id value = yes or no - map value = array or hash - first value = group-ID = group whose atoms will appear first in internal atom lists - sort values = Nfreq binsize - Nfreq = sort atoms spatially every this many time steps - binsize = bin size for spatial sorting (distance units) +map value = array or hash +first value = group-ID = group whose atoms will appear first in internal atom lists +sort values = Nfreq binsize + Nfreq = sort atoms spatially every this many time steps + binsize = bin size for spatial sorting (distance units)
args = none for any style except body and hybrid - body args = bstyle bstyle-args - bstyle = style of body particles - bstyle-args = additional arguments specific to the bstyle - see the body doc page for details - template args = template-ID - template-ID = ID of molecule template specified in a separate molecule command - hybrid args = list of one or more sub-styles, each with their args +body args = bstyle bstyle-args + bstyle = style of body particles + bstyle-args = additional arguments specific to the bstyle + see the body doc page for details +template args = template-ID + template-ID = ID of molecule template specified in a separate molecule command +hybrid args = list of one or more sub-styles, each with their args
x args = uniform or Px-1 numbers between 0 and 1 - uniform = evenly spaced cuts between processors in x dimension - numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension - x can be specified together with y or z - y args = uniform or Py-1 numbers between 0 and 1 - uniform = evenly spaced cuts between processors in y dimension - numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension - y can be specified together with x or z - z args = uniform or Pz-1 numbers between 0 and 1 - uniform = evenly spaced cuts between processors in z dimension - numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension - z can be specified together with x or y - shift args = dimstr Niter stopthresh - dimstr = sequence of letters containing "x" or "y" or "z", each not more than once - Niter = # of times to iterate within each dimension of dimstr sequence - stopthresh = stop balancing when this imbalance threshhold is reached - rcb args = none + uniform = evenly spaced cuts between processors in x dimension + numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension + x can be specified together with y or z +y args = uniform or Py-1 numbers between 0 and 1 + uniform = evenly spaced cuts between processors in y dimension + numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension + y can be specified together with x or z +z args = uniform or Pz-1 numbers between 0 and 1 + uniform = evenly spaced cuts between processors in z dimension + numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension + z can be specified together with x or y +shift args = dimstr Niter stopthresh + dimstr = sequence of letters containing "x" or "y" or "z", each not more than once + Niter = # of times to iterate within each dimension of dimstr sequence + stopthresh = stop balancing when this imbalance threshhold is reached +rcb args = none
out value = filename - filename = write each processor's sub-domain to a file + filename = write each processor's sub-domain to a file
args = none for any style except hybrid - hybrid args = list of one or more styles +hybrid args = list of one or more styles
p is periodic - f is non-periodic and fixed - s is non-periodic and shrink-wrapped - m is non-periodic and shrink-wrapped with a minimum value +f is non-periodic and fixed +s is non-periodic and shrink-wrapped +m is non-periodic and shrink-wrapped with a minimum value
units value = lattice or box - lattice = distances are defined in lattice units - box = distances are defined in simulation box units + lattice = distances are defined in lattice units + box = distances are defined in simulation box units
mode value = single or multi = communicate atoms within a single or multiple distances - cutoff value = Rcut (distance units) = communicate atoms from this far away - group value = group-ID = only communicate atoms in the group - vel value = yes or no = do or do not communicate velocity info with ghost atoms +cutoff value = Rcut (distance units) = communicate atoms from this far away +group value = group-ID = only communicate atoms in the group +vel value = yes or no = do or do not communicate velocity info with ghost atoms
theta = tabulate angles - eng = tabulate angle energies +eng = tabulate angle energies
type = atom type of the body particle - integer = 1,2,3,etc = index of fields defined by body style +integer = 1,2,3,etc = index of fields defined by body style
dist = bond distance - eng = bond energy - force = bond force +eng = bond energy +force = bond force
region value = region-ID - region-ID = ID of region atoms must be in to be part of a chunk - nchunk value = once or every - once = only compute the number of chunks once - every = re-compute the number of chunks whenever invoked - limit values = 0 or Nc max or Nc exact - 0 = no limit on the number of chunks - Nc max = limit number of chunks to be <= Nc - Nc exact = set number of chunks to exactly Nc - ids value = once or nfreq or every - once = assign chunk IDs to atoms only once, they persist thereafter - nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq) - every = assign chunk IDs to atoms whenever invoked - compress value = yes or no - yes = compress chunk IDs to eliminate IDs with no atoms - no = do not compress chunk IDs even if some IDs have no atoms - discard value = yes or no or mixed - yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0 - no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID - mixed = keep or discard such atoms according to spatial binning rule - bound values = x/y/z lo hi - x/y/z = x or y or z to bound sptial bins in this dimension - lo = lower or coordinate value (distance units) - hi = upper or coordinate value (distance units) - units value = box or lattice or reduced + region-ID = ID of region atoms must be in to be part of a chunk +nchunk value = once or every + once = only compute the number of chunks once + every = re-compute the number of chunks whenever invoked +limit values = 0 or Nc max or Nc exact + 0 = no limit on the number of chunks + Nc max = limit number of chunks to be <= Nc + Nc exact = set number of chunks to exactly Nc +ids value = once or nfreq or every + once = assign chunk IDs to atoms only once, they persist thereafter + nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq) + every = assign chunk IDs to atoms whenever invoked +compress value = yes or no + yes = compress chunk IDs to eliminate IDs with no atoms + no = do not compress chunk IDs even if some IDs have no atoms +discard value = yes or no or mixed + yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0 + no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID + mixed = keep or discard such atoms according to spatial binning rule +bound values = x/y/z lo hi + x/y/z = x or y or z to bound sptial bins in this dimension + lo = lower or coordinate value (distance units) + hi = upper or coordinate value (distance units) +units value = box or lattice or reduced
pair args = pstyle pparam I J v_delta - pstyle = pair style name, e.g. lj/cut - pparam = parameter to perturb - I,J = type pair(s) to set parameter for - v_delta = variable with perturbation to apply (in the units of the parameter) - atom args = aparam I v_delta - aparam = parameter to perturb - I = type to set parameter for - v_delta = variable with perturbation to apply (in the units of the parameter) + pstyle = pair style name, e.g. lj/cut + pparam = parameter to perturb + I,J = type pair(s) to set parameter for + v_delta = variable with perturbation to apply (in the units of the parameter) +atom args = aparam I v_delta + aparam = parameter to perturb + I = type to set parameter for + v_delta = variable with perturbation to apply (in the units of the parameter)
tail value = no or yes - no = ignore tail correction to pair energies (usually small in fep) - yes = include tail correction to pair energies - volume value = no or yes - no = ignore volume changes (e.g. in NVE or NVT trajectories) - yes = include volume changes (e.g. in NpT trajectories) + no = ignore tail correction to pair energies (usually small in fep) + yes = include tail correction to pair energies +volume value = no or yes + no = ignore volume changes (e.g. in NVE or NVT trajectories) + yes = include volume changes (e.g. in NpT trajectories)
pair value = yes or no - kspace value = yes or no - boundary value = yes or no +kspace value = yes or no +boundary value = yes or no
extra value = N - N = # of extra degrees of freedom to subtract - dynamic value = yes or no - yes/no = do or do not recompute the number of atoms contributing to the temperature - thermo value = yes or no - yes/no = do or do not add contributions from fixes to the potential energy + N = # of extra degrees of freedom to subtract +dynamic value = yes or no + yes/no = do or do not recompute the number of atoms contributing to the temperature +thermo value = yes or no + yes/no = do or do not add contributions from fixes to the potential energy
dist = pairwise distance - eng = pairwise energy - force = pairwise force - fx,*fy*,*fz* = components of pairwise force - pN = pair style specific quantities for allowed N values +eng = pairwise energy +force = pairwise force +fx,*fy*,*fz* = components of pairwise force +pN = pair style specific quantities for allowed N values
possible attributes = id, mol, proc, type, mass,
- x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, mu,
- radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz,
- shapex,shapey, shapez,
- quatw, quati, quatj, quatk, tqx, tqy, tqz,
- end1x, end1y, end1z, end2x, end2y, end2z,
- corner1x, corner1y, corner1z,
- corner2x, corner2y, corner2z,
- corner3x, corner3y, corner3z,
- nbonds,
- vfrac, s0,
- spin, eradius, ervel, erforce,
- rho, drho, e, de, cv,
- i_name, d_name
+ x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
+ q, mux, muy, muz, mu,
+ radius, diameter, omegax, omegay, omegaz,
+ angmomx, angmomy, angmomz,
+ shapex,shapey, shapez,
+ quatw, quati, quatj, quatk, tqx, tqy, tqz,
+ end1x, end1y, end1z, end2x, end2y, end2z,
+ corner1x, corner1y, corner1z,
+ corner2x, corner2y, corner2z,
+ corner3x, corner3y, corner3z,
+ nbonds,
+ vfrac, s0,
+ spin, eradius, ervel, erforce,
+ rho, drho, e, de, cv,
+ i_name, d_name
id = atom ID
- mol = molecule ID
- proc = ID of processor that owns atom
- type = atom type
- mass = atom mass
- x,y,z = unscaled atom coordinates
- xs,ys,zs = scaled atom coordinates
- xu,yu,zu = unwrapped atom coordinates
- ix,iy,iz = box image that the atom is in
- vx,vy,vz = atom velocities
- fx,fy,fz = forces on atoms
- q = atom charge
- mux,muy,muz = orientation of dipole moment of atom
- mu = magnitude of dipole moment of atom
- radius,diameter = radius,diameter of spherical particle
- omegax,omegay,omegaz = angular velocity of spherical particle
- angmomx,angmomy,angmomz = angular momentum of aspherical particle
- shapex,shapey,shapez = 3 diameters of aspherical particle
- quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
- tqx,tqy,tqz = torque on finite-size particles
- end12x, end12y, end12z = end points of line segment
- corner123x, corner123y, corner123z = corner points of triangle
- nbonds = number of bonds assigned to an atom
+mol = molecule ID
+proc = ID of processor that owns atom
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipole moment of atom
+mu = magnitude of dipole moment of atom
+radius,diameter = radius,diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+shapex,shapey,shapez = 3 diameters of aspherical particle
+quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
+tqx,tqy,tqz = torque on finite-size particles
+end12x, end12y, end12z = end points of line segment
+corner123x, corner123y, corner123z = corner points of triangle
+nbonds = number of bonds assigned to an atom
PERI package per-atom properties:
- vfrac = ???
- s0 = ???
+vfrac = ???
+s0 = ???
USER-EFF and USER-AWPMD package per-atom properties:
- spin = electron spin
- eradius = electron radius
- ervel = electron radial velocity
- erforce = electron radial force
+spin = electron spin
+eradius = electron radius
+ervel = electron radial velocity
+erforce = electron radial force
USER-SPH package per-atom properties:
- rho = ???
- drho = ???
- e = ???
- de = ???
- cv = ???
+rho = ???
+drho = ???
+e = ???
+de = ???
+cv = ???
fix property/atom per-atom properties: - i_name = custom integer vector with name - d_name = custom integer vector with name +i_name = custom integer vector with name +d_name = custom integer vector with name
attributes = count, id, coord1, coord2, coord3 - count = # of atoms in chunk - id = original chunk IDs before compression by compute chunk/atom - coord123 = coordinates for spatial bins calculated by compute chunk/atom + count = # of atoms in chunk + id = original chunk IDs before compression by compute chunk/atom + coord123 = coordinates for spatial bins calculated by compute chunk/atom
possible attributes = natom1 natom2 ntype1 ntype2
- patom1 patom2 ptype1 ptype2
- batom1 batom2 btype
- aatom1 aatom2 aatom3 atype
- datom1 datom2 datom3 dtype
- iatom1 iatom2 iatom3 itype
+ patom1 patom2 ptype1 ptype2
+ batom1 batom2 btype
+ aatom1 aatom2 aatom3 atype
+ datom1 datom2 datom3 dtype
+ iatom1 iatom2 iatom3 itype
natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
- ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
- patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
- ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
- batom1, batom2 = IDs of 2 atoms in each bond
- btype = bond type of each bond
- aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
- atype = angle type of each angle
- datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
- dtype = dihedral type of each dihedral
- iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
- itype = improper type of each improper
+ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
+patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
+ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
+batom1, batom2 = IDs of 2 atoms in each bond
+btype = bond type of each bond
+aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
+atype = angle type of each angle
+datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
+dtype = dihedral type of each dihedral
+iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
+itype = improper type of each improper
reduce arg = none - reduce/region arg = region-ID - region-ID = ID of region to use for choosing atoms +reduce/region arg = region-ID + region-ID = ID of region to use for choosing atoms
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
- c_ID = per-atom or local vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
- f_ID = per-atom or local vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
+c_ID = per-atom or local vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
+f_ID = per-atom or local vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
replace args = vec1 vec2 - vec1 = reduced value from this input vector will be replaced - vec2 = replace it with vec1[N] where N is index of max/min value from vec2 + vec1 = reduced value from this input vector will be replaced + vec2 = replace it with vec1[N] where N is index of max/min value from vec2
Kmax value = Maximum distance explored from reciprocal space origin - (inverse length units) - Zone values = z1 z2 z3 - z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all - reciprocal space will be meshed up to Kmax - dR_Ewald value = Thickness of Ewald sphere slice intercepting - reciprocal space (inverse length units) - c values = c1 c2 c3 - c1,c2,c3 = parameters to adjust the spacing of the reciprocal - lattice nodes in the h, k, and l directions respectively - manual = flag to use manual spacing of reciprocal lattice points - based on the values of the c parameters - echo = flag to provide extra output for debugging purposes + (inverse length units) +Zone values = z1 z2 z3 + z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all + reciprocal space will be meshed up to Kmax +dR_Ewald value = Thickness of Ewald sphere slice intercepting + reciprocal space (inverse length units) +c values = c1 c2 c3 + c1,c2,c3 = parameters to adjust the spacing of the reciprocal + lattice nodes in the h, k, and l directions respectively +manual = flag to use manual spacing of reciprocal lattice points + based on the values of the c parameters +echo = flag to provide extra output for debugging purposes
c_ID = global vector calculated by a compute with ID
- c_ID[I] = Ith column of global array calculated by a compute with ID
- f_ID = global vector calculated by a fix with ID
- f_ID[I] = Ith column of global array calculated by a fix with ID
+c_ID[I] = Ith column of global array calculated by a compute with ID
+f_ID = global vector calculated by a fix with ID
+f_ID[I] = Ith column of global array calculated by a fix with ID
diagonal value = 0 or 1 or 2 or 3 - 0 = all j1, j2, j <= twojmax, j2 <= j1 - 1 = subset satisfying j1 == j2 - 2 = subset satisfying j1 == j2 == j3 - 3 = subset satisfying j2 <= j1 <= j - rmin0 value = parameter in distance to angle conversion (distance units) - switchflag value = 0 or 1 - 0 = do not use switching function - 1 = use switching function + 0 = all j1, j2, j <= twojmax, j2 <= j1 + 1 = subset satisfying j1 == j2 + 2 = subset satisfying j1 == j2 == j3 + 3 = subset satisfying j2 <= j1 <= j +rmin0 value = parameter in distance to angle conversion (distance units) +switchflag value = 0 or 1 + 0 = do not use switching function + 1 = use switching function
bias value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - dof value = all or rotate - all = compute temperature of translational and rotational degrees of freedom - rotate = compute temperature of just rotational degrees of freedom + bias-ID = ID of a temperature compute that removes a velocity bias +dof value = all or rotate + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom
temp = temperature of each chunk
- kecom = kinetic energy of each chunk based on velocity of center of mass
- internal = internal kinetic energy of each chunk
+kecom = kinetic energy of each chunk based on velocity of center of mass
+internal = internal kinetic energy of each chunk
com value = yes or no - yes = subtract center-of-mass velocity from each chunk before calculating temperature - no = do not subtract center-of-mass velocity - bias value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - adof value = dof_per_atom - dof_per_atom = define this many degrees-of-freedom per atom - cdof value = dof_per_chunk - dof_per_chunk = define this many degrees-of-freedom per chunk + yes = subtract center-of-mass velocity from each chunk before calculating temperature + no = do not subtract center-of-mass velocity +bias value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias +adof value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom +cdof value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk
x arg = Nx - y arg = Ny - z arg = Nz - xy args = Nx Ny - yz args = Ny Nz - xz args = Nx Nz - xyz args = Nx Ny Nz - Nx,Ny,Nz = number of velocity bins in x,y,z dimensions +y arg = Ny +z arg = Nz +xy args = Nx Ny +yz args = Ny Nz +xz args = Nx Nz +xyz args = Nx Ny Nz + Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
bias value = bias-ID - bias-ID = ID of a temperature compute that removes a velocity bias - dof value = all or rotate - all = compute temperature of translational and rotational degrees of freedom - rotate = compute temperature of just rotational degrees of freedom + bias-ID = ID of a temperature compute that removes a velocity bias +dof value = all or rotate + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom
pair style args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is energy scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda - tail args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda - kspace args = atype v_name1 v_name2 - atype = atom type (see asterisk form below) - v_name1 = variable with name1 that is K-Space scale factor and function of lambda - v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is energy scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda +tail args = atype v_name1 v_name2 + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda +kspace args = atype v_name1 v_name2 + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is K-Space scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
only_group = no arg - occupation = no arg - surface arg = sgroup-ID - sgroup-ID = compute the dividing surface between group-ID and sgroup-ID - this keyword adds a third column to the compute output - radius arg = v_r - v_r = radius atom style variable for a poly-disperse Voronoi tessellation - edge_histo arg = maxedge - maxedge = maximum number of Voronoi cell edges to be accounted in the histogram - edge_threshold arg = minlength - minlength = minimum length for an edge to be counted - face_threshold arg = minarea - minarea = minimum area for a face to be counted +occupation = no arg +surface arg = sgroup-ID + sgroup-ID = compute the dividing surface between group-ID and sgroup-ID + this keyword adds a third column to the compute output +radius arg = v_r + v_r = radius atom style variable for a poly-disperse Voronoi tessellation +edge_histo arg = maxedge + maxedge = maximum number of Voronoi cell edges to be accounted in the histogram +edge_threshold arg = minlength + minlength = minimum length for an edge to be counted +face_threshold arg = minarea + minarea = minimum area for a face to be counted
2Theta values = Min2Theta Max2Theta - Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore - (radians or degrees) - c values = c1 c2 c3 - c1,c2,c3 = parameters to adjust the spacing of the reciprocal - lattice nodes in the h, k, and l directions respectively - LP value = switch to apply Lorentz-polarization factor - 0/1 = off/on - manual = flag to use manual spacing of reciprocal lattice points - based on the values of the c parameters - echo = flag to provide extra output for debugging purposes + Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore + (radians or degrees) +c values = c1 c2 c3 + c1,c2,c3 = parameters to adjust the spacing of the reciprocal + lattice nodes in the h, k, and l directions respectively +LP value = switch to apply Lorentz-polarization factor + 0/1 = off/on +manual = flag to use manual spacing of reciprocal lattice points + based on the values of the c parameters +echo = flag to provide extra output for debugging purposes
box args = none - region args = region-ID - region-ID = particles will only be created if contained in the region - single args = x y z - x,y,z = coordinates of a single particle (distance units) - random args = N seed region-ID - N = number of particles to create - seed = random # seed (positive integer) - region-ID = create atoms within this region, use NULL for entire simulation box +region args = region-ID + region-ID = particles will only be created if contained in the region +single args = x y z + x,y,z = coordinates of a single particle (distance units) +random args = N seed region-ID + N = number of particles to create + seed = random # seed (positive integer) + region-ID = create atoms within this region, use NULL for entire simulation box
