LAMMPS Input Commands

Return to top-level of LAMMPS documentation.

This page contains a complete list of valid LAMMPS inputs. It will be easiest to understand if you read it while looking at sample input files such as those in the examples directory.

The input file of commands is read by LAMMPS, one line at a time. Each command causes LAMMPS to take some action. Usually it simply causes some internal variable(s) to be set. Or it may cause a file to be read in or a simulation to be run. In general, commands can be listed in any order, although some commands require others to have been executed previously.

LAMMPS continues to read successive lines from the input command file until the end-of-file is reached which causes LAMMPS to terminate. Thus new simulations can be run or current simulations continued by simply specifying additional commands in the input command file.

The next section of this page gives an example of each command, some of which can be specified in multiple styles. Typically the commands take one or more parameters. The keyword for each command should begin in the leftmost column and all characters in the command and its parameters should be in lower-case. Parameters can be separated by arbitrary numbers of spaces and/or tabs (so long as the command fits on one line). The remainder of the line after the last parameter is ignored.

The final section of this page gives a more detailed description of each command with its associated parameters. It also lists the default parameters associated with each command. When performing a simulation, you only need specify a particular command if you do not want to use the default settings.


Categories of Commands withExamples


Basic Settings

comments

units                  real
dimension              3
periodicity            0 0 0
processor grid         10 10 10
newton flag            3
timestep               1.0
respa                  2 2 4
neighbor               2.0 0 1 10 1
special bonds          0.0 0.0 0.4

Output Control

thermo flag            50
thermo style           0
true flag              0

dump atoms             100 filename
dump velocities        100 filename
dump forces            100 filename

restart                1000 file1 file2
diagnostic             diffusion 100 filename 3 1.0 -1.0 2.5

Ensemble Control

temp control           none
temp control           rescale 300.0 300.0 100 20.0
temp control           replace 300.0 300.0 50 12345678
temp control           langevin 50.0 50.0 0.01 123456
temp control           nose/hoover 300.0 300.0 0.01

press control          none
press control          nose/hoover 1.0 1.0 0.001
press_x control        nose/hoover 1.0 1.0 0.001
press_y control        nose/hoover 1.0 1.0 0.001
press_z control        nose/hoover 1.0 1.0 0.001

Nonbond Force Field

nonbond style          none
nonbond style          lj/cutoff 10.0 0
nonbond coeff          1 2 1.0 3.45 10.0
nonbond style          lj/smooth 8.0 10.0
nonbond coeff          1 2 1.0 3.45 8.0 10.0
nonbond style          lj/shift 10.0 0
nonbond coeff          1 2 1.0 3.45 2.0 10.0
nonbond style          soft 2.5
nonbond coeff          1 2 1.0 30.0 2.5
nonbond style          class2/cutoff 10.0 0
nonbond coeff          1 2 1.0 3.45 10.0
mixing style           geometric

coulomb style          none
coulomb style          cutoff 10.0
coulomb style          smooth 8.0 10.0
coulomb style          ewald 10.0 1.0E-4
coulomb style          pppm 10.0 1.0E-4
pppm mesh              32 32 64
pppm order             5
dielectric             1.0

Bonded Force Field

bond style             none
bond style             harmonic
bond coeff             1 100.0 3.45
bond style             fene/standard
bond coeff             1 30.0 1.5 1.0 1.0
bond style             fene/shift
bond coeff             1 30.0 1.5 1.0 1.0 0.2
bond style             nonlinear
bond coeff             1 28.0 0.748308 0.166667
bond style             class2

angle style            none
angle style            harmonic
angle style            class2

dihedral style         none
dihedral style         harmonic
dihedral style         class2

improper style         none
improper style         harmonic
improper style         class2

Atom Creation

read data              filename
read restart           filename

Velocity Creation

create group           types 1 3
create group           region 0.0 1.0 0.0 1.0 INF 1.0
create group           remainder

create temp            uniform 300.0 12345678
create temp            gaussian 300.0 12345678
create temp            velocity 0.0 0.0 0.0

