compute ID group-ID msd/nongauss keyword values ...
ID, group-ID are documented in compute command
-msd/nongauss = style name of this compute command
-zero or more keyword/value pairs may be appended
-keyword = com
+com value = yes or no-
compute ID group-ID saed lambda type1 type2 ... typeN keyword value ...
ID, group-ID are documented in compute command
-saed = style name of this compute command
-lambda = wavelength of incident radiation (length units)
-type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)
-zero or more keyword/value pairs may be appended
-keyword = Kmax or Zone or dR_Ewald or c or manual or echo
+
Kmax value = Maximum distance explored from reciprocal space origin
(inverse length units)
@@ -314,8 +310,6 @@
based on the values of the c parameters
echo = flag to provide extra output for debugging purposes
-create_atoms type style args keyword values ...-
type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
-style = box or region or single or random
+box args = none region args = region-ID @@ -290,10 +290,10 @@ create_atoms type style args keyword values ... seed = random # seed (positive integer) region-ID = create atoms within this region, use NULL for entire simulation box-
zero or more keyword/value pairs may be appended
-keyword = mol or basis or remap or var or set or units
+mol value = template-ID seed template-ID = ID of molecule template specified in a separate molecule command @@ -313,8 +313,6 @@ create_atoms type style args keyword values ... lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units-
fix ID group-ID box/relax keyword value ...
ID, group-ID are documented in fix command
-box/relax = style name of this fix command
+
one or more keyword value pairs may be appended
keyword = iso or aniso or tri or x or y or z or xy or yz or xz or couple or nreset or vmax or dilate or scaleyz or scalexz or scalexy or fixedpoint
@@ -391,8 +391,6 @@ keyword = iso or aniso or tri or x or y<
fixedpoint values = x y z
x,y,z = perform relaxation dilation/contraction around this point (distance units)
-fix ID group-ID controller Nevery alpha Kp Ki Kd pvar setpoint cvar
ID, group-ID are documented in fix command
-controller = style name of this fix command
-Nevery = invoke controller every this many timesteps
-alpha = coupling constant for PID equation (see units discussion below)
-Kp = proportional gain in PID equation (unitless)
-Ki = integral gain in PID equation (unitless)
-Kd = derivative gain in PID equation (unitless)
-pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or 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 @@ -394,11 +388,9 @@ 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 = value calculated by an equal-style variable with name-
setpoint = desired value of process variable (same units as process variable)
-cvar = name of control variable
-fix ID group-ID ehex nevery F keyword value
ID, group-ID are documented in fix command
-ehex = style name of this fix command
-nevery = add/subtract heat every this many timesteps
-F = energy flux into the reservoir (energy/time units)
-zero or more keyword/value pairs may be appended to args
-keyword = region or constrain or com or hex
+region value = region-ID region-ID = ID of region (reservoir) atoms must be in for added thermostatting force @@ -393,8 +389,6 @@ hex value = none omit the coordinate correction to recover the HEX algorithm-
fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...-
ID, group-ID are documented in fix command
-gld = style name of this fix command
-Tstart,Tstop = desired temperature at start/end of run (temperature units)
-N_k = number of terms in the Prony series representation of the memory kernel
-seed = random number seed to use for white noise (positive integer)
-series = pprony is presently the only available option
-c_k = the weight of the kth term in the Prony series (mass per time units)
-tau_k = the time constant of the kth term in the Prony series (time units)
-zero or more keyword/value pairs may be appended
+
keyword = frozen or zero
frozen value = no or yes
@@ -399,8 +392,6 @@ keyword = frozen or zero
no = do not set total random force to zero
yes = set total random force to zero
-Apply a Langevin thermostat as described in (Schneider) +
Apply a Langevin thermostat as described in (Schneider) to a group of atoms which models an interaction with a background implicit solvent. Used with fix nve, this command performs Brownian dynamics (BD), since the total force on each atom @@ -452,7 +452,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired temperature, m is the mass of the particle, dt is the timestep size, and damp is the damping factor. Random numbers are used to randomize the direction and magnitude of this force as described in -(Dunweg), where a uniform random number is used (instead of +(Dunweg), where a uniform random number is used (instead of a Gaussian random number) for speed.