mol value = template-ID seed - template-ID = ID of molecule template specified in a separate molecule command - seed = random # seed (positive integer) - basis values = M itype - M = which basis atom - itype = atom type (1-N) to assign to this basis atom - remap value = yes or no - var value = name = variable name to evaluate for test of atom creation - set values = dim vname - dim = x or y or z - name = name of variable to set with x,y,z atom position - rotate values = Rx Ry Rz theta - Rx,Ry,Rz = rotation vector for single molecule - theta = rotation angle for single molecule (degrees) - units value = lattice or box - lattice = the geometry is defined in lattice units - box = the geometry is defined in simulation box units + template-ID = ID of molecule template specified in a separate molecule command + seed = random # seed (positive integer) +basis values = M itype + M = which basis atom + itype = atom type (1-N) to assign to this basis atom +remap value = yes or no +var value = name = variable name to evaluate for test of atom creation +set values = dim vname + dim = x or y or z + name = name of variable to set with x,y,z atom position +rotate values = Rx Ry Rz theta + Rx,Ry,Rz = rotation vector for single molecule + theta = rotation angle for single molecule (degrees) +units value = lattice or box + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units
bond/types value = # of bond types - angle/types value = # of angle types - dihedral/types value = # of dihedral types - improper/types value = # of improper types - extra/bond/per/atom value = # of bonds per atom - extra/angle/per/atom value = # of angles per atom - extra/dihedral/per/atom value = # of dihedrals per atom - extra/improper/per/atom value = # of impropers per atom - extra/special/per/atom value = # of special neighbors per atom +angle/types value = # of angle types +dihedral/types value = # of dihedral types +improper/types value = # of improper types +extra/bond/per/atom value = # of bonds per atom +extra/angle/per/atom value = # of angles per atom +extra/dihedral/per/atom value = # of dihedrals per atom +extra/improper/per/atom value = # of impropers per atom +extra/special/per/atom value = # of special neighbors per atom
group args = group-ID - region args = region-ID - overlap args = cutoff group1-ID group2-ID - cutoff = delete one atom from pairs of atoms within the cutoff (distance units) - group1-ID = one atom in pair must be in this group - group2-ID = other atom in pair must be in this group - porosity args = region-ID fraction seed - region-ID = region within which to perform deletions - fraction = delete this fraction of atoms - seed = random number seed (positive integer) +region args = region-ID +overlap args = cutoff group1-ID group2-ID + cutoff = delete one atom from pairs of atoms within the cutoff (distance units) + group1-ID = one atom in pair must be in this group + group2-ID = other atom in pair must be in this group +porosity args = region-ID fraction seed + region-ID = region within which to perform deletions + fraction = delete this fraction of atoms + seed = random number seed (positive integer)
compress value = no or yes - bond value = no or yes - mol value = no or yes +bond value = no or yes +mol value = no or yes
multi arg = none - atom arg = an atom type or range of types (see below) - bond arg = a bond type or range of types (see below) - angle arg = an angle type or range of types (see below) - dihedral arg = a dihedral type or range of types (see below) - improper arg = an improper type or range of types (see below) - stats arg = none +atom arg = an atom type or range of types (see below) +bond arg = a bond type or range of types (see below) +angle arg = an angle type or range of types (see below) +dihedral arg = a dihedral type or range of types (see below) +improper arg = an improper type or range of types (see below) +stats arg = none
move args = delx dely delz - delx,dely,delz = distance to displace in each dimension (distance units) - ramp args = ddim dlo dhi dim clo chi - ddim = x or y or z - dlo,dhi = displacement distance between dlo and dhi (distance units) - dim = x or y or z - clo,chi = lower and upper bound of domain to displace (distance units) - random args = dx dy dz seed - dx,dy,dz = random displacement magnitude in each dimension (distance units) - seed = random # seed (positive integer) - rotate args = Px Py Pz Rx Ry Rz theta - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - theta = angle of rotation (degrees) + delx,dely,delz = distance to displace in each dimension (distance units) +ramp args = ddim dlo dhi dim clo chi + ddim = x or y or z + dlo,dhi = displacement distance between dlo and dhi (distance units) + dim = x or y or z + clo,chi = lower and upper bound of domain to displace (distance units) +random args = dx dy dz seed + dx,dy,dz = random displacement magnitude in each dimension (distance units) + seed = random # seed (positive integer) +rotate args = Px Py Pz Rx Ry Rz theta + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + theta = angle of rotation (degrees)
keyword = units - value = box or lattice + value = box or lattice
atom args = none - atom/mpiio args = none - cfg args = same as custom args, see below - cfg/mpiio args = same as custom args, see below - dcd args = none - xtc args = none - xyz args = none +atom/mpiio args = none +cfg args = same as custom args, see below +cfg/mpiio args = same as custom args, see below +dcd args = none +xtc args = none +xyz args = none
xyz/mpiio args = none @@ -171,53 +171,53 @@
local args = list of local attributes - possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N] - index = enumeration of local values - c_ID = local vector calculated by a compute with ID - c_ID[N] = Nth column of local array calculated by a compute with ID - f_ID = local vector calculated by a fix with ID - f_ID[N] = Nth column of local array calculated by a fix with ID + possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N] + index = enumeration of local values + c_ID = local vector calculated by a compute with ID + c_ID[N] = Nth column of local array calculated by a compute with ID + f_ID = local vector calculated by a fix with ID + f_ID[N] = Nth column of local array calculated by a fix with ID
custom or custom/mpiio args = list of atom attributes - possible attributes = id, mol, proc, procp1, type, element, mass, - x, y, z, xs, ys, zs, xu, yu, zu, - xsu, ysu, zsu, ix, iy, iz, - vx, vy, vz, fx, fy, fz, - q, mux, muy, muz, mu, - radius, diameter, omegax, omegay, omegaz, - angmomx, angmomy, angmomz, tqx, tqy, tqz, - c_ID, c_ID[N], f_ID, f_ID[N], v_name + possible attributes = id, mol, proc, procp1, type, element, mass, + x, y, z, xs, ys, zs, xu, yu, zu, + xsu, ysu, zsu, ix, iy, iz, + vx, vy, vz, fx, fy, fz, + q, mux, muy, muz, mu, + radius, diameter, omegax, omegay, omegaz, + angmomx, angmomy, angmomz, tqx, tqy, tqz, + c_ID, c_ID[N], f_ID, f_ID[N], v_name
id = atom ID - mol = molecule ID - proc = ID of processor that owns atom - procp1 = ID+1 of processor that owns atom - type = atom type - element = name of atom element, as defined by dump_modify command - mass = atom mass - x,y,z = unscaled atom coordinates - xs,ys,zs = scaled atom coordinates - xu,yu,zu = unwrapped atom coordinates - xsu,ysu,zsu = scaled unwrapped atom coordinates - ix,iy,iz = box image that the atom is in - vx,vy,vz = atom velocities - fx,fy,fz = forces on atoms - q = atom charge - mux,muy,muz = orientation of dipole moment of atom - mu = magnitude of dipole moment of atom - radius,diameter = radius,diameter of spherical particle - omegax,omegay,omegaz = angular velocity of spherical particle - angmomx,angmomy,angmomz = angular momentum of aspherical particle - tqx,tqy,tqz = torque on finite-size particles - c_ID = per-atom vector calculated by a compute with ID - c_ID[N] = Nth column of per-atom array calculated by a compute with ID - f_ID = per-atom vector calculated by a fix with ID - f_ID[N] = Nth column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name - d_name = per-atom floating point vector with name, managed by fix property/atom - i_name = per-atom integer vector with name, managed by fix property/atom +mol = molecule ID +proc = ID of processor that owns atom +procp1 = ID+1 of processor that owns atom +type = atom type +element = name of atom element, as defined by dump_modify command +mass = atom mass +x,y,z = unscaled atom coordinates +xs,ys,zs = scaled atom coordinates +xu,yu,zu = unwrapped atom coordinates +xsu,ysu,zsu = scaled unwrapped atom coordinates +ix,iy,iz = box image that the atom is in +vx,vy,vz = atom velocities +fx,fy,fz = forces on atoms +q = atom charge +mux,muy,muz = orientation of dipole moment of atom +mu = magnitude of dipole moment of atom +radius,diameter = radius,diameter of spherical particle +omegax,omegay,omegaz = angular velocity of spherical particle +angmomx,angmomy,angmomz = angular momentum of aspherical particle +tqx,tqy,tqz = torque on finite-size particles +c_ID = per-atom vector calculated by a compute with ID +c_ID[N] = Nth column of per-atom array calculated by a compute with ID +f_ID = per-atom vector calculated by a fix with ID +f_ID[N] = Nth column of per-atom array calculated by a fix with ID +v_name = per-atom vector calculated by an atom-style variable with name +d_name = per-atom floating point vector with name, managed by fix property/atom +i_name = per-atom integer vector with name, managed by fix property/atom
adiam value = number = numeric value for atom diameter (distance units) - atom = yes/no = do or do not draw atoms - bond values = color width = color and width of bonds - color = atom or type or none - width = number or atom or type or none - number = numeric value for bond width (distance units) - size values = width height = size of images - width = width of image in # of pixels - height = height of image in # of pixels - view values = theta phi = view of simulation box - theta = view angle from +z axis (degrees) - phi = azimuthal view angle (degrees) - theta or phi can be a variable (see below) - center values = flag Cx Cy Cz = center point of image - flag = "s" for static, "d" for dynamic - Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) - Cx,Cy,Cz can be variables (see below) - up values = Ux Uy Uz = direction that is "up" in image - Ux,Uy,Uz = components of up vector - Ux,Uy,Uz can be variables (see below) - zoom value = zfactor = size that simulation box appears in image - zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink - zfactor can be a variable (see below) - persp value = pfactor = amount of "perspective" in image - pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed) - pfactor can be a variable (see below) - box values = yes/no diam = draw outline of simulation box - yes/no = do or do not draw simulation box lines - diam = diameter of box lines as fraction of shortest box length - axes values = yes/no length diam = draw xyz axes - yes/no = do or do not draw xyz axes lines next to simulation box - length = length of axes lines as fraction of respective box lengths - diam = diameter of axes lines as fraction of shortest box length - subbox values = yes/no diam = draw outline of processor sub-domains - yes/no = do or do not draw sub-domain lines - diam = diameter of sub-domain lines as fraction of shortest box length - shiny value = sfactor = shinyness of spheres and cylinders - sfactor = shinyness of spheres and cylinders from 0.0 to 1.0 - ssao value = yes/no seed dfactor = SSAO depth shading - yes/no = turn depth shading on/off - seed = random # seed (positive integer) - dfactor = strength of shading from 0.0 to 1.0 +atom = yes/no = do or do not draw atoms +bond values = color width = color and width of bonds + color = atom or type or none + width = number or atom or type or none + number = numeric value for bond width (distance units) +size values = width height = size of images + width = width of image in # of pixels + height = height of image in # of pixels +view values = theta phi = view of simulation box + theta = view angle from +z axis (degrees) + phi = azimuthal view angle (degrees) + theta or phi can be a variable (see below) +center values = flag Cx Cy Cz = center point of image + flag = "s" for static, "d" for dynamic + Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) + Cx,Cy,Cz can be variables (see below) +up values = Ux Uy Uz = direction that is "up" in image + Ux,Uy,Uz = components of up vector + Ux,Uy,Uz can be variables (see below) +zoom value = zfactor = size that simulation box appears in image + zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink + zfactor can be a variable (see below) +persp value = pfactor = amount of "perspective" in image + pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed) + pfactor can be a variable (see below) +box values = yes/no diam = draw outline of simulation box + yes/no = do or do not draw simulation box lines + diam = diameter of box lines as fraction of shortest box length +axes values = yes/no length diam = draw xyz axes + yes/no = do or do not draw xyz axes lines next to simulation box + length = length of axes lines as fraction of respective box lengths + diam = diameter of axes lines as fraction of shortest box length +subbox values = yes/no diam = draw outline of processor sub-domains + yes/no = do or do not draw sub-domain lines + diam = diameter of sub-domain lines as fraction of shortest box length +shiny value = sfactor = shinyness of spheres and cylinders + sfactor = shinyness of spheres and cylinders from 0.0 to 1.0 +ssao value = yes/no seed dfactor = SSAO depth shading + yes/no = turn depth shading on/off + seed = random # seed (positive integer) + dfactor = strength of shading from 0.0 to 1.0
append arg = yes or no - buffer arg = yes or no - element args = E1 E2 ... EN, where N = # of atom types - E1,...,EN = element name, e.g. C or Fe or Ga - every arg = N - N = dump every this many timesteps - N can be a variable (see below) - fileper arg = Np - Np = write one file for every this many processors - first arg = yes or no - format arg = C-style format string for one line of output - flush arg = yes or no - image arg = yes or no - label arg = string - string = character string (e.g. BONDS) to use in header of dump local file - nfile arg = Nf - Nf = write this many files, one from each of Nf processors - pad arg = Nchar = # of characters to convert timestep to - precision arg = power-of-10 value from 10 to 1000000 - region arg = region-ID or "none" - scale arg = yes or no - sfactor arg = coordinate scaling factor (> 0.0) - tfactor arg = time scaling factor (> 0.0) - sort arg = off or id or N or -N - off = no sorting of per-atom lines within a snapshot - id = sort per-atom lines by atom ID - N = sort per-atom lines in ascending order by the Nth column - -N = sort per-atom lines in descending order by the Nth column - thresh args = attribute operation value - attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style - operation = "<" or "<=" or ">" or ">=" or "==" or "!=" - value = numeric value to compare to - these 3 args can be replaced by the word "none" to turn off thresholding - unwrap arg = yes or no +buffer arg = yes or no +element args = E1 E2 ... EN, where N = # of atom types + E1,...,EN = element name, e.g. C or Fe or Ga +every arg = N + N = dump every this many timesteps + N can be a variable (see below) +fileper arg = Np + Np = write one file for every this many processors +first arg = yes or no +format arg = C-style format string for one line of output +flush arg = yes or no +image arg = yes or no +label arg = string + string = character string (e.g. BONDS) to use in header of dump local file +nfile arg = Nf + Nf = write this many files, one from each of Nf processors +pad arg = Nchar = # of characters to convert timestep to +precision arg = power-of-10 value from 10 to 1000000 +region arg = region-ID or "none" +scale arg = yes or no +sfactor arg = coordinate scaling factor (> 0.0) +tfactor arg = time scaling factor (> 0.0) +sort arg = off or id or N or -N + off = no sorting of per-atom lines within a snapshot + id = sort per-atom lines by atom ID + N = sort per-atom lines in ascending order by the Nth column + -N = sort per-atom lines in descending order by the Nth column +thresh args = attribute operation value + attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style + operation = "<" or "<=" or ">" or ">=" or "==" or "!=" + value = numeric value to compare to + these 3 args can be replaced by the word "none" to turn off thresholding +unwrap arg = yes or no
acolor args = type color - type = atom type or range of types (see below) - color = name of color or color1/color2/... - adiam args = type diam - type = atom type or range of types (see below) - diam = diameter of atoms of that type (distance units) - amap args = lo hi style delta N entry1 entry2 ... entryN - lo = number or min = lower bound of range of color map - hi = number or max = upper bound of range of color map - style = 2 letters = "c" or "d" or "s" plus "a" or "f" - "c" for continuous - "d" for discrete - "s" for sequential - "a" for absolute - "f" for fractional - delta = binsize (only used for style "s", otherwise ignored) - binsize = range is divided into bins of this width - N = # of subsequent entries - entry = value color (for continuous style) - value = number or min or max = single value within range - color = name of color used for that value - entry = lo hi color (for discrete style) - lo/hi = number or min or max = lower/upper bound of subset of range - color = name of color used for that subset of values - entry = color (for sequential style) - color = name of color used for a bin of values - backcolor arg = color - color = name of color for background - bcolor args = type color - type = bond type or range of types (see below) - color = name of color or color1/color2/... - bdiam args = type diam - type = bond type or range of types (see below) - diam = diameter of bonds of that type (distance units) - boxcolor arg = color - color = name of color for simulation box lines and processor sub-domain lines - color args = name R G B - name = name of color - R,G,B = red/green/blue numeric values from 0.0 to 1.0 - bitrate arg = rate - rate = target bitrate for movie in kbps - framerate arg = fps - fps = frames per second for movie + type = atom type or range of types (see below) + color = name of color or color1/color2/... +adiam args = type diam + type = atom type or range of types (see below) + diam = diameter of atoms of that type (distance units) +amap args = lo hi style delta N entry1 entry2 ... entryN + lo = number or min = lower bound of range of color map + hi = number or max = upper bound of range of color map + style = 2 letters = "c" or "d" or "s" plus "a" or "f" + "c" for continuous + "d" for discrete + "s" for sequential + "a" for absolute + "f" for fractional + delta = binsize (only used for style "s", otherwise ignored) + binsize = range is divided into bins of this width + N = # of subsequent entries + entry = value color (for continuous style) + value = number or min or max = single value within range + color = name of color used for that value + entry = lo hi color (for discrete style) + lo/hi = number or min or max = lower/upper bound of subset of range + color = name of color used for that subset of values + entry = color (for sequential style) + color = name of color used for a bin of values +backcolor arg = color + color = name of color for background +bcolor args = type color + type = bond type or range of types (see below) + color = name of color or color1/color2/... +bdiam args = type diam + type = bond type or range of types (see below) + diam = diameter of bonds of that type (distance units) +boxcolor arg = color + color = name of color for simulation box lines and processor sub-domain lines +color args = name R G B + name = name of color + R,G,B = red/green/blue numeric values from 0.0 to 1.0 +bitrate arg = rate + rate = target bitrate for movie in kbps +framerate arg = fps + fps = frames per second for movie
pair args = pstyle pparam I J v_name - pstyle = pair style name, e.g. lj/cut - pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for - v_name = variable with name that calculates value of pparam - kspace arg = v_name - v_name = variable with name that calculates scale factor on K-space terms - atom args = aparam v_name - aparam = parameter to adapt over time - v_name = variable with name that calculates value of aparam + pstyle = pair style name, e.g. lj/cut + pparam = parameter to adapt over time + I,J = type pair(s) to set parameter for + v_name = variable with name that calculates value of pparam +kspace arg = v_name + v_name = variable with name that calculates scale factor on K-space terms +atom args = aparam v_name + aparam = parameter to adapt over time + v_name = variable with name that calculates value of aparam
scale value = no or yes - no = the variable value is the new setting - yes = the variable value multiplies the original setting - reset value = no or yes - no = values will remain altered at the end of a run - yes = reset altered values to their original values at the end of a run + no = the variable value is the new setting + yes = the variable value multiplies the original setting +reset value = no or yes + no = values will remain altered at the end of a run + yes = reset altered values to their original values at the end of a run
pair args = pstyle pparam I J v_name - pstyle = pair style name, e.g. lj/cut - pparam = parameter to adapt over time - I,J = type pair(s) to set parameter for - v_name = variable with name that calculates value of pparam - kspace arg = v_name - v_name = variable with name that calculates scale factor on K-space terms - atom args = aparam v_name - aparam = parameter to adapt over time - I = type(s) to set parameter for - v_name = variable with name that calculates value of aparam + pstyle = pair style name, e.g. lj/cut + pparam = parameter to adapt over time + I,J = type pair(s) to set parameter for + v_name = variable with name that calculates value of pparam +kspace arg = v_name + v_name = variable with name that calculates scale factor on K-space terms +atom args = aparam v_name + aparam = parameter to adapt over time + I = type(s) to set parameter for + v_name = variable with name that calculates value of aparam
scale value = no or yes - no = the variable value is the new setting - yes = the variable value multiplies the original setting - reset value = no or yes - no = values will remain altered at the end of a run - yes = reset altered values to their original values at the end - of a run - after value = no or yes - no = parameters are adapted at timestep N - yes = parameters are adapted one timestep after N + no = the variable value is the new setting + yes = the variable value multiplies the original setting +reset value = no or yes + no = values will remain altered at the end of a run + yes = reset altered values to their original values at the end + of a run +after value = no or yes + no = parameters are adapted at timestep N + yes = parameters are adapted one timestep after N
every value = Nevery - Nevery = add force every this many timesteps - region value = region-ID - region-ID = ID of region atoms must be in to have added force - energy value = v_name - v_name = variable with name that calculates the potential energy of each atom in the added force field + Nevery = add force every this many timesteps +region value = region-ID + region-ID = ID of region atoms must be in to have added force +energy value = v_name + v_name = variable with name that calculates the potential energy of each atom in the added force field