Constraint Creation

fix style              none
fix style              1 setforce 0.0 NULL 0.0
fix style              1 addforce 1.0 0.0 0.0
fix style              1 aveforce 1.0 0.0 0.0
fix style              1 rescale 300.0 300.0 100 20.0
fix style              1 langevin 50.0 50.0 0.01 12345 1 1 1
fix style              1 nose/hoover 50.0 50.0 0.01
fix style              1 springforce 10.0 NULL NULL 1.0
fix style              1 dragforce 10.0 -5.0 NULL 2.0 1.0

assign fix             1 atom 200
assign fix             1 molecule 50
assign fix             1 type 2
assign fix             1 region 0.0 1.0 INF INF 0.0 1.0
assign fix             1 remainder

Dynamics or Minimization

reset timestep         0

run                    1000

min style              hftn
min file               filename
minimize               0.0001 9999 50000

Alphabetic Listing of Commands:


angle style

define style of angle interactions to use for all 3-body terms
angle style determines how many angle coefficients the program expects to
  find in a "Angle Coeffs" entry in the data file, 
  thus the style must be set (if not using default)
  before using the "read data" command (if the data file contains a 
  "Angle Coeffs" entry)
coefficients for all angle types must be defined in data (or restart)
  file by "Angle Coeffs" entry before a run is performed
style of "none" erases all previously defined angle coefficients, must
  reset style to something else before defining new coefficients

Default = harmonic

assign fix

styles:
coeffs:  atom
               (1) global atom #
         molecule
               (1) molecule #
         type
               (1) atom type
         region
               (1) lower x bound of region
               (2) upper x bound of region
               (3) lower y bound of region
               (4) upper y bound of region
               (5) lower z bound of region
               (6) upper z bound of region
         remainder
               no other parameters required

assign a group of atoms to a particular constraint
use appropriate number of coeffs for a particular style
the constraint itself is defined by the "fix style" command
multiple groups of atoms can be assigned to the same constraint
an atom can be assigned to multiple constraints, the constraints will be
  applied in the reverse order they are assigned to that atom
  (e.g. each timestep, the last fix assigned to an atom will be applied 
  to it first, then the next-to-last applied second, etc)
for style region, a coeff of INF means + or - infinity (all the way 
  to the boundary)

bond coeff

coeffs:   harmonic
               (1) K (energy units)
               (2) r0 (distance units)
          fene/standard
               (1) k for FENE portion (energy/distance^2 units)
               (2) r0 for FENE portion (distance units)
               (3) epsilon for LJ portion (energy units)
               (4) sigma for LJ portion (distance units)
          fene/shift
               (1) k for FENE (energy/distance^2 units)
               (2) r0 for FENE after shift is performed (distance units)
               (3) epsilon for LJ (energy units)
               (4) sigma for LJ after shift is performed (distance units)
               (5) delta shift distance (distance units)
          nonlinear
               (1) epsilon (energy units)
               (2) r0 (distance units)
               (3) lamda (distance units)
          class 2
               currently not enabled for "bond coeff" command
               must be specified in data file (see "read data" command)

define (or override) bond coefficients for an individual bond type
use appropriate number of coeffs for a particular style
these coefficients can also be set in data file 
  by "Bond Coeffs" entry, the most recently defined coefficients are used

Default = no settings

bond style

define style of bond interactions to use between all bonded atoms
bond style determines how many bond coefficients the program expects to
  find in a "Bond Coeffs" entry in the  data file or when using the 
  "bond coeff" command, thus the style must be set (if not using default)
  before using the "read data" command (if the data file contains a 
  "Bond Coeffs" entry)
coefficients for all bond types must be defined in data (or restart)
  file by "Bond Coeffs" entry or by "bond coeffs" commands before a run
  is performed
style of "none" erases all previously defined bond coefficients, must
  reset style to something else before defining new coefficients

