Second batch of spelling fixes in manual

         remainder

               no other parameters required

used with "create temp" commmand to initialize velocities of atoms

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

when the minimizer is invoked this command means create a restart file

  at the end of the minimization with the filename filename.timestep.min

a restart file stores atom and force-field information in binary form

allows program to restart from where it left off (see "read restart" commmand)

allows program to restart from where it left off (see "read restart" command)

Default = 0

</PRE>

         remainder

               no other parameters required

used with "create temp" commmand to initialize velocities of atoms

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

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" commmand)

allows program to restart from where it left off (see "read restart" command)

Default = 0

</PRE>

"timer"_timer.html,

"timestep"_timestep.html

Operations within timestepping (fixes) and diagnositics (computes):

Operations within timestepping (fixes) and diagnostics (computes):

"compute"_compute.html,

"compute_modify"_compute_modify.html,

LAMMPS failed to compute an initial guess for the PPPM_disp g_ewald_6

factor that partitions the computation between real space and k-space

for Disptersion interactions. :dd

for Dispersion interactions. :dd

{Cannot create an atom map unless atoms have IDs} :dt

{Cannot use fix reax/bonds without pair_style reax} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Cannot use fix rigid npt/nph and fix deform on same component of stress tensor} :dt

{Cannot use newton pair with born/gpu pair style} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Cannot use newton pair with buck/coul/cut/gpu pair style} :dt

{Cannot use newton pair with zbl/gpu pair style} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Cannot use non-zero forces in an energy minimization} :dt

{Compute chunk/atom bin/cylinder radius is too large for periodic box} :dt

Radius cannot be bigger than 1/2 of a non-axis  periodic dimention. :dd

Radius cannot be bigger than 1/2 of a non-axis  periodic dimension. :dd

{Compute chunk/atom bin/sphere radius is too large for periodic box} :dt

Radius cannot be bigger than 1/2 of any periodic dimention. :dd

Radius cannot be bigger than 1/2 of any periodic dimension. :dd

{Compute chunk/atom compute array is accessed out-of-range} :dt

{Compute chunk/atom stores no coord1 for compute property/chunk} :dt

Only certain binning options for comptue chunk/atom store coordinates. :dd

Only certain binning options for compute chunk/atom store coordinates. :dd

{Compute chunk/atom stores no coord2 for compute property/chunk} :dt

Only certain binning options for comptue chunk/atom store coordinates. :dd

Only certain binning options for compute chunk/atom store coordinates. :dd

{Compute chunk/atom stores no coord3 for compute property/chunk} :dt

Only certain binning options for comptue chunk/atom store coordinates. :dd

Only certain binning options for compute chunk/atom store coordinates. :dd

{Compute chunk/atom variable is not atom-style variable} :dt

{Compute cna/atom cutoff is longer than pairwise cutoff} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute cna/atom requires a pair style be defined} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute com/chunk does not use chunk/atom compute} :dt

{Compute contact/atom requires a pair style be defined} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute contact/atom requires atom style sphere} :dt

{Compute coord/atom requires a pair style be defined} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute damage/atom requires peridynamic potential} :dt

{Compute hexorder/atom requires a pair style be defined} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute improper/local used when impropers are not allowed} :dt

{Compute orientorder/atom requires a pair style be defined} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Compute pair must use group all} :dt

Pair styles accumlate energy on all atoms. :dd

Pair styles accumulate energy on all atoms. :dd

{Compute pe must use group all} :dt

{Compute property/local cannot use these inputs together} :dt

Only inputs that generate the same number of datums can be used

togther.  E.g. bond and angle quantities cannot be mixed. :dd

together.  E.g. bond and angle quantities cannot be mixed. :dd

{Compute property/local does not (yet) work with atom_style template} :dt

{Cutoffs missing in pair_style buck/long/coul/long} :dt

Self-exlanatory. :dd

Self-explanatory. :dd

{Cutoffs missing in pair_style lj/long/coul/long} :dt

{Fix ave/time compute does not calculate a scalar} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Fix ave/time compute does not calculate a vector} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Fix ave/time compute does not calculate an array} :dt