Note that unless you use the omega or angmom keywords, the thermostat effect of this fix is applied to only the translational diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index d3d4f63a2e..cb6d92d48b 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -372,23 +372,17 @@
fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ...
ID, group-ID are documented in fix command
-lb/fluid = style name of this fix command
-nevery = update the lattice-Boltzmann fluid every this many timesteps
-LBtype = 1 to use the standard finite difference LB integrator, -2 to use the LB integrator of Ollila et al.
-viscosity = the fluid viscosity (units of mass/(time*length)).
-density = the fluid density.
-zero or more keyword/value pairs may be appended
-keyword = setArea or setGamma or scaleGamma or dx or dm or a0 or noise or calcforce or trilinear or D3Q19 or read_restart or write_restart or zwall_velocity or bodyforce or printfluid
+
setArea values = type node_area
type = atom type (1-N)
@@ -415,8 +409,6 @@
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.
-fix ID group-ID pimd keyword value ...
ID, group-ID are documented in fix command
-pimd = style name of this fix command
-zero or more keyword/value pairs may be appended
-keyword = method or fmass or sp or temp or nhc
+method value = pimd or nmpimd or cmd fmass value = scaling factor on mass @@ -386,8 +384,6 @@ temp value = temperature (temperarate units) nhc value = Nc = number of chains in Nose-Hoover thermostat-
fix ID group-ID qbmsst dir shockvel keyword value ...
ID, group-ID are documented in fix command
-qbmsst = style name of this fix
-dir = x or y or z
-shockvel = shock velocity (strictly positive, velocity units)
-zero or more keyword/value pairs may be appended
-keyword = q or mu or p0 or v0 or e0 or tscale or damp or seedor f_max or N_f or eta or beta or T_init
+q value = cell mass-like parameter (mass^2/distance^4 units) mu value = artificial viscosity (mass/distance/time units) @@ -399,8 +395,6 @@ beta value = the quantum temperature is updated every beta time steps (positive integer) T_init value = quantum temperature for the initial state (temperature units)-
fix ID group-ID restrain keyword args ...
ID, group-ID are documented in fix command
-restrain = style name of this fix command
-one or more keyword/arg pairs may be appended
-keyword = bond or angle or dihedral
+bond args = atom1 atom2 Kstart Kstop r0 atom1,atom2 = IDs of 2 atoms in bond @@ -392,8 +390,6 @@ Kstart,Kstop = restraint coefficients at start/end of run (energy units) phi0 = equilibrium dihedral angle phi (degrees)-
fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...-
ID, group-ID are documented in fix command
-ti/rs = style name of this fix command
-lambda_initial/lambda_final = initial/final values of the coupling parameter
-t_switch/t_equil = number of steps of the switching/equilibration procedure
-keyword = function
+function value = function-ID function-ID = ID of the switching function (1, 2 or 3)-
Example:
fix ref all ti/rs 50.0 2000 1000
fix vf vacancy ti/rs 10.0 70000 50000 function 2
diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html
index 046489d447..ed0b6da5fc 100644
--- a/doc/html/fix_ttm.html
+++ b/doc/html/fix_ttm.html
@@ -375,14 +375,12 @@
fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
-ID, group-ID are documented in fix command
-style = ttm or ttm_mod
-seed = random number seed to use for white noise (positive integer)
-remaining arguments for fix ttm:
+C_e = electronic specific heat (energy/(electron*temperature) units) rho_e = electronic density (electrons/volume units) @@ -397,8 +395,9 @@ 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) @@ -408,8 +407,6 @@ 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)-
fix ID group-ID style face args ... keyword value ...
