files for doing particle dumps in XTC format.  This is only necessary

if your platform does have its own XDR files available.  See the

Restrictions section of the <a class="reference internal" href="dump.html"><em>dump</em></a> command for details.</p>

<p>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D-

DLAMMPS_SMALLSMALL settings.  The default is -DLAMMPS_SMALLBIG. These

<p>Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,

-DLAMMPS_SMALLSMALL settings.  The default is -DLAMMPS_SMALLBIG. These

settings refer to use of 4-byte (small) vs 8-byte (big) integers

within LAMMPS, as specified in src/lmptype.h.  The only reason to use

the BIGBIG setting is to enable simulation of huge molecular systems

like: &#8220;lmp_win_mpi -in in.lj&#8221;.</li>

</ul>

<hr class="docutils" />

<p>The screen output from LAMMPS is described in the next section.  As it

<p>The screen output from LAMMPS is described in a section below.  As it

runs, LAMMPS also writes a log.lammps file with the same information.</p>

<p>Note that this sequence of commands copies the LAMMPS executable

(lmp_linux) to the directory with the input files.  This may not be

atom_style style args :pre

style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \

        {electron} or {ellipsoid} or {full} or {line} or {meso} or \

        {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \

	{molecular} or {peri} or {smd} or {sphere} or {tri} or \

        {template} or {hybrid} :ulb,l

  args = none for any style except {body} and {hybrid}

  args = none for any style except the following

  {body} args = bstyle bstyle-args

    bstyle = style of body particles

    bstyle-args = additional arguments specific to the bstyle

"read_restart"_read_restart.html, or "create_box"_create_box.html

command.

NOTE: Many of the atom styles discussed here are only enabled if

LAMMPS was built with a specific package, as listed below in the

Restrictions section.

Once a style is assigned, it cannot be changed, so use a style general

enough to encompass all attributes.  E.g. with style {bond}, angular

terms cannot be used or added later to the model.  It is OK to use a

{bond} | bonds | bead-spring polymers |

{charge} | charge | atomic system with charges |

{dipole} | charge and dipole moment | system with dipolar particles |

{dpd} | internal temperature and internal energies | DPD particles |

{electron} | charge and spin and eradius | electronic force field |

{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |

{full} | molecular + charge | bio-molecules |

For the {peri} style, the particles are spherical and each stores a

per-particle mass and volume.

The {dpd} style is for dissipative particle dynamics (DPD) particles

which store the particle internal temperature (dpdTheta), internal

conductive energy (uCond) and internal mechanical energy (uMech).

The {meso} style is for smoothed particle hydrodynamics (SPH)

particles which store a density (rho), energy (e), and heat capacity

(cv).

This command cannot be used after the simulation box is defined by a

"read_data"_read_data.html or "create_box"_create_box.html command.

The {angle}, {bond}, {full}, {molecular}, and {template} styles are

part of the MOLECULE package.  The {line} and {tri} styles are part

of the ASPHERE pacakge.  The {body} style is part of the BODY package.

The {dipole} style is part of the DIPOLE package.  The {peri} style is

part of the PERI package for Peridynamics.  The {electron} style is

part of the USER-EFF package for "electronic force

fields"_pair_eff.html.  The {meso} style is part of the USER-SPH

package for smoothed particle hydrodyanmics (SPH).  See "this PDF

guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.  The

{wavepacket} style is part of the USER-AWPMD package for the

"antisymmetrized wave packet MD method"_pair_awpmd.html.  They are

only enabled if LAMMPS was built with that package.  See the "Making

Many of the styles listed above are only enabled if LAMMPS was built

with a specific package, as listed below.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info.

The {angle}, {bond}, {full}, {molecular}, and {template} styles are

part of the MOLECULE package.

The {line} and {tri} styles are part of the ASPHERE pacakge.

The {body} style is part of the BODY package.

The {dipole} style is part of the DIPOLE package.  

The {peri} style is part of the PERI package for Peridynamics.

The {electron} style is part of the USER-EFF package for "electronic

force fields"_pair_eff.html.

The {dpd} style is part of the USER-DPD package for dissipative

particle dynamics (DPD).

The {meso} style is part of the USER-SPH package for smoothed particle

hydrodyanmics (SPH).  See "this PDF

guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.

The {wavepacket} style is part of the USER-AWPMD package for the

"antisymmetrized wave packet MD method"_pair_awpmd.html.

[Related commands:]

"read_data"_read_data.html, "pair_style"_pair_style.html

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

compute dpd command :h3

[Syntax:]

compute ID group-ID dpd :pre

ID, group-ID are documented in "compute"_compute.html command

dpd = style name of this compute command :ul

[Examples:]

compute 1 all dpd :pre

[Description:]

Define a computation that accumulates the total internal conductive

energy (U_cond), the total internal mechanical energy (U_mech), the

total internal energy (U) and the {harmonic} average of the internal

temperature (dpdTheta) for the entire system of particles.  See the

"compute dpd/atom"_compute_dpd_atom.html command if you want

per-particle internal energies and internal temperatures.

The system internal properties are computed according to the following

relations:

:c,image(Eqs/compute_dpd.jpg)

where N is the number of particles in the system

:line

[Output info:]

This compute calculates a global vector of length 5 (U_cond, U_mech,

U, dpdTheta, N_particles), which can be accessed by indices 1-5.  See

"this section"_Section_howto.html#howto_15 for an overview of LAMMPS

output options.

The vector values will be in energy and temperature "units"_units.html.

[Restrictions:] 

The compute {dpd} is only available if LAMMPS is built with the

USER-DPD package and requires the "atom_style dpd"_atom_style.html.