Default = harmonic

comments

blank lines are ignored
everything on a line after the last parameter is ignored
lines starting with a # are echoed into the log file

coulomb style

styles:
coeffs:  none
               no other parameters required
         cutoff
               (1) cutoff distance (distance units)
         smooth
               (1) inner cutoff (distance units)
               (2) outer cutoff (distance units)
         ewald
               (1) cutoff distance for near-field portion (distance units)
               (2) accuracy criterion
         pppm
               (1) cutoff distance for near-field portion (distance units)
               (2) accuracy criterion

use appropriate number of coeffs for a particular style
if simulated system has no charges, must set "coulomb style none" to
  prevent LAMMPS from doing useless nonbond work
accuracy criterion means "one part in value" - e.g. 1.0E-4
Ewald and PPPM accuracy criterion are used in conjunction with cutoff
  to partition work between short-range and long-range routines
accuracy criterion effectively determines how many k-space vectors are used
  to approximate the energy and forces
for PPPM, accuracy criterion determines mesh spacing (see "particle mesh"
  command)
for PPPM, must be running on power-of-2 number of processors for FFTs
must use periodic boundary conditions in conjuction with Ewald and PPPM
cannot use any styles other than none with nonbond style = lj/shift or
  nonbond style = soft
Coulomb style = smooth should be used with nonbond style = lj/switch,
  and both should use same inner and outer cutoffs
for smooth style, outer cutoff must be > inner cutoff
for smooth style, atom pairs less than the inner cutoff distance use 
  usual Coulomb, pairs between inner and outer are smoothed, and the 
  potential goes to 0.0 at the outer cutoff
for smooth style, force is continuously differentiable everywhere

Default = cutoff 10.0

create group

styles:
coeffs:  types
               (1) lowest atom type
               (2) highest atom type
         region
               (1) lower x bound of region
               (2) upper x bound of region
               (3) lower y bound of region
               (4) upper y bound of region
               (5) lower z bound of region
               (6) upper z bound of region
         remainder
               no other parameters required
       
used with "create temp" command to initialize velocities of atoms
by default, the "create temp" command initializes the velocities of all atoms,
  this command limits the initialization to a group of atoms
this command is only in force for the next "create temp" command, any
  subsequent "create temp" command is applied to all atoms (unless the
  "create group" command is used again)
for style types, only atoms with a type such that lo-type <= type <= hi-type
  will be initialized by "create temp"
for style types, lo-type can equal hi-type if just want to specify one type
for style region, only atoms within the specified spatial region
  will be initialized by "create temp"
for style region, a coeff of INF means + or - infinity (all the way 
  to the boundary)
for style remainder, only previously uninitialized atoms
  will be initialized by "create temp"

create temp

styles: 
coeffs:  uniform
               (1) target T (temperature units)
               (2) random # seed (0 < seed <= 8 digits)
         gaussian
               (1) target T (temperature units)
               (2) random # seed (0 < seed <= 8 digits)
         velocity
               (1) x velocity component (velocity units)
               (2) y velocity component (velocity units)
               (3) z velocity component (velocity units)

initialize velocities of atoms to a specified temperature
use appropriate number of coeffs for a particular style
cannot be done before a data or restart file is read
by default, velocities are created for all atoms - this can be overridden
  by "create group" command
for uniform and Gaussian styles velocities are created in 
  processor-independent fashion - is slower but gives the same initial 
  state independent of # of processors
for uniform and Gaussian styles the momentum of the initialized atoms is
  also zeroed, but only if all atoms are being initialized 
for uniform and Gaussian styles, RN are generated with Park/Miller RNG
for velocity style in 2-d simulations, still specify z velocity component,
  even though it is ignored

diagnostic

call a user-defined diagnostic routine every this many timesteps
this command can be used multiple times to call different routines
  at different frequencies, that use different parameters, and that
  send output to different files
value of 0 for 2nd parameter means never call this particular routine
this command causes any previous file associated with this user routine
  to be closed
new filename can exist, will be overwritten
if the file name specified is "none", then no file is opened
each routine that is added to diagnostic.f and enabled with a
  "diagnostic" command will be called at the beginning and end of
  each "run" and every so many timesteps during the run
the diagnostic.f file has further information on how to create
  routines that operate on internal LAMMPS data, do their own file output,
  perform different operations (e.g. setup and clean-up) depending
  on when they are called, etc
the user routines must be compiled and linked into LAMMPS
the optional 5th-9th parameters are stored in program variables which
  can be accessed by the diagnostic routine

