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Note: this file is somewhat out-of-date for LAMMPS 99.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