{Initial temperatures not all set in fix ttm} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Input line quote not followed by whitespace} :dt

{Insufficient Jacobi rotations for triangle} :dt

The calculation of the intertia tensor of the triangle failed.  This

The calculation of the inertia tensor of the triangle failed.  This

should not happen if it is a reasonably shaped triangle. :dd

{Insufficient memory on accelerator} :dt

{Invalid attribute in dump custom command} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Invalid attribute in dump local command} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Invalid attribute in dump modify command} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Invalid basis setting in create_atoms command} :dt

Filenames used with the dump xyz style cannot be binary or cause files

to be written by each processor. :dd

{Invalid dump_modify threshhold operator} :dt

{Invalid dump_modify threshold operator} :dt

Operator keyword used for threshold specification in not recognized. :dd

{Invalid fix ave/time off column} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Invalid fix box/relax command for a 2d simulation} :dt

{LJ6 off not supported in pair_style buck/long/coul/long} :dt

Self-exlanatory. :dd

Self-explanatory. :dd

{Label wasn't found in input script} :dt

{Molecule template ID for create_atoms does not exist} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Molecule template ID for fix deposit does not exist} :dt

{Must use variable energy with fix addforce} :dt

Must define an energy vartiable when applyting a dynamic

Must define an energy variable when applying a dynamic

force during minimization. :dd

{Must use variable energy with fix efield} :dt

{Non digit character between brackets in variable} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Non integer # of swaps in temper command} :dt

{Pair style does not support compute group/group} :dt

The pair_style does not have a single() function, so it cannot be

invokded by the compute group/group command. :dd

invoked by the compute group/group command. :dd

{Pair style does not support compute pair/local} :dt

{Pair yukawa/colloid requires atom style sphere} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Pair yukawa/colloid requires atoms with same type have same radius} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Pair yukawa/colloid/gpu requires atom style sphere} :dt

{Threshhold for an atom property that isn't allocated} :dt

A dump threshhold has been requested on a quantity that is

A dump threshold has been requested on a quantity that is

not defined by the atom style used in this simulation. :dd

{Timestep must be >= 0} :dt

{Too many atom triplets for pair bop} :dt

The number of three atom groups for angle determinations exceeds the

expected number.  Check your atomic structrure to ensure that it is

expected number.  Check your atomic structure to ensure that it is

realistic. :dd

{Too many atoms for dump dcd} :dt

{Too many timesteps} :dt

The cummulative timesteps must fit in a 64-bit integer. :dd

The cumulative timesteps must fit in a 64-bit integer. :dd

{Too many timesteps for NEB} :dt

{Variable name for fix deform does not exist} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Variable name for fix efield does not exist} :dt

{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt

Self-explantory. :dd

Self-explanatory. :dd

{Calling write_dump before a full system init.} :dt

If a thermo_style command is used after a thermo_modify command, the

settings changed by the thermo_modify command will be reset to their

default values.  This is because the thermo_modify commmand acts on

default values.  This is because the thermo_modify command acts on

the currently defined thermo style, and a thermo_style command creates

a new style. :dd

{Using largest cutoff for buck/long/coul/long} :dt

Self-exlanatory. :dd

Self-explanatory. :dd

{Using largest cutoff for lj/long/coul/long} :dt

that mode of usage.

The SPC/E (extended) water model is the same, except

the partial charge assignemnts change:

the partial charge assignments change:

O charge = -0.8476

H charge = 0.4238 :all(b),p

tile a triclinic simulation box via the

"create_atoms"_create_atoms.html command.

A second use is to run Parinello-Rahman dyanamics via the "fix

A second use is to run Parinello-Rahman dynamics via the "fix

npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt

factors to compensate for off-diagonal components of the pressure

tensor.  The analalog for an "energy minimization"_minimize.html is

tensor.  The analog for an "energy minimization"_minimize.html is

the "fix box/relax"_fix_box_relax.html command.

