stored

• max_slist = biggest size swap list ever reached

• max_swap = most atoms ever sent in one swap

• mbin[xyz] = # of bins in my box with nearby atoms included

• mbin[xyz]lo = global bin indices (offset) at corner of extended box

• me(3) = which box I am (0 - pgrid-1) in each dimension

• mixflag = whether mixing style has been set or not

• mixstyle = style of mixing for nonbond coeffs (arith,geom,sixth)

• mpart(2,3)= node # of neighbor processor in each dimension

• nanglelocal = local # of angless to compute

• nangles = total # of angles

• nangletypes = total # of angle types

• natoms = total # of atoms

• nbin[xyz] # of global neighbor bins in each dimension

• nbondlocal = local # of bonds to compute

• nbonds = total # of bonds

• nbondtypes = total # of bond types

• ndanger = # of neighbor rebuilds triggered by 1st check

• ndiags = # of user-specified diagnostic routines

• ndihedlocal = local # of dihedrals to compute

• ndihedrals = total # of diheds

• ndihedtypes = total # of dihedral types

• need(3) how many processors I need neighbors from in each dim

• neighago = how many timesteps ago neighboring was done

• neighdelay = delay neighbor list build for this many steps

• neighfreq = build neighbor list every this many steps

• neighstyle = neighboring by (0) N^2 or (1) binning method

• neightop = last used position in neighbor list (nlist)

• neightrigger = always (0) do neighbor list or trigger (1) on atom move

• newton = flag for kind of Newton's 3rd law used (0,1,2,3)

• newton_bond = Newton's 3rd is not used (0) or (1) used for bonds

• newton_nonbond = Newton's 3rd is not used (0) or (1) used for nonbonds

• nfixes = # of constraints

• nimprolocal = local # of impropers to compute

• nimpropers = total # of impros

• nimprotypes = total # of improper types

• nlocal = # of atoms I currently own

• nother = # of nearby atoms I currently store

• node = my node #

• nonstyle = style on nonbond computation

• nprocs = total # of processors

• nsteps = # of timesteps to simulate

• nswap = # of swaps at each timestep

• ntimestep = current global timestep

• ntypes = total # of atom types

• numneigh = number of times reneighboring is done

• offsetflag = whether to include energy offset in LJ energy calc

• peratom = # of values/atom not including bond info

• perflagx[yz] = flag for periodic (0) or non-periodic (1) BC

• pgrid(3) = # of processors in each dimension

• readflag = whether atom input file has been read or not (1/0)

• restartfileflag = which restart file to open next (0/1)

• restartflag = write restart file every this many steps (0=never)

• t_every = rescale/replace temp every this many steps

• tempflag = constant temperature style flag

• thermoflag = print thermo info every this many steps (0 = never)

• thermostyle = style of thermo output (0 = full, 1 = reduced)

• trueflag = whether to dump remapped or true atom positions

• units = flag for real vs reduced LJ units

Variables (character):

• datafile = file to read atom and connectivity info from

• diagfile(maxdiag) = files to print user-specified diagnostics to

• diagname(maxdiag) = name of a user-specified diagnostic routine

• dumpfile = file to dump atom info to

• dumpforcefile = file to dump force info to

• dumpvelfile = file to dump velocity info to

• restart_in = file to read restart info from

• restart_out[12] = files to write restart info to