basis values = M itype - M = which basis atom - itype = atom type (1-N) to assign to this basis atom - size args = Lz - Lz = z size of lattice region appended in a single event(distance units) - freq args = freq - freq = the number of timesteps between append events - temp args = target damp seed extent - target = target temperature for the region between zhi-extent and zhi (temperature units) - damp = damping parameter (time units) - seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) - random args = xmax ymax zmax seed - xmax, ymax, zmax = maximum displacement in particular direction (distance units) - seed = random number seed for random displacement - units value = lattice or box - lattice = the wall position is defined in lattice units - box = the wall position is defined in simulation box units + M = which basis atom + itype = atom type (1-N) to assign to this basis atom +size args = Lz + Lz = z size of lattice region appended in a single event(distance units) +freq args = freq + freq = the number of timesteps between append events +temp args = target damp seed extent + target = target temperature for the region between zhi-extent and zhi (temperature units) + damp = damping parameter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) +random args = xmax ymax zmax seed + xmax, ymax, zmax = maximum displacement in particular direction (distance units) + seed = random number seed for random displacement +units value = lattice or box + lattice = the wall position is defined in lattice units + box = the wall position is defined in simulation box units
thermal = thermal coupling with fields: temperature - two_temperature = electron-phonon coupling with field: temperature and electron_temperature - hardy = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) - field = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) +two_temperature = electron-phonon coupling with field: temperature and electron_temperature +hardy = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) +field = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
# initial fix to designate coupling type and group to apply it to
- # tag group physics material_file
- fix AtC internal atc thermal Ar_thermal.mat
+# tag group physics material_file
+fix AtC internal atc thermal Ar_thermal.mat
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
- # nx ny nz region periodicity
- fix_modify AtC mesh create 12 2 2 mdRegion f p p
+# nx ny nz region periodicity
+fix_modify AtC mesh create 12 2 2 mdRegion f p p
# specify the control method for the type of coupling
- # physics control_type
- fix_modify AtC thermal control flux
+# physics control_type
+fix_modify AtC thermal control flux
# specify the initial values for the empirical field "temperature"
- # field node_group value
- fix_modify AtC initial temperature all 30
+# field node_group value
+fix_modify AtC initial temperature all 30
# create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output atc_fe_output 100
+# filename output_frequency
+fix_modify AtC output atc_fe_output 100
run 1000
@@ -196,32 +196,32 @@ fix AtC internal atc field
# initial fix to designate post-processing and the group to apply it to
- # no material file is allowed nor required
- fix AtC internal atc hardy
+# no material file is allowed nor required
+fix AtC internal atc hardy
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
- fix AtC kernel quartic_sphere 10.0
+fix AtC kernel quartic_sphere 10.0
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
- # with periodicity this effectively creats a system average
- fix_modify AtC mesh create 1 1 1 box p p p
+# with periodicity this effectively creats a system average
+fix_modify AtC mesh create 1 1 1 box p p p
# change from default lagrangian map to eulerian
- # refreshed every 100 steps
- fix_modify AtC atom_element_map eulerian 100
+# refreshed every 100 steps
+fix_modify AtC atom_element_map eulerian 100
# start with no field defined
- # add mass density, potential energy density, stress and temperature
- fix_modify AtC fields add density energy stress temperature
+# add mass density, potential energy density, stress and temperature
+fix_modify AtC fields add density energy stress temperature
# create an output stream for nodal fields
- # filename output_frequency
- fix_modify AtC output nvtFE 100 text
+# filename output_frequency
+fix_modify AtC output nvtFE 100 text
run 1000
diff --git a/doc/fix_atom_swap.html b/doc/fix_atom_swap.html
index db6450a67d..b24f358e5a 100644
--- a/doc/fix_atom_swap.html
+++ b/doc/fix_atom_swap.html
@@ -143,15 +143,15 @@
types values = two or more atom types
- delta_mu values = number_of_types-1 relative chemical potentials (energy units)
- ke value = no or yes
- no = no conservation of kinetic energy after atom swaps
- yes = kinetic energy is conserved after atom swaps
- semi-grand value = no or yes
- no = particle type counts and fractions conserved
- yes = semi-grand canonical ensemble, particle fractions not conserved
- region value = region-ID
- region-ID = ID of region to use as an exchange/move volume
+delta_mu values = number_of_types-1 relative chemical potentials (energy units)
+ke value = no or yes
+ no = no conservation of kinetic energy after atom swaps
+ yes = kinetic energy is conserved after atom swaps
+semi-grand value = no or yes
+ no = particle type counts and fractions conserved
+ yes = semi-grand canonical ensemble, particle fractions not conserved
+region value = region-ID
+ region-ID = ID of region to use as an exchange/move volume
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
- c_ID = per-atom vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
- density/number, density/mass = number or mass density
- temp = temperature
- c_ID = per-atom vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+temp = temperature
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
norm arg = all or sample or none = how output on Nfreq steps is normalized
- all = output is sum of atoms across all Nrepeat samples, divided by atom count
- sample = output is sum of Nrepeat sample averages, divided by Nrepeat
- none = output is sum of Nrepeat sums, divided by Nrepeat
- ave args = one or running or window M
- one = output new average value every Nfreq steps
- running = output cumulative average of all previous Nfreq steps
- window M = output average of M most recent Nfreq steps
- bias arg = bias-ID
- bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
- adof value = dof_per_atom
- dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
- cdof value = dof_per_chunk
- dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
- file arg = filename
- filename = file to write results to
- overwrite arg = none = overwrite output file with only latest output
- title1 arg = string
- string = text to print as 1st line of output file
- title2 arg = string
- string = text to print as 2nd line of output file
- title3 arg = string
- string = text to print as 3rd line of output file
+ all = output is sum of atoms across all Nrepeat samples, divided by atom count
+ sample = output is sum of Nrepeat sample averages, divided by Nrepeat
+ none = output is sum of Nrepeat sums, divided by Nrepeat
+ave args = one or running or window M
+ one = output new average value every Nfreq steps
+ running = output cumulative average of all previous Nfreq steps
+ window M = output average of M most recent Nfreq steps
+bias arg = bias-ID
+ bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
+adof value = dof_per_atom
+ dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
+cdof value = dof_per_chunk
+ dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
+file arg = filename
+ filename = file to write results to
+overwrite arg = none = overwrite output file with only latest output
+title1 arg = string
+ string = text to print as 1st line of output file
+title2 arg = string
+ string = text to print as 2nd line of output file
+title3 arg = string
+ string = text to print as 3rd line of output file
c_ID = global scalar calculated by a compute with ID
- c_ID[I] = Ith component of global vector calculated by a compute with ID
- f_ID = global scalar calculated by a fix with ID
- f_ID[I] = Ith component of global vector calculated by a fix with ID
- v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
type arg = auto or upper or lower or auto/upper or auto/lower or full - auto = correlate each value with itself - upper = correlate each value with each succeeding value - lower = correlate each value with each preceding value - auto/upper = auto + upper - auto/lower = auto + lower - full = correlate each value with every other value, including itself = auto + upper + lower - ave args = one or running - one = zero the correlation accumulation every Nfreq steps - running = accumulate correlations continuously - start args = Nstart - Nstart = start accumulating correlations on this timestep - prefactor args = value - value = prefactor to scale all the correlation data by - file arg = filename - filename = name of file to output correlation data to - overwrite arg = none = overwrite output file with only latest output - title1 arg = string - string = text to print as 1st line of output file - title2 arg = string - string = text to print as 2nd line of output file - title3 arg = string - string = text to print as 3rd line of output file + auto = correlate each value with itself + upper = correlate each value with each succeeding value + lower = correlate each value with each preceding value + auto/upper = auto + upper + auto/lower = auto + lower + full = correlate each value with every other value, including itself = auto + upper + lower +ave args = one or running + one = zero the correlation accumulation every Nfreq steps + running = accumulate correlations continuously +start args = Nstart + Nstart = start accumulating correlations on this timestep +prefactor args = value + value = prefactor to scale all the correlation data by +file arg = filename + filename = name of file to output correlation data to +overwrite arg = none = overwrite output file with only latest output +title1 arg = string + string = text to print as 1st line of output file +title2 arg = string + string = text to print as 2nd line of output file +title3 arg = string + string = text to print as 3rd line of output file
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
- c_ID = scalar or vector calculated by a compute with ID
- c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
- f_ID = scalar or vector calculated by a fix with ID
- f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
- v_name = value(s) calculated by an equal-style or atom-style variable with name
+c_ID = scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
+f_ID = scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
+v_name = value(s) calculated by an equal-style or atom-style variable with name
mode arg = scalar or vector - scalar = all input values are scalars - vector = all input values are vectors - file arg = filename - filename = name of file to output histogram(s) to - ave args = one or running or window - one = output a new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - start args = Nstart - Nstart = start averaging on this timestep - beyond arg = ignore or end or extra - ignore = ignore values outside histogram lo/hi bounds - end = count values outside histogram lo/hi bounds in end bins - extra = create 2 extra bins for value outside histogram lo/hi bounds - overwrite arg = none = overwrite output file with only latest output - title1 arg = string - string = text to print as 1st line of output file - title2 arg = string - string = text to print as 2nd line of output file - title3 arg = string - string = text to print as 3rd line of output file, only for vector mode + scalar = all input values are scalars + vector = all input values are vectors +file arg = filename + filename = name of file to output histogram(s) to +ave args = one or running or window + one = output a new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps +start args = Nstart + Nstart = start averaging on this timestep +beyond arg = ignore or end or extra + ignore = ignore values outside histogram lo/hi bounds + end = count values outside histogram lo/hi bounds in end bins + extra = create 2 extra bins for value outside histogram lo/hi bounds +overwrite arg = none = overwrite output file with only latest output +title1 arg = string + string = text to print as 1st line of output file +title2 arg = string + string = text to print as 2nd line of output file +title3 arg = string + string = text to print as 3rd line of output file, only for vector mode
dim = x or y or z - origin = lower or center or upper or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) +origin = lower or center or upper or coordinate value (distance units) +delta = thickness of spatial bins in dim (distance units)
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
- density/number, density/mass = number or mass density
- c_ID = per-atom vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
region arg = region-ID - bound args = x/y/z lo hi - x/y/z = x or y or z to bound bins in this dimension - lo = lower or coordinate value (distance units) - hi = upper or coordinate value (distance units) - discard arg = mixed or no or yes - mixed = discard atoms outside bins only if bin bounds are explicitly set - no = always keep out-of-bounds atoms - yes = always discard out-of-bounds atoms - norm arg = all or sample - region-ID = ID of region atoms must be in to contribute to spatial averaging - ave args = one or running or window M - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - units arg = box or lattice or reduced - file arg = filename - filename = file to write results to - overwrite arg = none = overwrite output file with only latest output - title1 arg = string - string = text to print as 1st line of output file - title2 arg = string - string = text to print as 2nd line of output file - title3 arg = string - string = text to print as 3rd line of output file +bound args = x/y/z lo hi + x/y/z = x or y or z to bound bins in this dimension + lo = lower or coordinate value (distance units) + hi = upper or coordinate value (distance units) +discard arg = mixed or no or yes + mixed = discard atoms outside bins only if bin bounds are explicitly set + no = always keep out-of-bounds atoms + yes = always discard out-of-bounds atoms +norm arg = all or sample + region-ID = ID of region atoms must be in to contribute to spatial averaging +ave args = one or running or window M + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps +units arg = box or lattice or reduced +file arg = filename + filename = file to write results to +overwrite arg = none = overwrite output file with only latest output +title1 arg = string + string = text to print as 1st line of output file +title2 arg = string + string = text to print as 2nd line of output file +title3 arg = string + string = text to print as 3rd line of output file
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
- density/number, density/mass = number or mass density
- c_ID = per-atom vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
+density/number, density/mass = number or mass density
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
region arg = region-ID - region-ID = ID of region atoms must be in to contribute to spatial averaging - norm arg = all or sample - units arg = box or lattice or reduced - ave args = one or running or window M - one = output new average value every Nfreq steps - running = output cumulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - file arg = filename - filename = file to write results to - overwrite arg = none = overwrite output file with only latest output - title1 arg = string - string = text to print as 1st line of output file - title2 arg = string - string = text to print as 2nd line of output file - title3 arg = string - string = text to print as 3rd line of output file + region-ID = ID of region atoms must be in to contribute to spatial averaging +norm arg = all or sample +units arg = box or lattice or reduced +ave args = one or running or window M + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps +file arg = filename + filename = file to write results to +overwrite arg = none = overwrite output file with only latest output +title1 arg = string + string = text to print as 1st line of output file +title2 arg = string + string = text to print as 2nd line of output file +title3 arg = string + string = text to print as 3rd line of output file
c_ID = global scalar, vector, or array calculated by a compute with ID
- c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
- f_ID = global scalar, vector, or array calculated by a fix with ID
- f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
- v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
+f_ID = global scalar, vector, or array calculated by a fix with ID
+f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
mode arg = scalar or vector - scalar = all input values are global scalars - vector = all input values are global vectors or global arrays - ave args = one or running or window M - one = output a new average value every Nfreq steps - running = output cummulative average of all previous Nfreq steps - window M = output average of M most recent Nfreq steps - start args = Nstart - Nstart = start averaging on this timestep - off arg = M = do not average this value - M = value # from 1 to Nvalues - file arg = filename - filename = name of file to output time averages to - overwrite arg = none = overwrite output file with only latest output - title1 arg = string - string = text to print as 1st line of output file - title2 arg = string - string = text to print as 2nd line of output file - title3 arg = string - string = text to print as 3rd line of output file, only for vector mode + scalar = all input values are global scalars + vector = all input values are global vectors or global arrays +ave args = one or running or window M + one = output a new average value every Nfreq steps + running = output cummulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps +start args = Nstart + Nstart = start averaging on this timestep +off arg = M = do not average this value + M = value # from 1 to Nvalues +file arg = filename + filename = name of file to output time averages to +overwrite arg = none = overwrite output file with only latest output +title1 arg = string + string = text to print as 1st line of output file +title2 arg = string + string = text to print as 2nd line of output file +title3 arg = string + string = text to print as 3rd line of output file, only for vector mode
region value = region-ID - region-ID = ID of region atoms must be in to have added force + region-ID = ID of region atoms must be in to have added force
shift args = dimstr Niter stopthresh
- dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
- Niter = # of times to iterate within each dimension of dimstr sequence
- stopthresh = stop balancing when this imbalance threshhold is reached
- rcb args = none
+ dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
+ Niter = # of times to iterate within each dimension of dimstr sequence
+ stopthresh = stop balancing when this imbalance threshhold is reached
+rcb args = none
out value = filename - filename = write each processor's sub-domain to a file, at each re-balancing + filename = write each processor's sub-domain to a file, at each re-balancing
prob values = fraction seed - fraction = break a bond with this probability if otherwise eligible - seed = random number seed (positive integer) + fraction = break a bond with this probability if otherwise eligible + seed = random number seed (positive integer)
iparam values = maxbond, newtype - maxbond = max # of bonds of bondtype the itype atom can have - newtype = change the itype atom to this type when maxbonds exist - jparam values = maxbond, newtype - maxbond = max # of bonds of bondtype the jtype atom can have - newtype = change the jtype atom to this type when maxbonds exist - prob values = fraction seed - fraction = create a bond with this probability if otherwise eligible - seed = random number seed (positive integer) - atype value = angletype - angletype = type of created angles - dtype value = dihedraltype - dihedraltype = type of created dihedrals - itype value = impropertype - impropertype = type of created impropers + maxbond = max # of bonds of bondtype the itype atom can have + newtype = change the itype atom to this type when maxbonds exist +jparam values = maxbond, newtype + maxbond = max # of bonds of bondtype the jtype atom can have + newtype = change the jtype atom to this type when maxbonds exist +prob values = fraction seed + fraction = create a bond with this probability if otherwise eligible + seed = random number seed (positive integer) +atype value = angletype + angletype = type of created angles +dtype value = dihedraltype + dihedraltype = type of created dihedrals +itype value = impropertype + impropertype = type of created impropers
input arg = colvars.state file name or prefix or NULL (default: NULL) - output arg = output filename prefix (default: out) - seed arg = seed for random number generator (default: 1966) - unwrap arg = yes or no - use unwrapped coordinates in collective variables (default: yes) - tstat arg = fix id of a thermostat or NULL (default: NULL) +output arg = output filename prefix (default: out) +seed arg = seed for random number generator (default: 1966) +unwrap arg = yes or no + use unwrapped coordinates in collective variables (default: yes) +tstat arg = fix id of a thermostat or NULL (default: NULL)
remap value = x or v or none - x = remap coords of atoms in group into deforming box - v = remap velocities of all atoms when they cross periodic boundaries - none = no remapping of x or v - flip value = yes or no - allow or disallow box flips when it becomes highly skewed - units value = lattice or box - lattice = distances are defined in lattice units - box = distances are defined in simulation box units + x = remap coords of atoms in group into deforming box + v = remap velocities of all atoms when they cross periodic boundaries + none = no remapping of x or v +flip value = yes or no + allow or disallow box flips when it becomes highly skewed +units value = lattice or box + lattice = distances are defined in lattice units + box = distances are defined in simulation box units