Default = none

dielectric

set dielectric constant to this value

Default = 1.0

dihedral style

define style of dihedral interactions to use for all 4-body terms
dihedral style determines how many dihedral coefficients the program expects to
  find in a "Dihedral Coeffs" entry in the data file, 
  thus the style must be set (if not using default)
  before using the "read data" command (if the data file contains a 
  "Dihedral Coeffs" entry)
coefficients for all dihedral types must be defined in data (or restart)
  file by "Dihedral Coeffs" entry before a run is performed
style of "none" erases all previously defined dihedral coefficients, must
  reset style to something else before defining new coefficients

Default = harmonic

dimension

for a 2-d run, assumes all z-coords are set to 0.0 in "read data" or
  "read restart" files and program creates no z velocities
this command sets the processor grid to default values for 2-d or 3-d
  so must be used before "processor grid" command
must be set before data or restart file is read

Default = 3

dump atoms

dump all atom positions to a file every this many timesteps
positions are also dumped at the start and end of every run
value of 0 means never dump
any previous file is closed
new filename can exist, will be overwritten
atom positions in dump file are in "box" units (0.0 to 1.0) in each dimension

Default = 0

dump forces

dump all atom forces to a file every this many timesteps
forces are also dumped at the start and end of every run
any previous file is closed
new filename can exist, will be overwritten
value of 0 means never dump

Default = 0

dump velocities

dump all atom velocities to a file every this many timesteps
velocities are also dumped at the start and end of every run
any previous file is closed
new filename can exist, will be overwritten
value of 0 means never dump

Default = 0

fix style

styles:
coeffs:  none
               no other parameters required (use "none" as 1st parameter)
         setforce
                (1) x component of set force (in force units)
                (2) y component of set force (in force units)
                (3) z component of set force (in force units)
         addforce
                (1) x component of added force (in force units)
                (2) y component of added force (in force units)
                (3) z component of added force (in force units)
         aveforce
                (1) x comp of added average force per atom (in force units)
                (2) y comp of added average force per atom (in force units)
                (3) z comp of added average force per atom (in force units)
         rescale
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) check for rescaling every this many timesteps
               (4) T window outside of which velocities will be rescaled
         langevin
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) Langevin damping parameter (inverse time units)
               (4) random seed to use for white noise (0 < seed <= 8 digits)
               (5) 0/1 = off/on x dimension
               (6) 0/1 = off/on y dimension
               (7) 0/1 = off/on z dimension
         nose/hoover
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) frequency constant for friction force (inverse time units)
         springforce
                (1) x position of spring origin
                (2) y position
                (3) z position
                (4) force constant k (so that k*distance = force units)
         dragforce
                (1) x position to drag atom towards
                (2) y position
                (3) z position
                (4) force magnitude f (in force units)
                (5) delta outside of which to apply force (in distance units)

define a constraint
cannot skip a constraint number, all must be used before a run is performed
use appropriate number of coeffs for a particular style
which atoms the constraint will affect is set by the "assign fix" command
all of the constraints (except for rescale) are applied every timestep
all specified temperatures are in temperature units
for style setforce, a coeff of NULL means do not alter that force component
for style aveforce, average force on the group of fixed atoms is computed,
  then new average force is added in and actual force on each atom is set
  to new total value -> has effect of applying same force to entire group
  of atoms
thermostatting constraints (rescale, langevin, nose/hoover) cannot be used in
  conjuction with global "temp control", since they conflict and will
  cause atom velocities to be reset twice
if multiple Langevin constraints are specified the Marsaglia RNG will
  only use the last RNG seed specified for initialization
meaning of thermostatting coefficients is same as in "temp control" command
style springforce is designed to be applied to an entire group of atoms
  en masse (e.g. an umbrella force on an entire molecule)
for style springforce, the center of mass r0 of the group of atoms is computed,
  then a restoring force = -k*(r-r0)*mass/masstotal is applied to each 
  atom in the group where mass = mass of the atom and masstotal = mass of
  all the atoms in the group - thus "k" should represent the total
  force on the group of atoms (not per atom)
for style springforce, a xyz position of NULL means do not include that
  dimension in the distance or force computation
for style dragforce, apply a drag force of magnitude f to each atom in the
  group in the direction (r-r0) where r0 = (x,y,z) - do not apply the force if
  the atom is within a distance delta of r0
for style dragforce, a xyz position of NULL means do not include that
  dimension in the distance or force computation