[Related commands:]

"compute dpd/atom"_compute_dpd_atom.html,

"thermo_style"_thermo_style.html

[Default:] none

:line

:link(Larentzos) 

[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

compute dpd/atom command :h3

[Syntax:]

compute ID group-ID dpd/atom :pre

ID, group-ID are documented in "compute"_compute.html command

dpd/atom = style name of this compute command :ul

[Examples:]

compute 1 all dpd/atom

[Description:]

Define a computation that accesses the per-particle internal

conductive energy (u_cond), internal mechanical energy (u_mech) and

internal temperatures (dpdTheta) for each particle in a group.  See

the "compute dpd"_compute_dpd.html command if you want the total

internal conductive energy, the total internal mechanical energy, and

average internal temperature of the entire system or group of dpd

particles.

[Output info:]

This compute calculates a per-particle array with 3 columns (u_cond,

u_mech, dpdTheta), which can be accessed by indices 1-3 by any command

that uses per-particle values from a compute as input.  See

"Section_howto15"_Section_howto.html#howto_15 for an overview of

LAMMPS output options.

The per-particle array values will be in energy (u_cond, u_mech) and

temperature (dpdTheta) "units"_units.html.

[Restrictions:] 

The compute {dpd/atom} is only available if LAMMPS is built with the

USER-DPD package.

[Related commands:]

"dump custom"_dump.html, "compute dpd"_compute_dpd.html

[Default:] none

:line

:link(Larentzos)

[(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and

W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative

Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research

Laboratory, Aberdeen Proving Ground, MD (2014).

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

compute temp/body command :h3

[Syntax:]

compute ID group-ID temp/body keyword value ... :pre

ID, group-ID are documented in "compute"_compute.html command :ulb,l

temp/body = style name of this compute command :l

zero or more keyword/value pairs may be appended :l

keyword = {bias} or {dof} :l

  {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 :pre

:ule

[Examples:]

compute 1 all temp/body

compute myTemp mobile temp/body bias tempCOM

compute myTemp mobile temp/body dof rotate :pre

[Description:]

Define a computation that calculates the temperature of a group of

body particles, including a contribution from both their

translational and rotational kinetic energy.  This differs from the

usual "compute temp"_compute_temp.html command, which assumes point

particles with only translational kinetic energy.

Only body particles can be included in the group.  For 3d particles,

each has 6 degrees of freedom (3 translational, 3 rotational).  For 2d

body particles, each has 3 degrees of freedom (2 translational, 1

rotational).

NOTE: This choice for degrees of freedom (dof) assumes that all body

particles in your model will freely rotate, sampling all their

rotational dof.  It is possible to use a combination of interaction

potentials and fixes that induce no torque or otherwise constrain some

of all of your particles so that this is not the case.  Then there are

less dof and you should use the "compute_modify

extra"_compute_modify.html command to adjust the dof accordingly.

The translational kinetic energy is computed the same as is described

by the "compute temp"_compute_temp.html command.  The rotational

kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor

for the aspherical particle and w is its angular velocity, which is

computed from its angular momentum.

A kinetic energy tensor, stored as a 6-element vector, is also

calculated by this compute.  The formula for the components of the

tensor is the same as the above formula, except that v^2 and w^2 are

replaced by vx*vy and wx*wy for the xy component, and the appropriate

elements of the inertia tensor are used.  The 6 components of the

vector are ordered xx, yy, zz, xy, xz, yz.

The number of atoms contributing to the temperature is assumed to be

constant for the duration of the run; use the {dynamic} option of the

"compute_modify"_compute_modify.html command if this is not the case.

This compute subtracts out translational degrees-of-freedom due to

fixes that constrain molecular motion, such as "fix

shake"_fix_shake.html and "fix rigid"_fix_rigid.html.  This means the

temperature of groups of atoms that include these constraints will be

computed correctly.  If needed, the subtracted degrees-of-freedom can

be altered using the {extra} option of the

"compute_modify"_compute_modify.html command.

See "this howto section"_Section_howto.html#howto_16 of the manual for

a discussion of different ways to compute temperature and perform

thermostatting.

:line

The keyword/value option pairs are used in the following ways.

For the {bias} keyword, {bias-ID} refers to the ID of a temperature

compute that removes a "bias" velocity from each atom.  This allows

compute temp/sphere to compute its thermal temperature after the

translational kinetic energy components have been altered in a

prescribed way, e.g. to remove a flow velocity profile.  Thermostats

that use this compute will work with this bias term.  See the doc

pages for individual computes that calculate a temperature and the doc

pages for fixes that perform thermostatting for more details.

For the {dof} keyword, a setting of {all} calculates a temperature

that includes both translational and rotational degrees of freedom.  A

setting of {rotate} calculates a temperature that includes only

rotational degrees of freedom.

:line

[Output info:]

This compute calculates a global scalar (the temperature) and a global

vector of length 6 (KE tensor), which can be accessed by indices 1-6.

These values can be used by any command that uses global scalar or

vector values from a compute as input.  See "this

section"_Section_howto.html#howto_15 for an overview of LAMMPS output

options.

The scalar value calculated by this compute is "intensive".  The

vector values are "extensive".

The scalar value will be in temperature "units"_units.html.  The

vector values will be in energy "units"_units.html.

[Restrictions:]

This compute is part of the BODY package.  It is only enabled if

LAMMPS was built with that package.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info.

This compute requires that atoms store angular momementum and a

quaternion as defined by the "atom_style body"_atom_style.html

command.

[Related commands:]

"compute temp"_compute_temp.html

[Default:] none