region value = region-ID - region-ID = ID of region to use as insertion volume - id value = max or next - max = atom ID for new atom(s) is max ID of all current atoms plus one - next = atom ID for new atom(s) increments by one for every deposition - global values = lo hi - lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units) - local values = lo hi delta - lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units) - delta = lateral distance within which a neighbor is considered "nearby" (distance units) - near value = R - R = only insert atom/molecule if further than R from existing particles (distance units) - attempt value = Q - Q = attempt a single insertion up to Q times - rate value = V - V = z velocity (y in 2d) at which insertion volume moves (velocity units) - vx values = vxlo vxhi - vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units) - vy values = vylo vyhi - vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units) - vz values = vzlo vzhi - vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) - target values = tx ty tz - tx,ty,tz = location of target point (distance units) - mol value = template-ID - template-ID = ID of molecule template specified in a separate molecule command - molfrac values = f1 f2 ... fN - f1 to fN = relative probability of creating each of N molecules in template-ID - rigid value = fix-ID - fix-ID = ID of fix rigid/small command - shake value = fix-ID - fix-ID = ID of fix shake command - units value = lattice or box - lattice = the geometry is defined in lattice units - box = the geometry is defined in simulation box units + region-ID = ID of region to use as insertion volume +id value = max or next + max = atom ID for new atom(s) is max ID of all current atoms plus one + next = atom ID for new atom(s) increments by one for every deposition +global values = lo hi + lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units) +local values = lo hi delta + lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units) + delta = lateral distance within which a neighbor is considered "nearby" (distance units) +near value = R + R = only insert atom/molecule if further than R from existing particles (distance units) +attempt value = Q + Q = attempt a single insertion up to Q times +rate value = V + V = z velocity (y in 2d) at which insertion volume moves (velocity units) +vx values = vxlo vxhi + vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units) +vy values = vylo vyhi + vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units) +vz values = vzlo vzhi + vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) +target values = tx ty tz + tx,ty,tz = location of target point (distance units) +mol value = template-ID + template-ID = ID of molecule template specified in a separate molecule command +molfrac values = f1 f2 ... fN + f1 to fN = relative probability of creating each of N molecules in template-ID +rigid value = fix-ID + fix-ID = ID of fix rigid/small command +shake value = fix-ID + fix-ID = ID of fix shake command +units value = lattice or box + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units
units value = lattice or box - lattice = Xmax is defined in lattice units - box = Xmax is defined in simulation box units + lattice = Xmax is defined in lattice units + box = Xmax is defined in simulation box units
region value = region-ID - region-ID = ID of region atoms must be in to have added force - energy value = v_name - v_name = variable with name that calculates the potential energy of each atom in the added E-field + region-ID = ID of region atoms must be in to have added force +energy value = v_name + v_name = variable with name that calculates the potential energy of each atom in the added E-field
pf/callback args = Ncall Napply - Ncall = make callback every Ncall steps - Napply = apply callback forces every Napply steps - pf/array args = Napply - Napply = apply array forces every Napply steps + Ncall = make callback every Ncall steps + Napply = apply callback forces every Napply steps +pf/array args = Napply + Napply = apply array forces every Napply steps
chute args = angle - angle = angle in +x away from -z or -y axis in 3d/2d (in degrees) - angle can be a variable (see below) - spherical args = phi theta - phi = azimuthal angle from +x axis (in degrees) - theta = angle from +z or +y axis in 3d/2d (in degrees) - phi or theta can be a variable (see below) - vector args = x y z - x y z = vector direction to apply the acceleration - x or y or z can be a variable (see below) + angle = angle in +x away from -z or -y axis in 3d/2d (in degrees) + angle can be a variable (see below) +spherical args = phi theta + phi = azimuthal angle from +x axis (in degrees) + theta = angle from +z or +y axis in 3d/2d (in degrees) + phi or theta can be a variable (see below) +vector args = x y z + x y z = vector direction to apply the acceleration + x or y or z can be a variable (see below)
region value = region-ID - region-ID = ID of region atoms must be in to have added force + region-ID = ID of region atoms must be in to have added force
unwrap arg = on or off - off = coordinates are wrapped back into the principal unit cell (default) - on = "unwrapped" coordinates using the image flags used - fscale arg = factor - factor = floating point number to scale IMD forces (default: 1.0) - trate arg = transmission rate of coordinate data sets (default: 1) - nowait arg = on or off - off = LAMMPS waits to be connected to an IMD client before continuing (default) - on = LAMMPS listens for an IMD client, but continues with the run + off = coordinates are wrapped back into the principal unit cell (default) + on = "unwrapped" coordinates using the image flags used +fscale arg = factor + factor = floating point number to scale IMD forces (default: 1.0) +trate arg = transmission rate of coordinate data sets (default: 1) +nowait arg = on or off + off = LAMMPS waits to be connected to an IMD client before continuing (default) + on = LAMMPS listens for an IMD client, but continues with the run
sphere args = x y z R - x,y,z = initial position of center of indenter (distance units) - R = sphere radius of indenter (distance units) - any of x,y,z,R can be a variable (see below) - cylinder args = dim c1 c2 R - dim = x or y or z = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) - R = cylinder radius of indenter (distance units) - any of c1,c2,R can be a variable (see below) - plane args = dim pos side - dim = x or y or z = plane perpendicular to this dimension - pos = position of plane in dimension x, y, or z (distance units) - pos can be a variable (see below) - side = lo or hi - side value = in or out - in = the indenter acts on particles inside the sphere or cylinder - out = the indenter acts on particles outside the sphere or cylinder - units value = lattice or box - lattice = the geometry is defined in lattice units - box = the geometry is defined in simulation box units + x,y,z = initial position of center of indenter (distance units) + R = sphere radius of indenter (distance units) + any of x,y,z,R can be a variable (see below) +cylinder args = dim c1 c2 R + dim = x or y or z = axis of cylinder + c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + R = cylinder radius of indenter (distance units) + any of c1,c2,R can be a variable (see below) +plane args = dim pos side + dim = x or y or z = plane perpendicular to this dimension + pos = position of plane in dimension x, y, or z (distance units) + pos can be a variable (see below) + side = lo or hi +side value = in or out + in = the indenter acts on particles inside the sphere or cylinder + out = the indenter acts on particles outside the sphere or cylinder +units value = lattice or box + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units
angmom value = no or scale - no = do not thermostat rotational degrees of freedom via the angular momentum - factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below - gjf value = no or yes - no = use standard formulation - yes = use Gronbech-Jensen/Farago formulation - omega value = no or yes - no = do not thermostat rotational degrees of freedom via the angular velocity - yes = do thermostat rotational degrees of freedom via the angular velocity - scale values = type ratio - type = atom type (1-N) - ratio = factor by which to scale the damping coefficient - tally value = no or yes - no = do not tally the energy added/subtracted to atoms - yes = do tally the energy added/subtracted to atoms - zero value = no or yes - no = do not set total random force to zero - yes = set total random force to zero + no = do not thermostat rotational degrees of freedom via the angular momentum + factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below +gjf value = no or yes + no = use standard formulation + yes = use Gronbech-Jensen/Farago formulation +omega value = no or yes + no = do not thermostat rotational degrees of freedom via the angular velocity + yes = do thermostat rotational degrees of freedom via the angular velocity +scale values = type ratio + type = atom type (1-N) + ratio = factor by which to scale the damping coefficient +tally value = no or yes + no = do not tally the energy added/subtracted to atoms + yes = do tally the energy added/subtracted to atoms +zero value = no or yes + no = do not set total random force to zero + yes = set total random force to zero
zero value = no or yes - no = do not set total random force on centers of mass to zero - yes = set total random force on centers of mass to zero + no = do not set total random force on centers of mass to zero + yes = set total random force on centers of mass to zero
zero value = no or yes - no = do not set total random force to zero - yes = set total random force to zero + no = do not set total random force to zero + yes = set total random force to zero
setArea values = type node_area - type = atom type (1-N) - node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default). - setGamma values = gamma - gamma = user set value for the force coupling constant. - scaleGamma values = type gammaFactor - type = atom type (1-N) - gammaFactor = factor to scale the setGamma gamma value by, for the specified atom type. - dx values = dx_LB = the lattice spacing. - dm values = dm_LB = the lattice-Boltzmann mass unit. - a0 values = a_0_real = the square of the speed of sound in the fluid. - noise values = Temperature seed - Temperature = fluid temperature. - seed = random number generator seed (positive integer) - calcforce values = N forcegroup-ID - N = output the force and torque every N timesteps - forcegroup-ID = ID of the particle group to calculate the force and torque of - trilinear values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil). - D3Q19 values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice). - read_restart values = restart file = name of the restart file to use to restart a fluid run. - write_restart values = N = write a restart file every N MD timesteps. - zwall_velocity values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax). - bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid. - printfluid values = N = print the fluid density and velocity at each grid point every N timesteps. + type = atom type (1-N) + node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default). +setGamma values = gamma + gamma = user set value for the force coupling constant. +scaleGamma values = type gammaFactor + type = atom type (1-N) + gammaFactor = factor to scale the setGamma gamma value by, for the specified atom type. +dx values = dx_LB = the lattice spacing. +dm values = dm_LB = the lattice-Boltzmann mass unit. +a0 values = a_0_real = the square of the speed of sound in the fluid. +noise values = Temperature seed + Temperature = fluid temperature. + seed = random number generator seed (positive integer) +calcforce values = N forcegroup-ID + N = output the force and torque every N timesteps + forcegroup-ID = ID of the particle group to calculate the force and torque of +trilinear values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil). +D3Q19 values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice). +read_restart values = restart file = name of the restart file to use to restart a fluid run. +write_restart values = N = write a restart file every N MD timesteps. +zwall_velocity values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax). +bodyforce values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid. +printfluid values = N = print the fluid density and velocity at each grid point every N timesteps.
linear values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension. + xflag,yflag,zflag = 0/1 to exclude/include each dimension.
force values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass force is active - torque values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass torque is active - innerNodes values = innergroup-ID - innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass force is active +torque values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass torque is active +innerNodes values = innergroup-ID + innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
temp value = compute ID that calculates a temperature - press value = compute ID that calculates a pressure - energy value = yes or no +press value = compute ID that calculates a pressure +energy value = yes or no
linear values = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension - angular values = none + xflag,yflag,zflag = 0/1 to exclude/include each dimension +angular values = none
rescale values = none diff --git a/doc/fix_move.html b/doc/fix_move.html index 70ddaa89e9..980af0410d 100644 --- a/doc/fix_move.html +++ b/doc/fix_move.html @@ -138,17 +138,17 @@linear args = Vx Vy Vz - Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL - wiggle args = Ax Ay Az period - Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL - period = period of oscillation (time units) - rotate args = Px Py Pz Rx Ry Rz period - Px,Py,Pz = origin point of axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector - period = period of rotation (time units) - variable args = v_dx v_dy v_dz v_vx v_vy v_vz - v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL - v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL +wiggle args = Ax Ay Az period + Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL + period = period of oscillation (time units) +rotate args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) +variable args = v_dx v_dy v_dz v_vx v_vy v_vz + v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL + v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
q value = cell mass-like parameter (mass^2/distance^4 units) - mu value = artificial viscosity (mass/length/time units) - p0 value = initial pressure in the shock equations (pressure units) - v0 value = initial simulation cell volume in the shock equations (distance^3 units) - e0 value = initial total energy (energy units) - tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) +mu value = artificial viscosity (mass/length/time units) +p0 value = initial pressure in the shock equations (pressure units) +v0 value = initial simulation cell volume in the shock equations (distance^3 units) +e0 value = initial total energy (energy units) +tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
update value = dipole - dipole = update orientation of dipole moment during integration + dipole = update orientation of dipole moment during integration
file0:
-0.798410432046075 1.785300000000000 1.596820864092150
- -0.798410432046075 1.785300000000000 -1.596820864092150
- 2.395231296138225 0.000000000000000 0.798410432046075
- 0.798410432046075 0.000000000000000 -2.395231296138225
- 1.596820864092150 1.785300000000000 -0.798410432046075
- 1.596820864092150 -1.785300000000000 -0.798410432046075
+ 0.798410432046075 1.785300000000000 1.596820864092150
+-0.798410432046075 1.785300000000000 -1.596820864092150
+ 2.395231296138225 0.000000000000000 0.798410432046075
+ 0.798410432046075 0.000000000000000 -2.395231296138225
+ 1.596820864092150 1.785300000000000 -0.798410432046075
+ 1.596820864092150 -1.785300000000000 -0.798410432046075
file1:
-0.798410432046075 1.785300000000000 1.596820864092150
- 0.798410432046075 1.785300000000000 -1.596820864092150
- 0.798410432046075 0.000000000000000 2.395231296138225
- 2.395231296138225 0.000000000000000 -0.798410432046075
- 1.596820864092150 1.785300000000000 0.798410432046075
- 1.596820864092150 -1.785300000000000 0.798410432046075
+ 0.798410432046075 1.785300000000000 -1.596820864092150
+ 0.798410432046075 0.000000000000000 2.395231296138225
+ 2.395231296138225 0.000000000000000 -0.798410432046075
+ 1.596820864092150 1.785300000000000 0.798410432046075
+ 1.596820864092150 -1.785300000000000 0.798410432046075
GAMMA flags to treate the whole simulation box as a unit cell, so that the mapping
- info can be generated internally. In this case, dynamical matrix at only the gamma-point
- will/can be evaluated.
+info can be generated internally. In this case, dynamical matrix at only the gamma-point
+will/can be evaluated.
sysdim value = d
- d = dimension of the system, usually the same as the MD model dimension
- nasr value = n
- n = number of iterations to enforce the acoustic sum rule
+ d = dimension of the system, usually the same as the MD model dimension
+nasr value = n
+ n = number of iterations to enforce the acoustic sum rule
method value = pimd or nmpimd or cmd - fmass value = scaling factor on mass - sp value = scaling factor on Planck constant - temp value = temperature (temperarate units) - nhc value = Nc = number of chains in Nose-Hoover thermostat +fmass value = scaling factor on mass +sp value = scaling factor on Planck constant +temp value = temperature (temperarate units) +nhc value = Nc = number of chains in Nose-Hoover thermostat
group values = list of group IDs - molecule values = none - file values = filename +molecule values = none +file values = filename
region value = region-ID - region-ID = ID of region to use as insertion volume - diam values = dstyle args - dstyle = one or range or poly - one args = D - D = single diameter for inserted particles (distance units) - range args = Dlo Dhi - Dlo,Dhi = range of diameters for inserted particles (distance units) - poly args = Npoly D1 P1 D2 P2 ... - Npoly = # of (D,P) pairs - D1,D2,... = diameter for subset of inserted particles (distance units) - P1,P2,... = percentage of inserted particles with this diameter (0-1) - vol values = fraction Nattempt - fraction = desired volume fraction for filling insertion volume - Nattempt = max # of insertion attempts per atom - rate value = V - V = z velocity (3d) or y velocity (2d) at which - insertion volume moves (velocity units) - vel values (3d) = vxlo vxhi vylo vyhi vz - vel values (2d) = vxlo vxhi vy - vxlo,vxhi = range of x velocities for inserted particles (velocity units) - vylo,vyhi = range of y velocities for inserted particles (velocity units) - vz = z velocity (3d) assigned to inserted particles (velocity units) - vy = y velocity (2d) assigned to inserted particles (velocity units) - mol value = template-ID - template-ID = ID of molecule template specified in a separate molecule command - molfrac values = f1 f2 ... fN - f1 to fN = relative probability of creating each of N molecules in template-ID - rigid value = fix-ID - fix-ID = ID of fix rigid/small command - shake value = fix-ID - fix-ID = ID of fix shake command + region-ID = ID of region to use as insertion volume +diam values = dstyle args + dstyle = one or range or poly + one args = D + D = single diameter for inserted particles (distance units) + range args = Dlo Dhi + Dlo,Dhi = range of diameters for inserted particles (distance units) + poly args = Npoly D1 P1 D2 P2 ... + Npoly = # of (D,P) pairs + D1,D2,... = diameter for subset of inserted particles (distance units) + P1,P2,... = percentage of inserted particles with this diameter (0-1) +vol values = fraction Nattempt + fraction = desired volume fraction for filling insertion volume + Nattempt = max # of insertion attempts per atom +rate value = V + V = z velocity (3d) or y velocity (2d) at which + insertion volume moves (velocity units) +vel values (3d) = vxlo vxhi vylo vyhi vz +vel values (2d) = vxlo vxhi vy + vxlo,vxhi = range of x velocities for inserted particles (velocity units) + vylo,vyhi = range of y velocities for inserted particles (velocity units) + vz = z velocity (3d) assigned to inserted particles (velocity units) + vy = y velocity (2d) assigned to inserted particles (velocity units) +mol value = template-ID + template-ID = ID of molecule template specified in a separate molecule command +molfrac values = f1 f2 ... fN + f1 to fN = relative probability of creating each of N molecules in template-ID +rigid value = fix-ID + fix-ID = ID of fix rigid/small command +shake value = fix-ID + fix-ID = ID of fix shake command
file value = filename - append value = filename - screen value = yes or no - title value = string - string = text to print as 1st line of output file +append value = filename +screen value = yes or no +title value = string + string = text to print as 1st line of output file
mol = molecule IDs - q = charge - i_name = new integer vector referenced by name - d_name = new floating-point vector referenced by name +q = charge +i_name = new integer vector referenced by name +d_name = new floating-point vector referenced by name
q value = cell mass-like parameter (mass^2/distance^4 units) - mu value = artificial viscosity (mass/distance/time units) - p0 value = initial pressure in the shock equations (pressure units) - v0 value = initial simulation cell volume in the shock equations (distance^3 units) - e0 value = initial total energy (energy units) - tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) - damp value = damping parameter (time units) inverse of friction <i>γ</i> - seed value = random number seed (positive integer) - f_max value = upper cutoff frequency of the vibration spectrum (1/time units) - N_f value = number of frequency bins (positive integer) - eta value = coupling constant between the shock system and the quantum thermal bath (positive unitless) - beta value = the quantum temperature is updated every beta time steps (positive integer) - T_init value = quantum temperature for the initial state (temperature units) +mu value = artificial viscosity (mass/distance/time units) +p0 value = initial pressure in the shock equations (pressure units) +v0 value = initial simulation cell volume in the shock equations (distance^3 units) +e0 value = initial total energy (energy units) +tscale value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) +damp value = damping parameter (time units) inverse of friction <i>γ</i> +seed value = random number seed (positive integer) +f_max value = upper cutoff frequency of the vibration spectrum (1/time units) +N_f value = number of frequency bins (positive integer) +eta value = coupling constant between the shock system and the quantum thermal bath (positive unitless) +beta value = the quantum temperature is updated every beta time steps (positive integer) +T_init value = quantum temperature for the initial state (temperature units)
file value = filename - filename = name of file to write QEQ equilibration info to + filename = name of file to write QEQ equilibration info to
temp value = target quantum temperature (temperature units) - damp value = damping parameter (time units) inverse of friction <i>&gamma</i>; - seed value = random number seed (positive integer) - f_max value = upper cutoff frequency of the vibration spectrum (1/time units) - N_f value = number of frequency bins (positive integer) +damp value = damping parameter (time units) inverse of friction <i>&gamma</i>; +seed value = random number seed (positive integer) +f_max value = upper cutoff frequency of the vibration spectrum (1/time units) +N_f value = number of frequency bins (positive integer)
cutoff value = I J Cutoff - I, J = atom types - Cutoff = Bond-order cutoff value for this pair of atom types - element value = Element1, Element2, ... - position value = posfreq filepos - posfreq = write position files every this many timestep - filepos = name of position output file + I, J = atom types + Cutoff = Bond-order cutoff value for this pair of atom types +element value = Element1, Element2, ... +position value = posfreq filepos + posfreq = write position files every this many timestep + filepos = name of position output file