Default = none

improper style

define style of improper interactions to use for all trigonal centers
in class2 case, dictates that angle-angle terms be included for all
  trigonal and tetrahedral centers
in above formulas, phi = improper torsion, chi = Wilson out-of-plane
improper style determines how many improper coefficients the program   
  expects to find in a "Improper Coeffs" entry in the data file, 
  thus the style must be set (if not using default)
  before using the "read data" command (if the data file contains a 
  "Improper Coeffs" entry)
coefficients for all improper types must be defined in data (or restart)
  file by "Improper Coeffs" entry before a run is performed
style of "none" erases all previously defined improper coefficients, must
  reset style to something else before defining new coefficients

Default = harmonic

min file

name of file to write minimization iteration info to
filename can exist, will be overwritten when minimization occurs
if no file is specified, no minimization output will be written to a file

Default = none

min style

choose minimization algorithm to use when "minimize" command is performed
currently, only htfn style is available

Default = htfn

minimize

perform an energy minimization of the atomic coordinates of the system
uses algorithm selected with "min style" command
minimization stops if any of 3 criteria are met:
  (1) largest force component < stopping tolerance
  (2) # of iterations > max iterations
  (3) # of force and energy evaluations > max evaluations
for good convergence, should specify use of smooth nonbond force fields 
  that have continuous second derivatives, set "coulomb style" to "smooth",
  set nonbond style to "lj/smooth" or use a long cutoff

mixing style

styles:
determine the kind of mixing rule that is applied to generate nonbond
  coefficients for interactions between type i and type j atoms
mixing rules are used only when nonbond coeffs are input in a "read data" file
for nonbond style "soft", only epsilons (prefactor A) are input - they are
  always mixed geometrically, regardless of mixing style setting

Default = geometric for all nonbond styles except class2/cutoff
         sixthpower for nonbond style class2/cutoff

neighbor

factors that affect how and when neighbor lists are constructed
skin must be large enough that all atoms needed for bond
  interactions are also acquired by interprocessor communication
last parameter incurs extra checking and communication to test against
  skin thickness, but may mean neighbor list is created less often
when RESPA is run, the 3rd and 4th parameters refer to the
  nonbond (short-range) timestepping
defaults = 2.0 0 1 10 1

newton flag

turn off or on Newton's 3rd law for bond and non-bond force computation
no Newton's 3rd law means more force computation and less communication
yes Newton's 3rd law means less force computation and more communication
which choice is faster is problem dependent on N, # of processors, 
  and cutoff length(s)
expect for round-off errors, setting this flag should not affect answers, 
  only run time
must be set before data or restart file is read

Default = 3

nonbond coeff

coeffs: lj/cutoff
               (1) epsilon (energy units)
               (2) sigma (distance units)
               (3) cutoff (distance units)
        lj/smooth
               (1) epsilon (energy units)
               (2) sigma (distance units)
               (3) inner cutoff (distance units)
               (4) outer cutoff (distance units)
        lj/shift
               (1) epsilon (energy units)
               (2) sigma (distance units)
               (3) delta shift distance (distance units)
               (4) cutoff (distance units)
        soft
               (1) prefactor A at start of run (energy units)
               (2) prefactor A at end of run (energy units)
               (3) cutoff (distance units)
        class2/cutoff
               (1) epsilon (energy units)
               (2) sigma (distance units)
               (3) cutoff (distance units)