ID, group-ID are documented in fix command
-style = wall/lj93 or wall/lj126 or wall/lj1043 or wall/colloid or wall/harmonic
-one or more face/arg pairs may be appended
-face = xlo or xhi or ylo or yhi or zlo or zhi
+
args = coord epsilon sigma cutoff
coord = position of wall = EDGE or constant or variable
@@ -404,10 +402,10 @@ args = coord epsilon sigma cutoff
sigma can be a variable (see below)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
-zero or more keyword/value pairs may be appended
-keyword = units or fld
+units value = lattice or box lattice = the wall position is defined in lattice units @@ -419,8 +417,6 @@ args = coord epsilon sigma cutoff yes = allow periodic boundary in a wall dimension no = require non-perioidic boundaries in any wall dimension-
-fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ... +fix ID group-ID wall/gran fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
ID, group-ID are documented in fix command
@@ -438,20 +438,21 @@ close enough to touch it. force between the wall and particles touching it is the same as the corresponding equation on the pair_style granular doc page, in the limit of one of the two particles going to infinite -radius and mass (flat wall). I.e. delta = radius - r = overlap of -particle with wall, m_eff = mass of particle, and sqrt(RiRj/Ri+Rj) -becomes sqrt(radius of particle). The units for Kn, Kt, gamma_n, and -gamma_t are as described on that doc page. The meaning of xmu and -dampflag are also as described on that page. Note that you can choose -a different force styles and/or different values for the 6 -wall/particle coefficients than for particle/particle interactions. -E.g. if you wish to model the wall as a different material. +radius and mass (flat wall). Specifically, delta = radius - r = +overlap of particle with wall, m_eff = mass of particle, and the +effective radius of contact = RiRj/Ri+Rj is just the radius of the +particle.The parameters Kn, Kt, gamma_n, gamma_t, xmu and dampflag -have the same meaning as those specified with the pair_style granular commands. This means a NULL can be used for -either Kt or gamma_t as described on that page. If a NULL is used -for Kt, then a default value is used where Kt = 2/7 Kn. If a -NULL is used for gamma_t, then a default value is used where -gamma_t = 1/2 gamma_n.
+have the same meaning and units as those specified with the +pair_style granular commands. This means a NULL can +be used for either Kt or gamma_t as described on that page. If a +NULL is used for Kt, then a default value is used where Kt = 2/7 +Kn. If a NULL is used for gamma_t, then a default value is used +where gamma_t = 1/2 gamma_n. +Note that you can choose a different force styles and/or different +values for the 6 wall/particle coefficients than for particle/particle +interactions. E.g. if you wish to model the wall as a different +material.
Note
As discussed on the doc page for pair_style granular, versions of LAMMPS before 9Jan09 used a diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html index 341610d806..b34251a0b0 100644 --- a/doc/html/fix_wall_reflect.html +++ b/doc/html/fix_wall_reflect.html @@ -310,7 +310,7 @@
Treat the surface of the geometric region defined by the region-ID as a bounding wall which interacts with nearby particles according to -the specified style. The distance between a particle and the surface -is the distance to the nearest point on the surface and the force the -wall exerts on the particle is along the direction between that point -and the particle, which is the direction normal to the surface at that -point. Note that if the region surface is comprised of multiple -“faces”, then each face can exert a force on the particle if it is -close enough. E.g. for region_style block, a particle -in the interior, near a corner of the block, could feel wall forces -from 1, 2, or 3 faces of the block.
+the specified style. +The distance between a particle and the surface is the distance to the +nearest point on the surface and the force the wall exerts on the +particle is along the direction between that point and the particle, +which is the direction normal to the surface at that point. Note that +if the region surface is comprised of multiple “faces”, then each face +can exert a force on the particle if it is close enough. E.g. for +region_style block, a particle in the interior, near a +corner of the block, could feel wall forces from 1, 2, or 3 faces of +the block.
Regions are defined using the region command. Note that the region volume can be interior or exterior to the bounding surface, which will determine in which direction the surface interacts with @@ -453,14 +454,15 @@ should not use the fix wall/region command with union or
Note
Similarly, you should not define union or intersert regions -for use with this command that share a common face, even if the face -is smooth. E.g. two regions of style block in a union region, where -the two blocks have the same face. This is because LAMMPS discards -points that are part of multiple sub-regions when calculating -wall/particle interactions, to avoid double-counting the interaction. -Having two coincident faces could cause the face to become invisible -to the particles. The solution is to make the two faces differ by -epsilon in their position.