shift value = group-ID - group-ID = group of atoms whose coords are shifted - units value = box or lattice or fraction + group-ID = group of atoms whose coords are shifted +units value = box or lattice or fraction
bond args = atom1 atom2 Kstart Kstop r0 - atom1,atom2 = IDs of 2 atoms in bond - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - r0 = equilibrium bond distance (distance units) - angle args = atom1 atom2 atom3 Kstart Kstop theta0 - atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - theta0 = equilibrium angle theta (degrees) - dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 - atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order - Kstart,Kstop = restraint coefficients at start/end of run (energy units) - phi0 = equilibrium dihedral angle phi (degrees) + atom1,atom2 = IDs of 2 atoms in bond + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + r0 = equilibrium bond distance (distance units) +angle args = atom1 atom2 atom3 Kstart Kstop theta0 + atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + theta0 = equilibrium angle theta (degrees) +dihedral args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + phi0 = equilibrium dihedral angle phi (degrees)
single args = none - molecule args = none - group args = N groupID1 groupID2 ... - N = # of groups - groupID1, groupID2, ... = list of N group IDs +molecule args = none +group args = N groupID1 groupID2 ... + N = # of groups + groupID1, groupID2, ... = list of N group IDs
langevin values = Tstart Tstop Tperiod seed - Tstart,Tstop = desired temperature at start/stop of run (temperature units) - Tdamp = temperature damping parameter (time units) - seed = random number seed to use for white noise (positive integer) - temp values = Tstart Tstop Tdamp - Tstart,Tstop = desired temperature at start/stop of run (temperature units) - Tdamp = temperature damping parameter (time units) - iso or aniso values = Pstart Pstop Pdamp - Pstart,Pstop = scalar external pressure at start/end of run (pressure units) - Pdamp = pressure damping parameter (time units) - x or y or z values = Pstart Pstop Pdamp - Pstart,Pstop = external stress tensor component at start/end of run (pressure units) - Pdamp = stress damping parameter (time units) - couple = none or xyz or xy or yz or xz - tparam values = Tchain Titer Torder - Tchain = length of Nose/Hoover thermostat chain - Titer = number of thermostat iterations performed - Torder = 3 or 5 = Yoshida-Suzuki integration parameters - pchain values = Pchain - Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat - dilate value = dilate-group-ID - dilate-group-ID = only dilate atoms in this group due to barostat volume changes - force values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass force is active - torque values = M xflag yflag zflag - M = which rigid body from 1-Nbody (see asterisk form below) - xflag,yflag,zflag = off/on if component of center-of-mass torque is active - infile filename - filename = file with per-body values of mass, center-of-mass, moments of inertia - mol value = template-ID - template-ID = ID of molecule template specified in a separate molecule command + Tstart,Tstop = desired temperature at start/stop of run (temperature units) + Tdamp = temperature damping parameter (time units) + seed = random number seed to use for white noise (positive integer) +temp values = Tstart Tstop Tdamp + Tstart,Tstop = desired temperature at start/stop of run (temperature units) + Tdamp = temperature damping parameter (time units) +iso or aniso values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) +x or y or z values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) +couple = none or xyz or xy or yz or xz +tparam values = Tchain Titer Torder + Tchain = length of Nose/Hoover thermostat chain + Titer = number of thermostat iterations performed + Torder = 3 or 5 = Yoshida-Suzuki integration parameters +pchain values = Pchain + Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat +dilate value = dilate-group-ID + dilate-group-ID = only dilate atoms in this group due to barostat volume changes +force values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass force is active +torque values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass torque is active +infile filename + filename = file with per-body values of mass, center-of-mass, moments of inertia +mol value = template-ID + template-ID = ID of molecule template specified in a separate molecule command
region value = region-ID - region-ID = ID of region atoms must be in to have added force + region-ID = ID of region atoms must be in to have added force
b values = one or more bond types - a values = one or more angle types - t values = one or more atom types - m value = one or more mass values +a values = one or more angle types +t values = one or more atom types +m value = one or more mass values
mol value = template-ID - template-ID = ID of molecule template specified in a separate molecule command + template-ID = ID of molecule template specified in a separate molecule command
cvel values = K vel - K = spring constant (force/distance units) - vel = velocity of pulling (distance/time units) - cfor values = force - force = pulling force (force units) + K = spring constant (force/distance units) + vel = velocity of pulling (distance/time units) +cfor values = force + force = pulling force (force units)
tether values = x y z R0 - x,y,z = point to which spring is tethered - R0 = distance of end of spring from tether point (distance units) - couple values = group-ID2 x y z R0 - group-ID2 = 2nd group to couple to fix group with a spring - x,y,z = direction of spring, automatically computed with 'auto' - R0 = distance of end of spring (distance units) + x,y,z = point to which spring is tethered + R0 = distance of end of spring from tether point (distance units) +couple values = group-ID2 x y z R0 + group-ID2 = 2nd group to couple to fix group with a spring + x,y,z = direction of spring, automatically computed with 'auto' + R0 = distance of end of spring (distance units)
tether values = K x y z R0 - K = spring constant (force/distance units) - x,y,z = point to which spring is tethered - R0 = equilibrium distance from tether point (distance units) - couple values = group-ID2 K x y z R0 - group-ID2 = 2nd group to couple to fix group with a spring - K = spring constant (force/distance units) - x,y,z = direction of spring - R0 = equilibrium distance of spring (distance units) + K = spring constant (force/distance units) + x,y,z = point to which spring is tethered + R0 = equilibrium distance from tether point (distance units) +couple values = group-ID2 K x y z R0 + group-ID2 = 2nd group to couple to fix group with a spring + K = spring constant (force/distance units) + x,y,z = direction of spring + R0 = equilibrium distance of spring (distance units)
lamda value = mean free path of SRD particles (distance units) - collision value = noslip or slip = collision model - overlap value = yes or no = whether big particles may overlap - inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated - exact value = yes or no - radius value = rfactor = scale collision radius by this factor - bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep - search value = sgrid = grid spacing for collision partner searching (distance units) - cubic values = style tolerance - style = error or warn - tolerance = fractional difference allowed (0 <= tol <= 1) - shift values = flag shiftseed - flag = yes or no or possible = SRD bin shifting for better statistics - yes = perform bin shifting each time SRD velocities are rescaled - no = no shifting - possible = shift depending on mean free path and bin size - shiftseed = random # seed (positive integer) - tstat value = yes or no = thermostat SRD particles or not - rescale value = yes or no or rotate or collide = rescaling of SRD velocities - yes = rescale during velocity rotation and collisions - no = no rescaling - rotate = rescale during velocity rotation, but not collisions - collide = rescale during collisions, but not velocity rotation +collision value = noslip or slip = collision model +overlap value = yes or no = whether big particles may overlap +inside value = error or warn or ignore = how SRD particles which end up inside a big particle are treated +exact value = yes or no +radius value = rfactor = scale collision radius by this factor +bounce value = Nbounce = max # of collisions an SRD particle can undergo in one timestep +search value = sgrid = grid spacing for collision partner searching (distance units) +cubic values = style tolerance + style = error or warn + tolerance = fractional difference allowed (0 <= tol <= 1) +shift values = flag shiftseed + flag = yes or no or possible = SRD bin shifting for better statistics + yes = perform bin shifting each time SRD velocities are rescaled + no = no shifting + possible = shift depending on mean free path and bin size + shiftseed = random # seed (positive integer) +tstat value = yes or no = thermostat SRD particles or not +rescale value = yes or no or rotate or collide = rescaling of SRD velocities + yes = rescale during velocity rotation and collisions + no = no rescaling + rotate = rescale during velocity rotation, but not collisions + collide = rescale during collisions, but not velocity rotation
possible attributes = id, mol, type, mass,
- x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz,
- radius, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- c_ID, c_ID[N], f_ID, f_ID[N], v_name,
- d_name, i_name
+ x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
+ q, mux, muy, muz,
+ radius, omegax, omegay, omegaz,
+ angmomx, angmomy, angmomz, tqx, tqy, tqz,
+ c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+ d_name, i_name
id = atom ID
- mol = molecule ID
- type = atom type
- mass = atom mass
- x,y,z = unscaled atom coordinates
- xs,ys,zs = scaled atom coordinates
- xu,yu,zu = unwrapped atom coordinates
- ix,iy,iz = box image that the atom is in
- vx,vy,vz = atom velocities
- fx,fy,fz = forces on atoms
- q = atom charge
- mux,muy,muz = orientation of dipolar atom
- radius = radius of spherical particle
- omegax,omegay,omegaz = angular velocity of spherical particle
- angmomx,angmomy,angmomz = angular momentum of aspherical particle
- tqx,tqy,tqz = torque on finite-size particles
- c_ID = per-atom vector calculated by a compute with ID
- c_ID[I] = Ith column of per-atom array calculated by a compute with ID
- f_ID = per-atom vector calculated by a fix with ID
- f_ID[I] = Ith column of per-atom array calculated by a fix with ID
- v_name = per-atom vector calculated by an atom-style variable with name
- d_name = per-atom floating point vector name, managed by fix property/atom
- i_name = per-atom integer vector name, managed by fix property/atom
+mol = molecule ID
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipolar atom
+radius = radius of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector name, managed by fix property/atom
+i_name = per-atom integer vector name, managed by fix property/atom
com args = xflag yflag zflag - xflag,yflag,zflag = 0/1 to exclude/include each dimension - rot args = none + xflag,yflag,zflag = 0/1 to exclude/include each dimension +rot args = none
function value = function-ID - function-ID = ID of the switching function (1, 2 or 3) + function-ID = ID of the switching function (1, 2 or 3)
Example:
fix ref all ti/rs 50.0 2000 1000
diff --git a/doc/fix_ti_spring.html b/doc/fix_ti_spring.html
index 22a08955ea..327b4b8a74 100644
--- a/doc/fix_ti_spring.html
+++ b/doc/fix_ti_spring.html
@@ -141,7 +141,7 @@
function value = function-ID
- function-ID = ID of the switching function (1 or 2)
+ function-ID = ID of the switching function (1 or 2)
Example:
fix ref all ti/spring 50.0 2000 1000 function 2
diff --git a/doc/fix_ttm.html b/doc/fix_ttm.html
index fcb4b3b523..45971a1cef 100644
--- a/doc/fix_ttm.html
+++ b/doc/fix_ttm.html
@@ -142,29 +142,29 @@ fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
remaining arguments for fix ttm:
C_e = electronic specific heat (energy/(electron*temperature) units)
- rho_e = electronic density (electrons/volume units)
- kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
- gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
- gamma_s = friction coefficient due to electronic stopping (mass/time units)
- v_0 = electronic stopping critical velocity (velocity units)
- Nx = number of thermal solve grid points in the x-direction (positive integer)
- Ny = number of thermal solve grid points in the y-direction (positive integer)
- Nz = number of thermal solve grid points in the z-direction (positive integer)
- T_infile = filename to read initial electronic temperature from
- N = dump TTM temperatures every this many timesteps, 0 = no dump
- T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+rho_e = electronic density (electrons/volume units)
+kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
+gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+gamma_s = friction coefficient due to electronic stopping (mass/time units)
+v_0 = electronic stopping critical velocity (velocity units)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
- remaining arguments for fix ttm/mod:
init_file = file with the parameters to TTM
- Nx = number of thermal solve grid points in the x-direction (positive integer)
- Ny = number of thermal solve grid points in the y-direction (positive integer)
- Nz = number of thermal solve grid points in the z-direction (positive integer)
- T_infile = filename to read initial electronic temperature from
- N = dump TTM temperatures every this many timesteps, 0 = no dump
- T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
diff --git a/doc/fix_vector.html b/doc/fix_vector.html
index 62dd1805b4..e6be5371d5 100644
--- a/doc/fix_vector.html
+++ b/doc/fix_vector.html
@@ -139,10 +139,10 @@
value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
c_ID = global scalar calculated by a compute with ID
- c_ID[I] = Ith component of global vector calculated by a compute with ID
- f_ID = global scalar calculated by a fix with ID
- f_ID[I] = Ith component of global vector calculated by a fix with ID
- v_name = global value calculated by an equal-style variable with name
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index 12a706717f..8f0eab262f 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -143,7 +143,7 @@
swap value = Nswap = number of swaps to perform every N steps
- vtarget value = V or INF = target velocity of swap partners (velocity units)
+vtarget value = V or INF = target velocity of swap partners (velocity units)
args = coord epsilon sigma cutoff - coord = position of wall = EDGE or constant or variable - EDGE = current lo or hi edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = equal-style variable like v_x or v_wiggle - epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) - epsilon can be a variable (see below) - sigma = size factor for wall-particle interaction (distance units) - sigma can be a variable (see below) - cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + coord = position of wall = EDGE or constant or variable + EDGE = current lo or hi edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = equal-style variable like v_x or v_wiggle + epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) + epsilon can be a variable (see below) + sigma = size factor for wall-particle interaction (distance units) + sigma can be a variable (see below) + cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
units value = lattice or box - lattice = the wall position is defined in lattice units - box = the wall position is defined in simulation box units - fld value = yes or no - yes = invoke the wall constraint to be compatible with implicit FLD - no = invoke the wall constraint in the normal way - pbc value = yes or no - yes = allow periodic boundary in a wall dimension - no = require non-perioidic boundaries in any wall dimension + lattice = the wall position is defined in lattice units + box = the wall position is defined in simulation box units +fld value = yes or no + yes = invoke the wall constraint to be compatible with implicit FLD + no = invoke the wall constraint in the normal way +pbc value = yes or no + yes = allow periodic boundary in a wall dimension + no = require non-perioidic boundaries in any wall dimension
xplane or yplane or zplane args = lo hi - lo,hi = position of lower and upper plane (distance units), either can be NULL) - zcylinder args = radius - radius = cylinder radius (distance units) + lo,hi = position of lower and upper plane (distance units), either can be NULL) +zcylinder args = radius + radius = cylinder radius (distance units)
wiggle values = dim amplitude period - dim = x or y or z - amplitude = size of oscillation (distance units) - period = time of oscillation (time units) - shear values = dim vshear - dim = x or y or z - vshear = magnitude of shear velocity (velocity units) + dim = x or y or z + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) +shear values = dim vshear + dim = x or y or z + vshear = magnitude of shear velocity (velocity units)
pos args = z - z = z coordinate at which the piston begins (distance units) - vel args = vz - vz = final velocity of the piston (velocity units) - ramp = use a linear velocity ramp from 0 to vz - temp args = target damp seed extent - target = target velocity for region immediately ahead of the piston - damp = damping paramter (time units) - seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) - units value = lattice or box - lattice = the wall position is defined in lattice units - box = the wall position is defined in simulation box units + z = z coordinate at which the piston begins (distance units) +vel args = vz + vz = final velocity of the piston (velocity units) +ramp = use a linear velocity ramp from 0 to vz +temp args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping paramter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) +units value = lattice or box + lattice = the wall position is defined in lattice units + box = the wall position is defined in simulation box units
xlo,*ylo*,*zlo* arg = EDGE or constant or variable - EDGE = current lo edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = equal-style variable like v_x or v_wiggle - xhi,*yhi*,*zhi* arg = EDGE or constant or variable - EDGE = current hi edge of simulation box - constant = number like 50.0 or 100.3 (distance units) - variable = equal-style variable like v_x or v_wiggle + EDGE = current lo edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = equal-style variable like v_x or v_wiggle +xhi,*yhi*,*zhi* arg = EDGE or constant or variable + EDGE = current hi edge of simulation box + constant = number like 50.0 or 100.3 (distance units) + variable = equal-style variable like v_x or v_wiggle
units value = lattice or box - lattice = the wall position is defined in lattice units - box = the wall position is defined in simulation box units + lattice = the wall position is defined in lattice units + box = the wall position is defined in simulation box units
xlo,*ylo*,*zlo* arg = EDGE or constant or variable - EDGE = current lo edge of simulation box - constant = number like 0.0 or -30.0 (distance units) - variable = equal-style variable like v_x or v_wiggle - xhi,*yhi*,*zhi* arg = EDGE or constant or variable - EDGE = current hi edge of simulation box - constant = number like 50.0 or 100.3 (distance units) - variable = equal-style variable like v_x or v_wiggle + EDGE = current lo edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = equal-style variable like v_x or v_wiggle +xhi,*yhi*,*zhi* arg = EDGE or constant or variable + EDGE = current hi edge of simulation box + constant = number like 50.0 or 100.3 (distance units) + variable = equal-style variable like v_x or v_wiggle
units value = lattice or box - lattice = the wall position is defined in lattice units - box = the wall position is defined in simulation box units + lattice = the wall position is defined in lattice units + box = the wall position is defined in simulation box units
delete = no args - clear = no args - region args = region-ID - type or id or molecule - args = list of one or more atom types, atom IDs, or molecule IDs - any entry in list can be a sequence formatted as A:B or A:B:C where - A = starting index, B = ending index, - C = increment between indices, 1 if not specified - args = logical value - logical = "<" or "<=" or ">" or ">=" or "==" or "!=" - value = an atom type or atom ID or molecule ID (depending on style) - args = logical value1 value2 - logical = "<>" - value1,value2 = atom types or atom IDs or molecule IDs (depending on style) - variable args = variable-name - include args = molecule - molecule = add atoms to group with same molecule ID as atoms already in group - subtract args = two or more group IDs - union args = one or more group IDs - intersect args = two or more group IDs - dynamic args = parent-ID keyword value ... - one or more keyword/value pairs may be appended - keyword = region or var or every - region value = region-ID - var value = name of variable - every value = N = update group every this many timesteps - static = no args +clear = no args +region args = region-ID +type or id or molecule + args = list of one or more atom types, atom IDs, or molecule IDs + any entry in list can be a sequence formatted as A:B or A:B:C where + A = starting index, B = ending index, + C = increment between indices, 1 if not specified + args = logical value + logical = "<" or "<=" or ">" or ">=" or "==" or "!=" + value = an atom type or atom ID or molecule ID (depending on style) + args = logical value1 value2 + logical = "<>" + value1,value2 = atom types or atom IDs or molecule IDs (depending on style) +variable args = variable-name +include args = molecule + molecule = add atoms to group with same molecule ID as atoms already in group +subtract args = two or more group IDs +union args = one or more group IDs +intersect args = two or more group IDs +dynamic args = parent-ID keyword value ... + one or more keyword/value pairs may be appended + keyword = region or var or every + region value = region-ID + var value = name of variable + every value = N = update group every this many timesteps +static = no args