define (or override) nonbond coefficients for an individual atom type pair
use appropriate number of coeffs for a particular style
1st atom type must be <= 2nd atom type
all cutoffs are in global units, not local sigma units
  (e.g. in reduced units a setting of "lj/cutoff 1.0 1.2 2.5" means a 
  cutoff of 2.5, not 1.2*2.5)
turn off a particular type pair interaction by setting the
  cutoff to 0.0 (both cutoffs to zero for lj/smooth option)
for soft style, prefactor A is ramped from starting value to
  ending value during run
these coefficients (except the cutoffs) can also be set in data file 
  by "Nonbond Coeffs" entry and associated mixing rules, the cutoffs can
  be set (globally) via the "nonbond style" command, the most
  recently defined coefficients/cutoffs are used

Default = no settings

nonbond style

styles: 
coeffs:  none
               no other parameters required
         lj/cutoff
               (1) cutoff (distance units)
               (2) offset flag (0 or 1)
         lj/smooth
               (1) inner cutoff (distance units)
               (2) outer cutoff (distance units)
         lj/shift
               (1) cutoff (distance units)
               (2) offset flag (0 or 1)
         soft
               (1) cutoff (distance units)
         class2/cutoff
               (1) cutoff (distance units)
               (2) offset flag (0 or 1)

define style of pairwise nonbond interactions to use between all atom types
use appropriate number of coeffs for a particular style
this is separate from charge interactions (see "coulomb style" command)
nonbond style determines how many nonbond coefficients the program expects to
  find in a "Nonbond Coeffs" entry in the data file or when using the 
  "nonbond coeff" command, thus the style must be set (if not using default)
  before using the "read data" command (if the data file contains a 
  "Nonbond Coeffs" entry)
coefficients for all atom type pairs must be defined in data (or restart)
  file by "Nonbond Coeffs" entry or by "nonbond coeffs" commands before a run
  is performed
style of "none" erases all previously defined nonbond coefficients, must
  reset style to something else before defining new coefficients
for all styles (except none), this command sets the cutoff(s) for all type
  pair interactions, thus overriding any previous settings by a "nonbond
  coeff" command or that were read in from a restart file
for lj/cutoff, lj/shift, class2/cutoff styles, 
  offset flag only affects printout of thermodynamic energy
  (not forces or dynamics), determines whether offset energy 
  is added in to LJ potential to make value at cutoff = 0.0,
  flag = 0 -> do not add in offset energy,
  flag = 1 -> add in offset energy 
for lj/smooth style, outer cutoff must be > inner cutoff
for lj/smooth style, atom pairs less than the inner cutoff distance use 
  straight LJ, pairs between inner and outer use a smoothed LJ, and the 
  potential goes to 0.0 at the outer cutoff
for lj/smooth style, energy and forces are continuous at inner cutoff and go
  smoothly to zero at outer cutoff
for lj/shift and soft styles, must set "coulomb style" to "none"
for lj/shift style, delta shift distances for each atom pair are set by
  "Nonbond Coeffs" entry in data file or by "nonbond coeffs" command
for soft style, values of the prefactor "A", which is ramped from one
  value to another during the run, are set by "Nonbond Coeffs" entry
  in data file or by "nonbond coeffs" command

Default = lj/cutoff 10.0 0

periodicity

turn on/off periodicity in any of three dimensions
used in inter-particle distance computation and when particles move
  to map (or not map) them back into periodic box
for a 2-d run (see "dimension" command), 3rd parameter must be 
  specified, but doesn't matter if it is 0 or 1
must be set before data or restart file is read

Default = 0 0 0 (periodic in all dimensions)

pppm mesh

specify the mesh size used by coulomb style pppm
mesh dimensions that are power-of-two are fastest for FFTs, but any size
  can be used that are supported by native machine libraries
this command is optional - if not used, a default
  mesh size will be chosen to satisfy accuracy criterion - if used, the
  specified mesh size will override the default

Default = none

pppm order

specify the order of the interpolation function that is used by coulomb
  style pppm to map particle charge to the particle mesh
order is roughly equivalent to how many mesh points a point charge
  overlaps onto