A third use is to shear a bulk solid to study the response of the

There is also a "dump local"_dump.html format where the user specifies

what local values to output.  A pre-defined index keyword can be

specified to enumuerate the local values.  Two additional kinds of

specified to enumerate the local values.  Two additional kinds of

keywords can also be specified (c_ID, f_ID), where a

"compute"_compute.html or "fix"_fix.html or "variable"_variable.html

provides the values to be output.  In each case, the compute or fix

velocities but also rotational velocities for spherical and aspherical

particles.

DPD thermostatting alters pairwise interactions in a manner analagous

DPD thermostatting alters pairwise interactions in a manner analogous

to the per-particle thermostatting of "fix

langevin"_fix_langevin.html.

Any of the thermostatting fixes can use temperature computes that

remove bias which has two effects.  First, the current calculated

temperature, which is compared to the requested target temperature, is

caluclated with the velocity bias removed.  Second, the thermostat

calculated with the velocity bias removed.  Second, the thermostat

adjusts only the thermal temperature component of the particle's

velocities, which are the velocities with the bias removed.  The

removed bias is then added back to the adjusted velocities.  See the

section"_Section_howto.html#howto_21 of the manual for an analogous

discussion for viscosity.

The thermal conducitivity tensor kappa is a measure of the propensity

The thermal conductivity tensor kappa is a measure of the propensity

of a material to transmit heat energy in a diffusive manner as given

by Fourier's law

moving in another direction, normal to the area through which the

momentum flows.  Viscosity thus has units of pressure-time.

The first method is to perform a non-equlibrium MD (NEMD) simulation

The first method is to perform a non-equilibrium MD (NEMD) simulation

by shearing the simulation box via the "fix deform"_fix_deform.html

command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to

thermostat the fluid via the SLLOD equations of motion.

swapped between atoms in two different layers of the simulation box in

a different dimension.  This induces a velocity gradient which can be

monitored with the "fix ave/chunk"_fix_ave_chunk.html command.

The fix tallies the cummulative momentum transfer that it performs.

The fix tallies the cumulative momentum transfer that it performs.

See the "fix viscosity"_fix_viscosity.html command for details.

The fourth method is based on the Green-Kubo (GK) formula which

Example calculations with chunks :h5

Here are eaxmples using chunk commands to calculate various

Here are examples using chunk commands to calculate various

properties:

(1) Average velocity in each of 1000 2d spatial bins:

The first approach is to set desired real-space an kspace accuracies

via the {kspace_modify force/disp/real} and {kspace_modify

force/disp/kspace} commands. Note that the accuracies have to be

specified in force units and are thus dependend on the chosen unit

specified in force units and are thus dependent on the chosen unit

settings. For real units, 0.0001 and 0.002 seem to provide reasonable

accurate and efficient computations for the real-space and kspace

accuracies.  0.002 and 0.05 work well for most systems using lj

The computational overhead can be reduced using the {kspace_modify

mix/disp geom} and {kspace_modify splittol} commands. The first

command simply enforces geometric mixing of the dispersion

coeffiecients in kspace computations.  This introduces some error in

coefficients in kspace computations.  This introduces some error in

the computations but will also significantly speed-up the

simulations. The second keyword sets the accuracy with which the

dispersion coefficients are approximated using a matrix factorization

6.25 Polarizable models :link(howto_25),h4

In polarizable force fields the charge distributions in molecules and

materials respond to their electrostatic environements. Polarizable

materials respond to their electrostatic environments. Polarizable

systems can be simulated in LAMMPS using three methods:

the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html

the pairs.  This can be done by using the {bias} keyword of the

"velocity create"_velocity.html command and assigning the "compute

temp/cs"_compute_temp_cs.html command to the {temp} keyword of the

"velocity"_velocity.html commmand, e.g.

"velocity"_velocity.html command, e.g.

velocity all create 1427 134 bias yes temp CSequ

velocity all scale 1427 temp CSequ :pre