none value = none - ewald value = accuracy - accuracy = desired relative error in forces - ewald/disp value = accuracy - accuracy = desired relative error in forces - ewald/omp value = accuracy - accuracy = desired relative error in forces - pppm value = accuracy - accuracy = desired relative error in forces - pppm/cg value = accuracy (smallq) - accuracy = desired relative error in forces - smallq = cutoff for charges to be considered (optional) (charge units) - pppm/disp value = accuracy - accuracy = desired relative error in forces - pppm/tip4p value = accuracy - accuracy = desired relative error in forces - pppm/disp/tip4p value = accuracy - accuracy = desired relative error in forces - pppm/gpu value = accuracy - accuracy = desired relative error in forces - pppm/omp value = accuracy - accuracy = desired relative error in forces - pppm/cg/omp value = accuracy - accuracy = desired relative error in forces - pppm/tip4p/omp value = accuracy - accuracy = desired relative error in forces - pppm/stagger value = accuracy - accuracy = desired relative error in forces - msm value = accuracy - accuracy = desired relative error in forces - msm/cg value = accuracy (smallq) - accuracy = desired relative error in forces - smallq = cutoff for charges to be considered (optional) (charge units) - msm/omp value = accuracy - accuracy = desired relative error in forces - msm/cg/omp value = accuracy (smallq) - accuracy = desired relative error in forces - smallq = cutoff for charges to be considered (optional) (charge units) +ewald value = accuracy + accuracy = desired relative error in forces +ewald/disp value = accuracy + accuracy = desired relative error in forces +ewald/omp value = accuracy + accuracy = desired relative error in forces +pppm value = accuracy + accuracy = desired relative error in forces +pppm/cg value = accuracy (smallq) + accuracy = desired relative error in forces + smallq = cutoff for charges to be considered (optional) (charge units) +pppm/disp value = accuracy + accuracy = desired relative error in forces +pppm/tip4p value = accuracy + accuracy = desired relative error in forces +pppm/disp/tip4p value = accuracy + accuracy = desired relative error in forces +pppm/gpu value = accuracy + accuracy = desired relative error in forces +pppm/omp value = accuracy + accuracy = desired relative error in forces +pppm/cg/omp value = accuracy + accuracy = desired relative error in forces +pppm/tip4p/omp value = accuracy + accuracy = desired relative error in forces +pppm/stagger value = accuracy + accuracy = desired relative error in forces +msm value = accuracy + accuracy = desired relative error in forces +msm/cg value = accuracy (smallq) + accuracy = desired relative error in forces + smallq = cutoff for charges to be considered (optional) (charge units) +msm/omp value = accuracy + accuracy = desired relative error in forces +msm/cg/omp value = accuracy (smallq) + accuracy = desired relative error in forces + smallq = cutoff for charges to be considered (optional) (charge units)
scale = reduced density rho* (for LJ units)
- scale = lattice constant in distance units (for all other units)
+scale = lattice constant in distance units (for all other units)
origin values = x y z - x,y,z = fractions of a unit cell (0 <= x,y,z < 1) - orient values = dim i j k - dim = x or y or z - i,j,k = integer lattice directions - spacing values = dx dy dz - dx,dy,dz = lattice spacings in the x,y,z box directions - a1,*a2*,*a3* values = x y z - x,y,z = primitive vector components that define unit cell - basis values = x y z - x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) + x,y,z = fractions of a unit cell (0 <= x,y,z < 1) +orient values = dim i j k + dim = x or y or z + i,j,k = integer lattice directions +spacing values = dx dy dz + dx,dy,dz = lattice spacings in the x,y,z box directions +a1,*a2*,*a3* values = x y z + x,y,z = primitive vector components that define unit cell +basis values = x y z + x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1)
offset values = toff boff aoff doff ioff - toff = offset to add to atom types - boff = offset to add to bond types - aoff = offset to add to angle types - doff = offset to add to dihedral types - ioff = offset to add to improper types + toff = offset to add to atom types + boff = offset to add to bond types + aoff = offset to add to angle types + doff = offset to add to dihedral types + ioff = offset to add to improper types
final arg = filename - filename = file with initial coords for final replica - coords for intermediate replicas are linearly interpolated between first and last replica - each arg = filename - filename = unique filename for each replica (except first) with its initial coords - none arg = no argument - all replicas assumed to already have their initial coords + filename = file with initial coords for final replica + coords for intermediate replicas are linearly interpolated between first and last replica +each arg = filename + filename = unique filename for each replica (except first) with its initial coords +none arg = no argument + all replicas assumed to already have their initial coords
cuda args = Ngpu keyword value ... - Ngpu = # of GPUs per node - zero or more keyword/value pairs may be appended - keywords = newton or gpuID or timing or test or thread - newton = off or on - off = set Newton pairwise and bonded flags off (default) - on = set Newton pairwise and bonded flags on - gpuID values = gpu1 .. gpuN - gpu1 .. gpuN = IDs of the Ngpu GPUs to use - timing values = none - test values = id - id = atom-ID of a test particle - thread = auto or tpa or bpa - auto = test whether tpa or bpa is faster - tpa = one thread per atom - bpa = one block per atom - gpu args = Ngpu keyword value ... - Ngpu = # of GPUs per node - zero or more keyword/value pairs may be appended - keywords = neigh or newton or binsize or split or gpuID or tpa or device - neigh value = yes or no - yes = neighbor list build on GPU (default) - no = neighbor list build on CPU - newton = off or on - off = set Newton pairwise flag off (default and required) - on = set Newton pairwise flag on (currently not allowed) - binsize value = size - size = bin size for neighbor list construction (distance units) - split = fraction - fraction = fraction of atoms assigned to GPU (default = 1.0) - gpuID values = first last - first = ID of first GPU to be used on each node - last = ID of last GPU to be used on each node - tpa value = Nthreads - Nthreads = # of GPU threads used per atom - device value = device_type - device_type = kepler or fermi or cypress or generic - intel args = NPhi keyword value ... - Nphi = # of coprocessors per node - zero or more keyword/value pairs may be appended - keywords = omp or mode or balance or ghost or tpc or tptask or no_affinity - omp value = Nthreads - Nthreads = number of OpenMP threads to use on CPU (default = 0) - mode value = single or mixed or double - single = perform force calculations in single precision - mixed = perform force calculations in mixed precision - double = perform force calculations in double precision - balance value = split - split = fraction of work to offload to coprocessor, -1 for dynamic - ghost value = yes or no - yes = include ghost atoms for offload - no = do not include ghost atoms for offload - tpc value = Ntpc - Ntpc = max number of coprocessor threads per coprocessor core (default = 4) - tptask value = Ntptask - Ntptask = max number of coprocessor threads per MPI task (default = 240) - no_affinity values = none - kokkos args = keyword value ... - zero or more keyword/value pairs may be appended - keywords = neigh or newton or binsize or comm or comm/exchange or comm/forward - neigh value = full or half/thread or half or n2 or full/cluster - full = full neighbor list - half/thread = half neighbor list built in thread-safe manner - half = half neighbor list, not thread-safe, only use when 1 thread/MPI task - n2 = non-binning neighbor list build, O(N^2) algorithm - full/cluster = full neighbor list with clustered groups of atoms - newton = off or on - off = set Newton pairwise and bonded flags off (default) - on = set Newton pairwise and bonded flags on - binsize value = size - size = bin size for neighbor list construction (distance units) - comm value = no or host or device - use value for both comm/exchange and comm/forward - comm/exchange value = no or host or device - comm/forward value = no or host or device - no = perform communication pack/unpack in non-KOKKOS mode - host = perform pack/unpack on host (e.g. with OpenMP threading) - device = perform pack/unpack on device (e.g. on GPU) - omp args = Nthreads keyword value ... - Nthread = # of OpenMP threads to associate with each MPI process - zero or more keyword/value pairs may be appended - keywords = neigh - neigh value = yes or no - yes = threaded neighbor list build (default) - no = non-threaded neighbor list build + Ngpu = # of GPUs per node + zero or more keyword/value pairs may be appended + keywords = newton or gpuID or timing or test or thread + newton = off or on + off = set Newton pairwise and bonded flags off (default) + on = set Newton pairwise and bonded flags on + gpuID values = gpu1 .. gpuN + gpu1 .. gpuN = IDs of the Ngpu GPUs to use + timing values = none + test values = id + id = atom-ID of a test particle + thread = auto or tpa or bpa + auto = test whether tpa or bpa is faster + tpa = one thread per atom + bpa = one block per atom +gpu args = Ngpu keyword value ... + Ngpu = # of GPUs per node + zero or more keyword/value pairs may be appended + keywords = neigh or newton or binsize or split or gpuID or tpa or device + neigh value = yes or no + yes = neighbor list build on GPU (default) + no = neighbor list build on CPU + newton = off or on + off = set Newton pairwise flag off (default and required) + on = set Newton pairwise flag on (currently not allowed) + binsize value = size + size = bin size for neighbor list construction (distance units) + split = fraction + fraction = fraction of atoms assigned to GPU (default = 1.0) + gpuID values = first last + first = ID of first GPU to be used on each node + last = ID of last GPU to be used on each node + tpa value = Nthreads + Nthreads = # of GPU threads used per atom + device value = device_type + device_type = kepler or fermi or cypress or generic +intel args = NPhi keyword value ... + Nphi = # of coprocessors per node + zero or more keyword/value pairs may be appended + keywords = omp or mode or balance or ghost or tpc or tptask or no_affinity + omp value = Nthreads + Nthreads = number of OpenMP threads to use on CPU (default = 0) + mode value = single or mixed or double + single = perform force calculations in single precision + mixed = perform force calculations in mixed precision + double = perform force calculations in double precision + balance value = split + split = fraction of work to offload to coprocessor, -1 for dynamic + ghost value = yes or no + yes = include ghost atoms for offload + no = do not include ghost atoms for offload + tpc value = Ntpc + Ntpc = max number of coprocessor threads per coprocessor core (default = 4) + tptask value = Ntptask + Ntptask = max number of coprocessor threads per MPI task (default = 240) + no_affinity values = none +kokkos args = keyword value ... + zero or more keyword/value pairs may be appended + keywords = neigh or newton or binsize or comm or comm/exchange or comm/forward + neigh value = full or half/thread or half or n2 or full/cluster + full = full neighbor list + half/thread = half neighbor list built in thread-safe manner + half = half neighbor list, not thread-safe, only use when 1 thread/MPI task + n2 = non-binning neighbor list build, O(N^2) algorithm + full/cluster = full neighbor list with clustered groups of atoms + newton = off or on + off = set Newton pairwise and bonded flags off (default) + on = set Newton pairwise and bonded flags on + binsize value = size + size = bin size for neighbor list construction (distance units) + comm value = no or host or device + use value for both comm/exchange and comm/forward + comm/exchange value = no or host or device + comm/forward value = no or host or device + no = perform communication pack/unpack in non-KOKKOS mode + host = perform pack/unpack on host (e.g. with OpenMP threading) + device = perform pack/unpack on device (e.g. on GPU) +omp args = Nthreads keyword value ... + Nthread = # of OpenMP threads to associate with each MPI process + zero or more keyword/value pairs may be appended + keywords = neigh + neigh value = yes or no + yes = threaded neighbor list build (default) + no = non-threaded neighbor list build
hartree value = none - dproduct value = none - uhf value = none - free value = none - pbc value = Plen - Plen = periodic width of electron = -1 or positive value (distance units) - fix value = Flen - Flen = fixed width of electron = -1 or positive value (distance units) - harm value = width - width = harmonic width constraint - ermscale value = factor - factor = scaling between electron mass and width variable mass - flex_press value = none +dproduct value = none +uhf value = none +free value = none +pbc value = Plen + Plen = periodic width of electron = -1 or positive value (distance units) +fix value = Flen + Flen = fixed width of electron = -1 or positive value (distance units) +harm value = width + width = harmonic width constraint +ermscale value = factor + factor = scaling between electron mass and width variable mass +flex_press value = none
born args = cutoff - cutoff = global cutoff for non-Coulombic interactions (distance units) - born/coul/long or born/coul/long/cs args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - born/coul/msm args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - born/coul/wolf args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for non-Coulombic interactions (distance units) +born/coul/long or born/coul/long/cs args = cutoff (cutoff2) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +born/coul/msm args = cutoff (cutoff2) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +born/coul/wolf args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
buck args = cutoff - cutoff = global cutoff for Buckingham interactions (distance units) - buck/coul/cut args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - buck/coul/long or buck/coul/long/cs args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - buck/coul/msm args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for Buckingham interactions (distance units) +buck/coul/cut args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +buck/coul/long or buck/coul/long/cs args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +buck/coul/msm args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
long = use Kspace long-range summation for the dispersion term 1/r^6 - cut = use a cutoff +cut = use a cutoff
long = use Kspace long-range summation for the Coulombic term 1/r - off = omit the Coulombic term +off = omit the Coulombic term
lj/charmm/coul/charmm args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) - lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) - lj/charmm/coul/long args = inner outer (cutoff) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) - lj/charmm/coul/msm args = inner outer (cutoff) - inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) + inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) + inner2, outer2 = global switching cutoffs for Coulombic (optional) +lj/charmm/coul/charmm/implicit args = inner outer (inner2) (outer2) + inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) + inner2, outer2 = global switching cutoffs for Coulombic (optional) +lj/charmm/coul/long args = inner outer (cutoff) + inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) + cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) +lj/charmm/coul/msm args = inner outer (cutoff) + inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args) + cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
lj/class2 args = cutoff - cutoff = global cutoff for class 2 interactions (distance units) - lj/class2/coul/cut args = cutoff (cutoff2) - cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/class2/coul/long args = cutoff (cutoff2) - cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for class 2 interactions (distance units) +lj/class2/coul/cut args = cutoff (cutoff2) + cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/class2/coul/long args = cutoff (cutoff2) + cutoff = global cutoff for class 2 (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
born/coul/long/cs args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - buck/coul/long/cs args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +buck/coul/long/cs args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
long = use long-range damping on dispersion 1/r^6 term - cut = use a cutoff on dispersion 1/r^6 term - off = omit disperion 1/r^6 term entirely +cut = use a cutoff on dispersion 1/r^6 term +off = omit disperion 1/r^6 term entirely
long = use long-range damping on Coulombic 1/r and point-dipole terms - off = omit Coulombic and point-dipole terms entirely +off = omit Coulombic and point-dipole terms entirely
lj/gromacs args = inner outer - inner, outer = global switching cutoffs for Lennard Jones - lj/gromacs/coul/gromacs args = inner outer (inner2) (outer2) - inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) - inner2, outer2 = global switching cutoffs for Coulombic (optional) + inner, outer = global switching cutoffs for Lennard Jones +lj/gromacs/coul/gromacs args = inner outer (inner2) (outer2) + inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args) + inner2, outer2 = global switching cutoffs for Coulombic (optional)
ID1 = atom ID of first atom
- ID2 = atom ID of second atom
- style = style of interaction
- coeffs = list of coeffs
- cutoff = cutoff for interaction (optional)
+ID2 = atom ID of second atom
+style = style of interaction
+coeffs = list of coeffs
+cutoff = cutoff for interaction (optional)
The cutoff parameter is optional. If not specified, the global cutoff diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 7101fd7f99..977c5eb706 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -236,36 +236,36 @@
lj/cut args = cutoff - cutoff = global cutoff for Lennard Jones interactions (distance units) - lj/cut/coul/cut args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/coul/debye args = kappa cutoff (cutoff2) - kappa = inverse of the Debye length (inverse distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/coul/dsf args = alpha cutoff (cutoff2) - alpha = damping parameter (inverse distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (distance units) - lj/cut/coul/long args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/coul/msm args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/tip4p/cut args = otype htype btype atype qdist cutoff (cutoff2) - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/tip4p/long args = otype htype btype atype qdist cutoff (cutoff2) - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for Lennard Jones interactions (distance units) +lj/cut/coul/cut args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/coul/debye args = kappa cutoff (cutoff2) + kappa = inverse of the Debye length (inverse distance units) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/coul/dsf args = alpha cutoff (cutoff2) + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (distance units) +lj/cut/coul/long args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/coul/msm args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/tip4p/cut args = otype htype btype atype qdist cutoff (cutoff2) + otype,htype = atom types for TIP4P O and H + btype,atype = bond and angle types for TIP4P waters + qdist = distance from O atom to massless charge (distance units) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/tip4p/long args = otype htype btype atype qdist cutoff (cutoff2) + otype,htype = atom types for TIP4P O and H + btype,atype = bond and angle types for TIP4P waters + qdist = distance from O atom to massless charge (distance units) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
lj/long/coul/long args = flag_lj flag_coul cutoff (cutoff2) - flag_lj = long or cut or off - long = use Kspace long-range summation for dispersion 1/r^6 term - cut = use a cutoff on dispersion 1/r^6 term - off = omit disperion 1/r^6 term entirely - flag_coul = long or off - long = use Kspace long-range summation for Coulombic 1/r term - off = omit Coulombic term - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2) - flag_lj = long or cut - long = use Kspace long-range summation for dispersion 1/r^6 term - cut = use a cutoff - flag_coul = long or off - long = use Kspace long-range summation for Coulombic 1/r term - off = omit Coulombic term - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + flag_lj = long or cut or off + long = use Kspace long-range summation for dispersion 1/r^6 term + cut = use a cutoff on dispersion 1/r^6 term + off = omit disperion 1/r^6 term entirely + flag_coul = long or off + long = use Kspace long-range summation for Coulombic 1/r term + off = omit Coulombic term + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/long/tip4p/long args = flag_lj flag_coul otype htype btype atype qdist cutoff (cutoff2) + flag_lj = long or cut + long = use Kspace long-range summation for dispersion 1/r^6 term + cut = use a cutoff + flag_coul = long or off + long = use Kspace long-range summation for Coulombic 1/r term + off = omit Coulombic term + otype,htype = atom types for TIP4P O and H + btype,atype = bond and angle types for TIP4P waters + qdist = distance from O atom to massless charge (distance units) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
lj/cut/soft args = n alpha_lj cutoff - n, alpha_LJ = parameters of soft-core potential - cutoff = global cutoff for Lennard-Jones interactions (distance units) - lj/cut/coul/cut/soft args = n alpha_LJ alpha_C cutoff (cutoff2) - n, alpha_LJ, alpha_C = parameters of soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/coul/long/soft args = n alpha_LJ alpha_C cutoff - n, alpha_LJ, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/cut/tip4p/long/soft args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2) - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - n, alpha_LJ, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - lj/charmm/coul/long/soft args = n alpha_LJ alpha_C inner outer (cutoff) - n, alpha_LJ, alpha_C = parameters of the soft-core potential - inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args) - cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args) - coul/cut/soft args = n alpha_C cutoff - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) - coul/long/soft args = n alpha_C cutoff - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) - tip4p/long/soft args = otype htype btype atype qdist n alpha_C cutoff - otype,htype = atom types for TIP4P O and H - btype,atype = bond and angle types for TIP4P waters - qdist = distance from O atom to massless charge (distance units) - n, alpha_C = parameters of the soft-core potential - cutoff = global cutoff for Coulomb interactions (distance units) + n, alpha_LJ = parameters of soft-core potential + cutoff = global cutoff for Lennard-Jones interactions (distance units) +lj/cut/coul/cut/soft args = n alpha_LJ alpha_C cutoff (cutoff2) + n, alpha_LJ, alpha_C = parameters of soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/coul/long/soft args = n alpha_LJ alpha_C cutoff + n, alpha_LJ, alpha_C = parameters of the soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/cut/tip4p/long/soft args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2) + otype,htype = atom types for TIP4P O and H + btype,atype = bond and angle types for TIP4P waters + qdist = distance from O atom to massless charge (distance units) + n, alpha_LJ, alpha_C = parameters of the soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +lj/charmm/coul/long/soft args = n alpha_LJ alpha_C inner outer (cutoff) + n, alpha_LJ, alpha_C = parameters of the soft-core potential + inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args) + cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args) +coul/cut/soft args = n alpha_C cutoff + n, alpha_C = parameters of the soft-core potential + cutoff = global cutoff for Coulomb interactions (distance units) +coul/long/soft args = n alpha_C cutoff + n, alpha_C = parameters of the soft-core potential + cutoff = global cutoff for Coulomb interactions (distance units) +tip4p/long/soft args = otype htype btype atype qdist n alpha_C cutoff + otype,htype = atom types for TIP4P O and H + btype,atype = bond and angle types for TIP4P waters + qdist = distance from O atom to massless charge (distance units) + n, alpha_C = parameters of the soft-core potential + cutoff = global cutoff for Coulomb interactions (distance units)