Default = 5

press control

styles:
coeffs:   none
               no other parameters required
          nose/hoover
               (1) desired P at beginning of run
               (2) desired P at end of run
               (3) frequency constant for volume adjust (inverse time units)

use appropriate number of coeffs for a particular style
all specified pressures are in pressure units
target pressure at intermediate points during run is a ramped value
  between the beginning and ending pressure
for nose/hoover style, frequency constant is like an inverse "piston" 
  mass which determines how rapidly the pressure fluctuates in response to a
  restoring force, large frequency -> small mass -> rapid fluctations
for nose/hoover style, units of frequency/damping constant are
  inverse time, so a value of 0.001 means relax in a timespan on the 
  order of 1000 fmsec (real units) or 1000 tau (LJ units)

Default = none

press_x control

press_y control

press_z control

styles: 
coeffs: none
                no other parameters required
        nose/hoover
                (1) desired P at beginning of run
                (2) desired P at end of run
                (3) frequency constant for volume adjust (inverse time units)

commands for anisotropic pressure control, any combination is allowed
for a component with style = none, the cell dimension in that direction
  is held constant (constant volume)
use appropriate number of coeffs for a particular style
all specified pressures are in pressure units
target pressure at intermediate points during run is a ramped value
  between the beginning and ending pressure
cannot be used with isotropic "press control" command
for nose/hoover style, frequency constant is like an inverse "piston"
  mass which determines how rapidly the pressure fluctuates in response to a
  restoring force, large frequency -> small mass -> rapid fluctations
for nose/hoover style, units of frequency/damping constant are
  inverse time, so a value of 0.001 means relax in a timespan on the
  order of 1000 fmsec (real units) or 1000 tau (LJ units)

Default = none

processor grid

specify 3-d grid of processors to map to physical simulation domain
for 2-d problem, specify N by M by 1 grid
program will choose these values to best map processor grid to physical
  simulation box, only use this command if wish to override program choice
product of 3 parameters must equal total # of processors
must be set before data or restart file is read

Default = none

read data

read the initial atom positions and bond info from the specified file
the format for the data file is specified in the file data_format
if a "Coeffs" entry is in data file, the appropriate "style" command
  command must be used first (unless default setting is used) to tell 
  LAMMPS how many coefficients to expect
most "Coeffs" entries must be present in this file if a particular "style"
  is desired, an exception are the "Nonbond Coeffs" and "Bond Coeffs" entries
  which can be omitted if all the settings are made via "nonbond coeff"
  and "bond coeff" commands
a "Nonbond Coeffs" entry only contains one set of coefficients for each
  atom type, after being read-in the appropriate class I or class II mixing
  rules are applied to compute the cross-type coefficients (see the file
  data_format for more information)

read restart

read atom positions and velocities and nonbond and bond coefficients
  from specified file
allows continuation of a previous run
file is binary to enable exact restarts
do not have to restart on same # of processors, but can only do exact
  restarts on same # of processors
when restart file is read, warnings are issued if certain parameters
  in the restart file do not match current settings (e.g. newton flag,
  dimension, periodicity, units) - this usually indicates an error
the restart file stores all nonbond and many-body styles and coefficients,
  so reading the file will overwrite any current settings
the restart file stores the constraint assignments for each atom, but
  not the constraints themselves, so they must still be specified with
  the "fix style" command
for a restart do not use the "read data" and "create temp" commands

reset timestep

explicitly reset the timestep to this value
the "read data" and "read restart" commands set the timestep to zero
  and file value respectively, so this should be done after those commands

respa

factors that affect sub-cycling of force calculations within RESPA hierarchy
bonded intramolecular forces are calculated every innermost sub-timestep
bonded 3- and 4-body forces are computed every 1st parameter sub-timesteps
short-range nonbond pairwise forces (LJ, Coulombic) are computed every 
  (2nd parameter * 1st parameter) sub-timesteps
long-range (Ewald, PPPM) forces are computed every 
  (3rd parameter * 2nd parameter * 1st parameter) sub-timesteps
the timestepping for all 3 inner loops (bond, 3/4-body, nonbond) is performed
  as sub-cycling within the long-range timestepping loop
the fastest (innermost) timestep size is set by the "timestep" command
when running RESPA, all input commands that specify numbers of timesteps
  (e.g. run, thermo flag, restart flag, etc) refer to the outermost loop
  of long-range timestepping
the only exception to this rule is the "neighbor" command, where the timestep
  parameters refer to the nonbond (short-range) timestepping
setting all 3 parameters to 1 turns off RESPA