+for use with this command that share an overlapping common face that +is part of the overall outer boundary (interior boundary is OK), even +if the face is smooth. E.g. two regions of style block in a union +region, where the two blocks overlap on one or more of their faces. +This is because LAMMPS discards points that are part of multiple +sub-regions when calculating wall/particle interactions, to avoid +double-counting the interaction. Having two coincident faces could +cause the face to become invisible to the particles. The solution is +to make the two faces differ by epsilon in their position.The energy of wall-particle interactions depends on the specified style.
diff --git a/doc/html/group.html b/doc/html/group.html index f184e61d1b..7648bd9867 100644 --- a/doc/html/group.html +++ b/doc/html/group.html @@ -214,7 +214,7 @@pair_style eff/cut cutoff keyword args ...-
cutoff = global cutoff for Coulombic interactions
-zero or more keyword/value pairs may be appended
+
keyword = limit/eradius or pressure/evirials or ecp
limit/eradius args = none
@@ -541,8 +541,6 @@ keyword = limit/eradius or pressure/evirials or ecp
type = LAMMPS atom type (1 to Ntypes)
element = element symbol (e.g. H, Si)
-The format of the list file is as follows:
-one line per pair of atoms
-empty lines will be ignored
-comment text starts with a ‘#’ character
-line syntax: ID1 ID2 style coeffs cutoff
+ID1 = atom ID of first atom
ID2 = atom ID of second atom
style = style of interaction
@@ -575,8 +573,6 @@ Morse and a harmonic potential.
cutoff = cutoff for interaction (optional)
The cutoff parameter is optional. If not specified, the global cutoff is used.
Here is an example file:
diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html index 76ca3c09a7..d725697c9a 100644 --- a/doc/html/pair_mdf.html +++ b/doc/html/pair_mdf.html @@ -534,10 +534,10 @@pair_style style args-
style = lj/mdf or buck/mdf or lennard/mdf
-args = list of arguments for a particular style
+lj/mdf args = cutoff1 cutoff2 cutoff1 = inner cutoff for the start of the tapering function @@ -549,8 +549,6 @@ pair_style style args cutoff1 = inner cutoff for the start of the tapering function cutoff1 = out cutoff for the end of the tapering function-
pair_style srp cutoff btype dist keyword value ...
-cutoff = global cutoff for SRP interactions (distance units)
-btype = bond type to apply SRP interactions to (can be wildcard, see below)
-distance = min or mid
-zero or more keyword/value pairs may be appended
-keyword = exclude
+bptype value = atom type for bond particles exclude value = yes or no-
For the bitmap style, the specified N is used to create interpolation tables that are 2^N in length. The distance R is used to index into the table via a fast bit-mapping technique due to -(Wolff), and a linear interpolation is performed between +(Wolff), and a linear interpolation is performed between adjacent table values.
The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html index 85e8c61689..9aa9b491e1 100644 --- a/doc/html/pair_thole.html +++ b/doc/html/pair_thole.html @@ -467,7 +467,7 @@
This function results from an adaptation to point charges -(Noskov) of the dipole screening scheme originally proposed -by Thole. The scaling coefficient \(s_{ij}\) is determined +(Noskov) of the dipole screening scheme originally proposed +by Thole. The scaling coefficient \(s_{ij}\) is determined by the polarizability of the atoms, \(\alpha_i\), and by a Thole damping parameter \(a\). This Thole damping parameter usually takes a value of 2.6, but in certain force fields the value can depend upon diff --git a/doc/html/partition.html b/doc/html/partition.html index 2b0248a26e..d261d0c9fd 100644 --- a/doc/html/partition.html +++ b/doc/html/partition.html @@ -213,7 +213,7 @@