0 => G = sqrt(1+Gamma)
- 1 => G = exp(Gamma/2)
- 2 => not implemented
- 3 => G = 2/(1+exp(-Gamma))
- 4 => G = sqrt(1+Gamma)
- -5 => G = +-sqrt(abs(1+Gamma))
+ 0 => G = sqrt(1+Gamma)
+ 1 => G = exp(Gamma/2)
+ 2 => not implemented
+ 3 => G = 2/(1+exp(-Gamma))
+ 4 => G = sqrt(1+Gamma)
+-5 => G = +-sqrt(abs(1+Gamma))
If used, the MEAM parameter file contains settings that override or
diff --git a/doc/pair_modify.html b/doc/pair_modify.html
index 1bf713ad94..df61d1d294 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -137,23 +137,23 @@
pair values = sub-style N special which w1 wt2 wt3
- sub-style = sub-style of pair hybrid
- N = which instance of sub-style (only if sub-style is used multiple times)
- special values = flavor w1 w2 w3
- flavor = lj/coul or lj or coul
- w1,w2,w3 = weights from 0.0 to 1.0 inclusive
- mix value = geometric or arithmetic or sixthpower
- shift value = yes or no
- table value = N
- 2^N = # of values in table
- table/disp value = N
- 2^N = # of values in table
- tabinner value = cutoff
- cutoff = inner cutoff at which to begin table (distance units)
- tabinner/disp value = cutoff
- cutoff = inner cutoff at which to begin table (distance units)
- tail value = yes or no
- compute value = yes or no
+ sub-style = sub-style of pair hybrid
+ N = which instance of sub-style (only if sub-style is used multiple times)
+special values = flavor w1 w2 w3
+ flavor = lj/coul or lj or coul
+ w1,w2,w3 = weights from 0.0 to 1.0 inclusive
+mix value = geometric or arithmetic or sixthpower
+shift value = yes or no
+table value = N
+ 2^N = # of values in table
+table/disp value = N
+ 2^N = # of values in table
+tabinner value = cutoff
+ cutoff = inner cutoff at which to begin table (distance units)
+tabinner/disp value = cutoff
+ cutoff = inner cutoff at which to begin table (distance units)
+tail value = yes or no
+compute value = yes or no
nm/cut args = cutoff - cutoff = global cutoff for Pair interactions (distance units) - nm/cut/coul/cut args = cutoff (cutoff2) - cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - nm/cut/coul/long args = cutoff (cutoff2) - cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for Pair interactions (distance units) +nm/cut/coul/cut args = cutoff (cutoff2) + cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) +nm/cut/coul/long args = cutoff (cutoff2) + cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
lj/sdk args = cutoff - cutoff = global cutoff for Lennard Jones interactions (distance units) - lj/sdk/coul/long args = cutoff (cutoff2) - cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) + cutoff = global cutoff for Lennard Jones interactions (distance units) +lj/sdk/coul/long args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units)
variable zblcutinner equal 4
- variable zblcutouter equal 4.8
- variable zblz equal 73
- pair_style hybrid/overlay &
- zbl ${zblcutinner} ${zblcutouter} snap
- pair_coeff * * zbl 0.0
- pair_coeff 1 1 zbl ${zblz}
- pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
- ../potentials/Ta06A.snapparam Ta
+variable zblcutouter equal 4.8
+variable zblz equal 73
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} snap
+pair_coeff * * zbl 0.0
+pair_coeff 1 1 zbl ${zblz}
+pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+../potentials/Ta06A.snapparam Ta
It is convenient to keep these commands in a separate file that can diff --git a/doc/prd.html b/doc/prd.html index 65833d8c0c..07420fc597 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -144,18 +144,18 @@
min values = etol ftol maxiter maxeval - etol = stopping tolerance for energy, used in quenching - ftol = stopping tolerance for force, used in quenching - maxiter = max iterations of minimize, used in quenching - maxeval = max number of force/energy evaluations, used in quenching - temp value = Tdephase - Tdephase = target temperature for velocity randomization, used in dephasing - vel values = loop dist - loop = all or local or geom, used in dephasing - dist = uniform or gaussian, used in dephasing - time value = step or clock - step = simulation runs for N timesteps on each replica (default) - clock = simulation runs for N timesteps across all replicas + etol = stopping tolerance for energy, used in quenching + ftol = stopping tolerance for force, used in quenching + maxiter = max iterations of minimize, used in quenching + maxeval = max number of force/energy evaluations, used in quenching +temp value = Tdephase + Tdephase = target temperature for velocity randomization, used in dephasing +vel values = loop dist + loop = all or local or geom, used in dephasing + dist = uniform or gaussian, used in dephasing +time value = step or clock + step = simulation runs for N timesteps on each replica (default) + clock = simulation runs for N timesteps across all replicas
file value = filename - append value = filename - screen value = yes or no +append value = filename +screen value = yes or no
grid arg = gstyle params ... - gstyle = onelevel or twolevel or numa or custom - onelevel params = none - twolevel params = Nc Cx Cy Cz - Nc = number of cores per node - Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node - numa params = none - custom params = infile - infile = file containing grid layout - map arg = cart or cart/reorder or xyz or xzy or yxz or yzx or zxy or zyx - cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 - cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 - xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering - numa arg = none - part args = Psend Precv cstyle - Psend = partition # (1 to Np) which will send its processor layout - Precv = partition # (1 to Np) which will recv the processor layout - cstyle = multiple - multiple = Psend grid will be multiple of Precv grid in each dimension - file arg = outfile - outfile = name of file to write 3d grid of processors to + gstyle = onelevel or twolevel or numa or custom + onelevel params = none + twolevel params = Nc Cx Cy Cz + Nc = number of cores per node + Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node + numa params = none + custom params = infile + infile = file containing grid layout +map arg = cart or cart/reorder or xyz or xzy or yxz or yzx or zxy or zyx + cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 + cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 + xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering +numa arg = none +part args = Psend Precv cstyle + Psend = partition # (1 to Np) which will send its processor layout + Precv = partition # (1 to Np) which will recv the processor layout + cstyle = multiple + multiple = Psend grid will be multiple of Precv grid in each dimension +file arg = outfile + outfile = name of file to write 3d grid of processors to
# loop N times, increasing cutoff each time
for i in range(N):
- cut = cut0 + i*0.1
- lmp.set_variable("cut",cut) # set a variable in LAMMPS
- lmp.command("pair_style lj/cut $*cut*") # LAMMPS commands
- lmp.command("pair_coeff * * 1.0 1.0")
- lmp.command("run 100")
- """
+ for i in range(N):
+ cut = cut0 + i*0.1
+ lmp.set_variable("cut",cut) # set a variable in LAMMPS
+ lmp.command("pair_style lj/cut $*cut*") # LAMMPS commands
+ lmp.command("pair_coeff * * 1.0 1.0")
+ lmp.command("run 100")
+"""
for i in range(N):
- cut = cut0 + i*0.1
+ cut = cut0 + i*0.1
lmp.set_variable("cut",cut) # set a variable in LAMMPS
- lmp.command("pair_style lj/cut $*cut*") # LAMMPS command
- #lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
+lmp.set_variable("cut",cut) # set a variable in LAMMPS
+lmp.command("pair_style lj/cut $*cut*") # LAMMPS command
+#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
lmp.command("pair_coeff * * 1.0 1.0") # ditto
- lmp.command("run 10") # ditto
- pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
- print "PE",pe/natoms,thresh
- if pe/natoms < thresh: return
+lmp.command("run 10") # ditto
+pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
+print "PE",pe/natoms,thresh
+if pe/natoms < thresh: return
with these input script commands:
diff --git a/doc/read_data.html b/doc/read_data.html
index 42e8f24302..01d1b92d48 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -138,28 +138,28 @@
add arg = append or Nstart or merge
- append = add new atoms with IDs appended to current IDs
- Nstart = add new atoms with IDs starting with Nstart
- merge = add new atoms with their IDs unchanged
- offset args = toff boff aoff doff ioff
- toff = offset to add to atom types
- boff = offset to add to bond types
- aoff = offset to add to angle types
- doff = offset to add to dihedral types
- ioff = offset to add to improper types
- shift args = Sx Sy Sz
- Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
- extra/atom/types arg = # of extra atom types
- extra/bond/types arg = # of extra bond types
- extra/angle/types arg = # of extra angle types
- extra/dihedral/types arg = # of extra dihedral types
- extra/improper/types arg = # of extra improper types
- group args = groupID
- groupID = add atoms in data file to this group
- fix args = fix-ID header-string section-string
- fix-ID = ID of fix to process header lines and sections of data file
- header-string = header lines containing this string will be passed to fix
- section-string = section names with this string will be passed to fix
+ append = add new atoms with IDs appended to current IDs
+ Nstart = add new atoms with IDs starting with Nstart
+ merge = add new atoms with their IDs unchanged
+offset args = toff boff aoff doff ioff
+ toff = offset to add to atom types
+ boff = offset to add to bond types
+ aoff = offset to add to angle types
+ doff = offset to add to dihedral types
+ ioff = offset to add to improper types
+shift args = Sx Sy Sz
+ Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
+extra/atom/types arg = # of extra atom types
+extra/bond/types arg = # of extra bond types
+extra/angle/types arg = # of extra angle types
+extra/dihedral/types arg = # of extra dihedral types
+extra/improper/types arg = # of extra improper types
+group args = groupID
+ groupID = add atoms in data file to this group
+fix args = fix-ID header-string section-string
+ fix-ID = ID of fix to process header lines and sections of data file
+ header-string = header lines containing this string will be passed to fix
+ section-string = section names with this string will be passed to fix
ID = angle type (1-N)
- coeffs = list of coeffs
+coeffs = list of coeffs
ID = improper type (1-N) - coeffs = list of coeffs (see improper_coeff) +coeffs = list of coeffs (see improper_coeff)
AngleAngleTorsion Coeffs section:
@@ -562,7 +562,7 @@ ID = improper type (1-N)ID = dihedral type (1-N) - coeffs = list of coeffs (see dihedral_coeff) +coeffs = list of coeffs (see dihedral_coeff)
Angles section:
@@ -571,8 +571,8 @@ ID = dihedral type (1-N)ID = number of angle (1-Nangles)
- type = angle type (1-Nangletype)
- atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
+type = angle type (1-Nangletype)
+atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
example: @@ -593,7 +593,7 @@ integers (1, not 1.0).
ID = dihedral type (1-N) - coeffs = list of coeffs (see dihedral_coeff) +coeffs = list of coeffs (see dihedral_coeff)
Atoms section:
@@ -815,7 +815,7 @@ script.ninteger = # of integer quantities for this particle
- ndouble = # of floating-point quantities for this particle
+ndouble = # of floating-point quantities for this particle
12 3 6
- 2 3 2
- 1.0 2.0 3.0 1.0 2.0 4.0
+2 3 2
+1.0 2.0 3.0 1.0 2.0 4.0
12 0 14
- 1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
- 2.0 4.0 4.0 2.0
+1.0 2.0 3.0 1.0 2.0 4.0 1.0 2.0 3.0 1.0
+2.0 4.0 4.0 2.0
The Bodies section must appear if atom_style body @@ -863,7 +863,7 @@ e.g. there are no integer lines in the last example above.
ID = bond type (1-N)
- coeffs = list of coeffs
+coeffs = list of coeffs
ID = angle type (1-N) - coeffs = list of coeffs (see class 2 section of angle_coeff) +coeffs = list of coeffs (see class 2 section of angle_coeff)
BondBond Coeffs section:
@@ -895,7 +895,7 @@ ID = angle type (1-N)ID = angle type (1-N) - coeffs = list of coeffs (see class 2 section of angle_coeff) +coeffs = list of coeffs (see class 2 section of angle_coeff)
BondBond13 Coeffs section:
@@ -905,7 +905,7 @@ ID = angle type (1-N)ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of dihedral_coeff) +coeffs = list of coeffs (see class 2 section of dihedral_coeff)
Bonds section:
@@ -914,8 +914,8 @@ ID = dihedral type (1-N)ID = bond number (1-Nbonds)
- type = bond type (1-Nbondtype)
- atom1,atom2 = IDs of 1st,2nd atoms in bond
+type = bond type (1-Nbondtype)
+atom1,atom2 = IDs of 1st,2nd atoms in bond
ID = dihedral type (1-N)
- coeffs = list of coeffs
+coeffs = list of coeffs
ID = number of dihedral (1-Ndihedrals)
- type = dihedral type (1-Ndihedraltype)
- atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
+type = dihedral type (1-Ndihedraltype)
+atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
atom-ID = ID of atom which is an ellipsoid
- shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
- quatw,quati,quatj,quatk = quaternion components for orientation of atom
+shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
+quatw,quati,quatj,quatk = quaternion components for orientation of atom
ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of dihedral_coeff) +coeffs = list of coeffs (see class 2 section of dihedral_coeff)
Improper Coeffs section:
@@ -1020,7 +1020,7 @@ ID = dihedral type (1-N)ID = improper type (1-N)
- coeffs = list of coeffs
+coeffs = list of coeffs
ID = number of improper (1-Nimpropers)
- type = improper type (1-Nimpropertype)
- atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
+type = improper type (1-Nimpropertype)
+atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
atom-ID = ID of atom which is a line segment
- x1,y1 = 1st end point
- x2,y2 = 2nd end point
+x1,y1 = 1st end point
+x2,y2 = 2nd end point
ID = atom type (1-N)
- mass = mass value
+mass = mass value
ID = dihedral type (1-N) - coeffs = list of coeffs (see class 2 section of dihedral_coeff) +coeffs = list of coeffs (see class 2 section of dihedral_coeff)
Pair Coeffs section:
@@ -1121,7 +1121,7 @@ ID = dihedral type (1-N)ID = atom type (1-N)
- coeffs = list of coeffs
+coeffs = list of coeffs
ID1 = atom type I = 1-N
- ID2 = atom type J = I-N, with I <= J
- coeffs = list of coeffs
+ID2 = atom type J = I-N, with I <= J
+coeffs = list of coeffs
3 3 0.022 2.35197 0.022 2.35197
- 3 5 0.022 2.35197 0.022 2.35197
+3 5 0.022 2.35197 0.022 2.35197
This section must have N*(N+1)/2 lines where N = # of atom types. The @@ -1172,9 +1172,9 @@ script.
atom-ID = ID of atom which is a line segment
- x1,y1,z1 = 1st corner point
- x2,y2,z2 = 2nd corner point
- x3,y3,z3 = 3rd corner point
+x1,y1,z1 = 1st corner point
+x2,y2,z2 = 2nd corner point
+x3,y3,z3 = 3rd corner point
box value = yes or no = replace simulation box with dump box - replace value = yes or no = overwrite atoms with dump atoms - purge value = yes or no = delete all atoms before adding dump atoms - trim value = yes or no = trim atoms not in dump snapshot - add value = yes or no = add new dump atoms to system - label value = field column - field = one of the listed fields or id or type - column = label on corresponding column in dump file - scaled value = yes or no = coords in dump file are scaled/unscaled - wrapped value = yes or no = coords in dump file are wrapped/unwrapped - format values = format of dump file, must be last keyword if used - native = native LAMMPS dump file - xyz = XYZ file - molfile style path = VMD molfile plugin interface - style = dcd or xyz or others supported by molfile plugins - path = optional path for location of molfile plugins +replace value = yes or no = overwrite atoms with dump atoms +purge value = yes or no = delete all atoms before adding dump atoms +trim value = yes or no = trim atoms not in dump snapshot +add value = yes or no = add new dump atoms to system +label value = field column + field = one of the listed fields or id or type + column = label on corresponding column in dump file +scaled value = yes or no = coords in dump file are scaled/unscaled +wrapped value = yes or no = coords in dump file are wrapped/unwrapped +format values = format of dump file, must be last keyword if used + native = native LAMMPS dump file + xyz = XYZ file + molfile style path = VMD molfile plugin interface + style = dcd or xyz or others supported by molfile plugins + path = optional path for location of molfile plugins
delete = no args - block args = xlo xhi ylo yhi zlo zhi - xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units) - cone args = dim c1 c2 radlo radhi lo hi - dim = x or y or z = axis of cone - c1,c2 = coords of cone axis in other 2 dimensions (distance units) - radlo,radhi = cone radii at lo and hi end (distance units) - lo,hi = bounds of cone in dim (distance units) - cylinder args = dim c1 c2 radius lo hi - dim = x or y or z = axis of cylinder - c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) - radius = cylinder radius (distance units) - radius can be a variable (see below) - lo,hi = bounds of cylinder in dim (distance units) - plane args = px py pz nx ny nz - px,py,pz = point on the plane (distance units) - nx,ny,nz = direction normal to plane (distance units) - prism args = xlo xhi ylo yhi zlo zhi xy xz yz - xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units) - xy = distance to tilt y in x direction (distance units) - xz = distance to tilt z in x direction (distance units) - yz = distance to tilt z in y direction (distance units) - sphere args = x y z radius - x,y,z = center of sphere (distance units) - radius = radius of sphere (distance units) - radius can be a variable (see below) - union args = N reg-ID1 reg-ID2 ... - N = # of regions to follow, must be 2 or greater - reg-ID1,reg-ID2, ... = IDs of regions to join together - intersect args = N reg-ID1 reg-ID2 ... - N = # of regions to follow, must be 2 or greater - reg-ID1,reg-ID2, ... = IDs of regions to intersect +block args = xlo xhi ylo yhi zlo zhi + xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units) +cone args = dim c1 c2 radlo radhi lo hi + dim = x or y or z = axis of cone + c1,c2 = coords of cone axis in other 2 dimensions (distance units) + radlo,radhi = cone radii at lo and hi end (distance units) + lo,hi = bounds of cone in dim (distance units) +cylinder args = dim c1 c2 radius lo hi + dim = x or y or z = axis of cylinder + c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + radius = cylinder radius (distance units) + radius can be a variable (see below) + lo,hi = bounds of cylinder in dim (distance units) +plane args = px py pz nx ny nz + px,py,pz = point on the plane (distance units) + nx,ny,nz = direction normal to plane (distance units) +prism args = xlo xhi ylo yhi zlo zhi xy xz yz + xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units) + xy = distance to tilt y in x direction (distance units) + xz = distance to tilt z in x direction (distance units) + yz = distance to tilt z in y direction (distance units) +sphere args = x y z radius + x,y,z = center of sphere (distance units) + radius = radius of sphere (distance units) + radius can be a variable (see below) +union args = N reg-ID1 reg-ID2 ... + N = # of regions to follow, must be 2 or greater + reg-ID1,reg-ID2, ... = IDs of regions to join together +intersect args = N reg-ID1 reg-ID2 ... + N = # of regions to follow, must be 2 or greater + reg-ID1,reg-ID2, ... = IDs of regions to intersect
side value = in or out - in = the region is inside the specified geometry - out = the region is outside the specified geometry - units value = lattice or box - lattice = the geometry is defined in lattice units - box = the geometry is defined in simulation box units - move args = v_x v_y v_z - v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time - rotate args = v_theta Px Py Pz Rx Ry Rz - v_theta = equal-style variable for rotaton of region over time (in radians) - Px,Py,Pz = origin for axis of rotation (distance units) - Rx,Ry,Rz = axis of rotation vector + in = the region is inside the specified geometry + out = the region is outside the specified geometry +units value = lattice or box + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units +move args = v_x v_y v_z + v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time +rotate args = v_theta Px Py Pz Rx Ry Rz + v_theta = equal-style variable for rotaton of region over time (in radians) + Px,Py,Pz = origin for axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector
fileper arg = Np - Np = write one file for every this many processors - nfile arg = Nf - Nf = write this many files, one from each of Nf processors + Np = write one file for every this many processors +nfile arg = Nf + Nf = write this many files, one from each of Nf processors
upto value = none - start value = N1 - N1 = timestep at which 1st run started - stop value = N2 - N2 = timestep at which last run will end - pre value = no or yes - post value = no or yes - every values = M c1 c2 ... - M = break the run into M-timestep segments and invoke one or more commands between each segment - c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes - c1 = NULL means no command will be invoked +start value = N1 + N1 = timestep at which 1st run started +stop value = N2 + N2 = timestep at which last run will end +pre value = no or yes +post value = no or yes +every values = M c1 c2 ... + M = break the run into M-timestep segments and invoke one or more commands between each segment + c1,c2,...,cN = one or more LAMMPS commands, each enclosed in quotes + c1 = NULL means no command will be invoked
verlet args = none - verlet/split args = none - respa args = N n1 n2 ... keyword values ... - N = # of levels of rRESPA - n1, n2, ... = loop factor between rRESPA levels (N-1 values) - zero or more keyword/value pairings may be appended to the loop factors - keyword = bond or angle or dihedral or improper or - pair or inner or middle or outer or hybrid or kspace - bond value = M - M = which level (1-N) to compute bond forces in - angle value = M - M = which level (1-N) to compute angle forces in - dihedral value = M - M = which level (1-N) to compute dihedral forces in - improper value = M - M = which level (1-N) to compute improper forces in - pair value = M - M = which level (1-N) to compute pair forces in - inner values = M cut1 cut2 - M = which level (1-N) to compute pair inner forces in - cut1 = inner cutoff between pair inner and - pair middle or outer (distance units) - cut2 = outer cutoff between pair inner and - pair middle or outer (distance units) - middle values = M cut1 cut2 - M = which level (1-N) to compute pair middle forces in - cut1 = inner cutoff between pair middle and pair outer (distance units) - cut2 = outer cutoff between pair middle and pair outer (distance units) - outer value = M - M = which level (1-N) to compute pair outer forces in - hybrid values = M1 [M2 ...] (as many values as there are hybrid sub-styles - M1 = which level (1-N) to compute the first pair_style hybrid sub-style in - M2 = which level (1-N) to compute the second pair_style hybrid sub-style in - ... - kspace value = M - M = which level (1-N) to compute kspace forces in +verlet/split args = none +respa args = N n1 n2 ... keyword values ... + N = # of levels of rRESPA + n1, n2, ... = loop factor between rRESPA levels (N-1 values) + zero or more keyword/value pairings may be appended to the loop factors + keyword = bond or angle or dihedral or improper or + pair or inner or middle or outer or hybrid or kspace + bond value = M + M = which level (1-N) to compute bond forces in + angle value = M + M = which level (1-N) to compute angle forces in + dihedral value = M + M = which level (1-N) to compute dihedral forces in + improper value = M + M = which level (1-N) to compute improper forces in + pair value = M + M = which level (1-N) to compute pair forces in + inner values = M cut1 cut2 + M = which level (1-N) to compute pair inner forces in + cut1 = inner cutoff between pair inner and + pair middle or outer (distance units) + cut2 = outer cutoff between pair inner and + pair middle or outer (distance units) + middle values = M cut1 cut2 + M = which level (1-N) to compute pair middle forces in + cut1 = inner cutoff between pair middle and pair outer (distance units) + cut2 = outer cutoff between pair middle and pair outer (distance units) + outer value = M + M = which level (1-N) to compute pair outer forces in + hybrid values = M1 [M2 ...] (as many values as there are hybrid sub-styles + M1 = which level (1-N) to compute the first pair_style hybrid sub-style in + M2 = which level (1-N) to compute the second pair_style hybrid sub-style in + ... + kspace value = M + M = which level (1-N) to compute kspace forces in