Default = 1 1 1 (no RESPA)

restart

create a restart file every this many timesteps
value of 0 means never create one
program will toggle between 2 filenames as the run progresses
  so always have at least one good file even if the program dies in mid-write
restart file stores atom positions and velocities in binary form
allows program to restart from where it left off (see "read restart" command)

Default = 0

run

run or continue dynamics for specified # of timesteps
must have performed "read data"/"create temp" or "read restart"
  commands first

special bonds

weighting factors to turn on/off nonbond interactions of atom pairs that
  are "close" in the molecular topology
1st nearest neighbors are a pair of atoms connected by a bond
2nd nearest neighbors are a pair of atoms 2 hops away, etc.
weight values are from 0.0 to 1.0 and are used to multiply the
  energy and force interaction (both Coulombic and LJ) between the 2 atoms
weight of 0.0 means no interaction
weight of 1.0 means full interaction

Default = 0.0 0.0 0.4 (CHARMM standard)

temp control

styles:  
coeffs:  none
               no other parameters required
         rescale
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) check for rescaling every this many timesteps
               (4) T window outside of which velocities will be rescaled
         replace
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) do Gaussian replacement every this many timesteps
               (4) random # seed to use for replacement (0 < seed <= 8 digits)
         langevin
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) Langevin damping parameter (inverse time units)
               (4) random seed to use for white noise (0 < seed <= 8 digits)
         nose/hoover
               (1) desired T at beginning of run
               (2) desired T at end of run
               (3) frequency constant for friction force (inverse time units)

use appropriate number of coeffs for a particular style
all specified temperatures are in temperature units
target temperature at intermediate points during run is a ramped value
  between the beginning and ending temperatures
for rescale style, temperature is controlled by explicitly rescaling
  velocities to exactly the target temperature
for rescale style, rescaling is only done if current temperature is
  beyond the target temperature plus or minus the window value
for replace style, Gaussian RNs from the Marsaglia RNG are used
for langevin style, uniform RNs from the Marsaglia RNG are used
for replace and langevin styles, the seed is used to initialize the
  Marsaglia RNG, on successive runs the RNG will just continue on
for replace and langevin styles, generated RNs depend on # of processors
  so will not get same answers independent of # of processors
for replace and langevin styles, RNG states are not saved in restart file,
  so cannot do an exact restart
for langevin style, damping parameter means small value -> less damping
for nose/hoover style, frequency constant is like an inverse "piston" 
  mass which determines how rapidly the temperature fluctuates in response to a
  restoring force, large frequency -> small mass -> rapid fluctations
for langevin and nose/hoover styles, units of frequency/damping constant are
  inverse time, so a value of 0.01 means relax in a timespan on the 
  order of 100 fmsec (real units) or 100 tau (LJ units)

Default = none

thermo flag

print thermodynamic info to screen and log file every this many timesteps
value of 0 means never print

Default = 0

thermo style

determines format of thermodynamic output to screen and log file
Default = 0

timestep

timestep size for MD run (time units)
when RESPA is run, the timestep size is for the innermost (bond) loop

Default = 1.0

true flag

read atom positions (see "read data" command) and dump atom positions
  (see "dump flag" command) in one of 2 formats
for each dimension, box count of "n" means add that many box lengths
  to get "true" un-remapped position, "n" can be positive, negative, or zero

Default = 0

units

set units to one of two options for all subsequent input parameters

option real = conventional units:
option lj = LJ reduced units:
for LJ units, LAMMPS sets global epsilon,sigma,mass all equal to 1.0
subsequent input numbers in data and command file must be in these units
output numbers to screen and log and dump files will be in these units
must be set before data or restart file is read

Default = real