type value = atom type - value can be an atom-style variable (see below) - type/fraction values = type fraction seed - type = new atom type - fraction = fraction of selected atoms to set to new atom type - seed = random # seed (positive integer) - mol value = molecule ID - value can be an atom-style variable (see below) - x,*y*,*z* value = atom coordinate (distance units) - value can be an atom-style variable (see below) - charge value = atomic charge (charge units) - value can be an atom-style variable (see below) - dipole values = x y z - x,y,z = orientation of dipole moment vector - any of x,y,z can be an atom-style variable (see below) - dipole/random value = seed Dlen - seed = random # seed (positive integer) for dipole moment orientations - Dlen = magnitude of dipole moment (dipole units) - quat values = a b c theta - a,b,c = unit vector to rotate particle around via right-hand rule - theta = rotation angle (degrees) - any of a,b,c,theta can be an atom-style variable (see below) - quat/random value = seed - seed = random # seed (positive integer) for quaternion orientations - diameter value = diameter of spherical particle (distance units) - value can be an atom-style variable (see below) - shape value = Sx Sy Sz - Sx,Sy,Sz = 3 diameters of ellipsoid (distance units) - length value = len - len = length of line segment (distance units) - len can be an atom-style variable (see below) - tri value = side - side = side length of equilateral triangle (distance units) - side can be an atom-style variable (see below) - theta value = angle (degrees) - angle = orientation of line segment with respect to x-axis - angle can be an atom-style variable (see below) - angmom values = Lx Ly Lz - Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units) - any of Lx,Ly,Lz can be an atom-style variable (see below) - mass value = per-atom mass (mass units) - value can be an atom-style variable (see below) - density value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) - value can be an atom-style variable (see below) - volume value = particle volume for Peridynamic particle (distance^3 units) - value can be an atom-style variable (see below) - image nx ny nz - nx,ny,nz = which periodic image of the simulation box the atom is in - bond value = bond type for all bonds between selected atoms - angle value = angle type for all angles between selected atoms - dihedral value = dihedral type for all dihedrals between selected atoms - improper value = improper type for all impropers between selected atoms - meso_e value = energy of SPH particles (need units) - value can be an atom-style variable (see below) - meso_cv value = heat capacity of SPH particles (need units) - value can be an atom-style variable (see below) - meso_rho value = density of SPH particles (need units) - value can be an atom-style variable (see below) - i_name value = value for custom integer vector with name - value can be an atom-style variable (see below) - d_name value = value for custom floating-point vector with name - value can be an atom-style variable (see below) + value can be an atom-style variable (see below) +type/fraction values = type fraction seed + type = new atom type + fraction = fraction of selected atoms to set to new atom type + seed = random # seed (positive integer) +mol value = molecule ID + value can be an atom-style variable (see below) +x,*y*,*z* value = atom coordinate (distance units) + value can be an atom-style variable (see below) +charge value = atomic charge (charge units) + value can be an atom-style variable (see below) +dipole values = x y z + x,y,z = orientation of dipole moment vector + any of x,y,z can be an atom-style variable (see below) +dipole/random value = seed Dlen + seed = random # seed (positive integer) for dipole moment orientations + Dlen = magnitude of dipole moment (dipole units) +quat values = a b c theta + a,b,c = unit vector to rotate particle around via right-hand rule + theta = rotation angle (degrees) + any of a,b,c,theta can be an atom-style variable (see below) +quat/random value = seed + seed = random # seed (positive integer) for quaternion orientations +diameter value = diameter of spherical particle (distance units) + value can be an atom-style variable (see below) +shape value = Sx Sy Sz + Sx,Sy,Sz = 3 diameters of ellipsoid (distance units) +length value = len + len = length of line segment (distance units) + len can be an atom-style variable (see below) +tri value = side + side = side length of equilateral triangle (distance units) + side can be an atom-style variable (see below) +theta value = angle (degrees) + angle = orientation of line segment with respect to x-axis + angle can be an atom-style variable (see below) +angmom values = Lx Ly Lz + Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units) + any of Lx,Ly,Lz can be an atom-style variable (see below) +mass value = per-atom mass (mass units) + value can be an atom-style variable (see below) +density value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) + value can be an atom-style variable (see below) +volume value = particle volume for Peridynamic particle (distance^3 units) + value can be an atom-style variable (see below) +image nx ny nz + nx,ny,nz = which periodic image of the simulation box the atom is in +bond value = bond type for all bonds between selected atoms +angle value = angle type for all angles between selected atoms +dihedral value = dihedral type for all dihedrals between selected atoms +improper value = improper type for all impropers between selected atoms +meso_e value = energy of SPH particles (need units) + value can be an atom-style variable (see below) +meso_cv value = heat capacity of SPH particles (need units) + value can be an atom-style variable (see below) +meso_rho value = density of SPH particles (need units) + value can be an atom-style variable (see below) +i_name value = value for custom integer vector with name + value can be an atom-style variable (see below) +d_name value = value for custom floating-point vector with name + value can be an atom-style variable (see below)
cd arg = dir - dir = directory to change to - mkdir args = dir1 dir2 ... - dir1,dir2 = one or more directories to create - mv args = old new - old = old filename - new = new filename - rm args = file1 file2 ... - file1,file2 = one or more filenames to delete - rmdir args = dir1 dir2 ... - dir1,dir2 = one or more directories to delete - putenv args = var1=value1 var2=value2 - var=value = one of more definitions of environment variables - anything else is passed as a command to the shell for direct execution + dir = directory to change to +mkdir args = dir1 dir2 ... + dir1,dir2 = one or more directories to create +mv args = old new + old = old filename + new = new filename +rm args = file1 file2 ... + file1,file2 = one or more filenames to delete +rmdir args = dir1 dir2 ... + dir1,dir2 = one or more directories to delete +putenv args = var1=value1 var2=value2 + var=value = one of more definitions of environment variables +anything else is passed as a command to the shell for direct execution
amber values = none - charmm values = none - dreiding values = none - fene values = none - lj/coul values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions - lj values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions - coul values = w1,w2,w3 - w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions - angle value = yes or no - dihedral value = yes or no - extra value = N - N = number of extra 1-2,1-3,1-4 interactions to save space for +charmm values = none +dreiding values = none +fene values = none +lj/coul values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions +lj values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions +coul values = w1,w2,w3 + w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions +angle value = yes or no +dihedral value = yes or no +extra value = N + N = number of extra 1-2,1-3,1-4 interactions to save space for
Examples:
special_bonds amber
diff --git a/doc/tad.html b/doc/tad.html
index aa0bff9b8e..843fc4a7bb 100644
--- a/doc/tad.html
+++ b/doc/tad.html
@@ -144,20 +144,20 @@
min values = etol ftol maxiter maxeval
- etol = stopping tolerance for energy (energy units)
- ftol = stopping tolerance for force (force units)
- maxiter = max iterations of minimize
- maxeval = max number of force/energy evaluations
- neb values = ftol N1 N2 Nevery
- etol = stopping tolerance for energy (energy units)
- ftol = stopping tolerance for force (force units)
- N1 = max # of iterations (timesteps) to run initial NEB
- N2 = max # of iterations (timesteps) to run barrier-climbing NEB
- Nevery = print NEB statistics every this many timesteps
- neb_style value = quickmin or fire
- neb_step value = dtneb
- dtneb = timestep for NEB damped dynamics minimization
- neb_log value = file where NEB statistics are printed
+ etol = stopping tolerance for energy (energy units)
+ ftol = stopping tolerance for force (force units)
+ maxiter = max iterations of minimize
+ maxeval = max number of force/energy evaluations
+neb values = ftol N1 N2 Nevery
+ etol = stopping tolerance for energy (energy units)
+ ftol = stopping tolerance for force (force units)
+ N1 = max # of iterations (timesteps) to run initial NEB
+ N2 = max # of iterations (timesteps) to run barrier-climbing NEB
+ Nevery = print NEB statistics every this many timesteps
+neb_style value = quickmin or fire
+neb_step value = dtneb
+ dtneb = timestep for NEB damped dynamics minimization
+neb_log value = file where NEB statistics are printed
one args = none - multi args = none - custom args = list of keywords - possible keywords = step, elapsed, elaplong, dt, time, - cpu, tpcpu, spcpu, cpuremain, part, - atoms, temp, press, pe, ke, etotal, enthalpy, - evdwl, ecoul, epair, ebond, eangle, edihed, eimp, - emol, elong, etail, - vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, - xy, xz, yz, xlat, ylat, zlat, - bonds, angles, dihedrals, impropers, - pxx, pyy, pzz, pxy, pxz, pyz, - fmax, fnorm, nbuild, ndanger, - cella, cellb, cellc, cellalpha, cellbeta, cellgamma, - c_ID, c_ID[I], c_ID[I][J], - f_ID, f_ID[I], f_ID[I][J], - v_name - step = timestep - elapsed = timesteps since start of this run - elaplong = timesteps since start of initial run in a series of runs - dt = timestep size - time = simulation time - cpu = elapsed CPU time in seconds - tpcpu = time per CPU second - spcpu = timesteps per CPU second - cpuremain = estimated CPU time remaining in run - part = which partition (0 to Npartition-1) this is - atoms = # of atoms - temp = temperature - press = pressure - pe = total potential energy - ke = kinetic energy - etotal = total energy (pe + ke) - enthalpy = enthalpy (etotal + press*vol) - evdwl = VanderWaal pairwise energy - ecoul = Coulombic pairwise energy - epair = pairwise energy (evdwl + ecoul + elong + etail) - ebond = bond energy - eangle = angle energy - edihed = dihedral energy - eimp = improper energy - emol = molecular energy (ebond + eangle + edihed + eimp) - elong = long-range kspace energy - etail = VanderWaal energy long-range tail correction - vol = volume - density = mass density of system - lx,ly,lz = box lengths in x,y,z - xlo,xhi,ylo,yhi,zlo,zhi = box boundaries - xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes - xlat,ylat,zlat = lattice spacings as calculated by lattice command - bonds,angles,dihedrals,impropers = # of these interactions defined - pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor - fmax = max component of force on any atom in any dimension - fnorm = length of force vector for all atoms - nbuild = # of neighbor list builds - ndanger = # of dangerous neighbor list builds - cella,cellb,cellc = periodic cell lattice constants a,b,c - cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma - c_ID = global scalar value calculated by a compute with ID - c_ID[I] = Ith component of global vector calculated by a compute with ID - c_ID[I][J] = I,J component of global array calculated by a compute with ID - f_ID = global scalar value calculated by a fix with ID - f_ID[I] = Ith component of global vector calculated by a fix with ID - f_ID[I][J] = I,J component of global array calculated by a fix with ID - v_name = scalar value calculated by an equal-style variable with name +multi args = none +custom args = list of keywords + possible keywords = step, elapsed, elaplong, dt, time, + cpu, tpcpu, spcpu, cpuremain, part, + atoms, temp, press, pe, ke, etotal, enthalpy, + evdwl, ecoul, epair, ebond, eangle, edihed, eimp, + emol, elong, etail, + vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi, + xy, xz, yz, xlat, ylat, zlat, + bonds, angles, dihedrals, impropers, + pxx, pyy, pzz, pxy, pxz, pyz, + fmax, fnorm, nbuild, ndanger, + cella, cellb, cellc, cellalpha, cellbeta, cellgamma, + c_ID, c_ID[I], c_ID[I][J], + f_ID, f_ID[I], f_ID[I][J], + v_name + step = timestep + elapsed = timesteps since start of this run + elaplong = timesteps since start of initial run in a series of runs + dt = timestep size + time = simulation time + cpu = elapsed CPU time in seconds + tpcpu = time per CPU second + spcpu = timesteps per CPU second + cpuremain = estimated CPU time remaining in run + part = which partition (0 to Npartition-1) this is + atoms = # of atoms + temp = temperature + press = pressure + pe = total potential energy + ke = kinetic energy + etotal = total energy (pe + ke) + enthalpy = enthalpy (etotal + press*vol) + evdwl = VanderWaal pairwise energy + ecoul = Coulombic pairwise energy + epair = pairwise energy (evdwl + ecoul + elong + etail) + ebond = bond energy + eangle = angle energy + edihed = dihedral energy + eimp = improper energy + emol = molecular energy (ebond + eangle + edihed + eimp) + elong = long-range kspace energy + etail = VanderWaal energy long-range tail correction + vol = volume + density = mass density of system + lx,ly,lz = box lengths in x,y,z + xlo,xhi,ylo,yhi,zlo,zhi = box boundaries + xy,xz,yz = box tilt for triclinic (non-orthogonal) simulation boxes + xlat,ylat,zlat = lattice spacings as calculated by lattice command + bonds,angles,dihedrals,impropers = # of these interactions defined + pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor + fmax = max component of force on any atom in any dimension + fnorm = length of force vector for all atoms + nbuild = # of neighbor list builds + ndanger = # of dangerous neighbor list builds + cella,cellb,cellc = periodic cell lattice constants a,b,c + cellalpha, cellbeta, cellgamma = periodic cell angles alpha,beta,gamma + c_ID = global scalar value calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID + c_ID[I][J] = I,J component of global array calculated by a compute with ID + f_ID = global scalar value calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID + f_ID[I][J] = I,J component of global array calculated by a fix with ID + v_name = scalar value calculated by an equal-style variable with name
delete = no args - index args = one or more strings - loop args = N - N = integer size of loop, loop from 1 to N inclusive - loop args = N pad - N = integer size of loop, loop from 1 to N inclusive - pad = all values will be same length, e.g. 001, 002, ..., 100 - loop args = N1 N2 - N1,N2 = loop from N1 to N2 inclusive - loop args = N1 N2 pad - N1,N2 = loop from N1 to N2 inclusive - pad = all values will be same length, e.g. 050, 051, ..., 100 - world args = one string for each partition of processors - universe args = one or more strings - uloop args = N - N = integer size of loop - uloop args = N pad - N = integer size of loop - pad = all values will be same length, e.g. 001, 002, ..., 100 - string arg = one string - format args = vname fstr - vname = name of equal-style variable to evaluate - fstr = C-style format string - getenv arg = one string - file arg = filename - atomfile arg = filename - python arg = function - equal or atom args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references - numbers = 0.0, 100, -5.4, 2.8e-4, etc - constants = PI - thermo keywords = vol, ke, press, etc from thermo_style - math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, - x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x - math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), - sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), - random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) - ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), - stride(x,y,z), stride2(x,y,z,a,b,c), - vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) - group functions = count(group), mass(group), charge(group), - xcm(group,dim), vcm(group,dim), fcm(group,dim), - bound(group,dir), gyration(group), ke(group), - angmom(group,dim), torque(group,dim), - inertia(group,dimdim), omega(group,dim) - region functions = count(group,region), mass(group,region), charge(group,region), - xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region), - bound(group,dir,region), gyration(group,region), ke(group,reigon), - angmom(group,dim,region), torque(group,dim,region), - inertia(group,dimdim,region), omega(group,dim,region) - special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) - atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] - atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q - compute references = c_ID, c_ID[i], c_ID[i][j] - fix references = f_ID, f_ID[i], f_ID[i][j] - variable references = v_name, v_name[i] +index args = one or more strings +loop args = N + N = integer size of loop, loop from 1 to N inclusive +loop args = N pad + N = integer size of loop, loop from 1 to N inclusive + pad = all values will be same length, e.g. 001, 002, ..., 100 +loop args = N1 N2 + N1,N2 = loop from N1 to N2 inclusive +loop args = N1 N2 pad + N1,N2 = loop from N1 to N2 inclusive + pad = all values will be same length, e.g. 050, 051, ..., 100 +world args = one string for each partition of processors +universe args = one or more strings +uloop args = N + N = integer size of loop +uloop args = N pad + N = integer size of loop + pad = all values will be same length, e.g. 001, 002, ..., 100 +string arg = one string +format args = vname fstr + vname = name of equal-style variable to evaluate + fstr = C-style format string +getenv arg = one string +file arg = filename +atomfile arg = filename +python arg = function +equal or atom args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute/fix/variable references + numbers = 0.0, 100, -5.4, 2.8e-4, etc + constants = PI + thermo keywords = vol, ke, press, etc from thermo_style + math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, + x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x + math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), + sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), + random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) + ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), + stride(x,y,z), stride2(x,y,z,a,b,c), + vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) + group functions = count(group), mass(group), charge(group), + xcm(group,dim), vcm(group,dim), fcm(group,dim), + bound(group,dir), gyration(group), ke(group), + angmom(group,dim), torque(group,dim), + inertia(group,dimdim), omega(group,dim) + region functions = count(group,region), mass(group,region), charge(group,region), + xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region), + bound(group,dir,region), gyration(group,region), ke(group,reigon), + angmom(group,dim,region), torque(group,dim,region), + inertia(group,dimdim,region), omega(group,dim,region) + special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) + atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] + atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q + compute references = c_ID, c_ID[i], c_ID[i][j] + fix references = f_ID, f_ID[i], f_ID[i][j] + variable references = v_name, v_name[i]
create args = temp seed - temp = temperature value (temperature units) - seed = random # seed (positive integer) - set args = vx vy vz - vx,vy,vz = velocity value or NULL (velocity units) - any of vx,vy,vz van be a variable (see below) - scale arg = temp - temp = temperature value (temperature units) - ramp args = vdim vlo vhi dim clo chi - vdim = vx or vy or vz - vlo,vhi = lower and upper velocity value (velocity units) - dim = x or y or z - clo,chi = lower and upper coordinate bound (distance units) - zero arg = linear or angular - linear = zero the linear momentum - angular = zero the angular momentum + temp = temperature value (temperature units) + seed = random # seed (positive integer) +set args = vx vy vz + vx,vy,vz = velocity value or NULL (velocity units) + any of vx,vy,vz van be a variable (see below) +scale arg = temp + temp = temperature value (temperature units) +ramp args = vdim vlo vhi dim clo chi + vdim = vx or vy or vz + vlo,vhi = lower and upper velocity value (velocity units) + dim = x or y or z + clo,chi = lower and upper coordinate bound (distance units) +zero arg = linear or angular + linear = zero the linear momentum + angular = zero the angular momentum
dist value = uniform or gaussian - sum value = no or yes - mom value = no or yes - rot value = no or yes - temp value = temperature compute ID - bias value = no or yes - loop value = all or local or geom - rigid value = fix-ID - fix-ID = ID of rigid body fix - units value = box or lattice +sum value = no or yes +mom value = no or yes +rot value = no or yes +temp value = temperature compute ID +bias value = no or yes +loop value = all or local or geom +rigid value = fix-ID + fix-ID = ID of rigid body fix +units value = box or lattice
nocoeff = do not write out force field info - pair value = ii or ij - ii = write one line of pair coefficient info per atom type - ij = write one line of pair coefficient info per IJ atom type pair +pair value = ii or ij + ii = write one line of pair coefficient info per atom type + ij = write one line of pair coefficient info per IJ atom type pair
fileper arg = Np - Np = write one file for every this many processors - nfile arg = Nf - Nf = write this many files, one from each of Nf processors + Np = write one file for every this many processors +nfile arg = Nf + Nf = write this many files, one from each of Nf processors