Merge pull request #634 from craabreu/master

fix-ID = ID of the fix to modify :ulb,l

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

keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l

keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l

  {temp} value = compute ID that calculates a temperature

  {press} value = compute ID that calculates a pressure

  {energy} value = {yes} or {no}

  {virial} value = {yes} or {no}

  {respa} value = {1} to {max respa level} or {0} (for outermost level)

  {dynamic/dof} value = {yes} or {no}

    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre

    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature

  {bodyforces} value = {early} or {late}

    early/late = compute rigid-body forces/torques early or late in the timestep :pre

:ule

[Examples:]

relaxation criteria, although this seems unlikely.

NOTE: This option is only supported by fixes that explicitly say

so. For some of these (e.g. the

"fix shake"_fix_shake.html command) the default setting is

{virial yes}, for others it is {virial no}.

so. For some of these (e.g. the "fix shake"_fix_shake.html command)

the default setting is {virial yes}, for others it is {virial no}.

For fixes that set or modify forces, it may be possible to select at

which "r-RESPA"_run_style.html level the fix operates via the {respa}

dynamic/dof"_compute_modify.html command for a similar way to insure

correct temperature normalization for those thermostats.

The {bodyforces} keyword determines whether the forces and torques

acting on rigid bodies are computed {early} at the post-force stage of

each timestep (right after per-atom forces have been computed and

communicated among processors), or {late} at the final-integrate stage

of each timestep (after any other fixes have finished their post-force

tasks).  Only the rigid-body integration fixes use this option, which

includes "fix rigid"_fix_rigid.html and "fix

rigid/small"_fix_rigid.html, and their variants, and also "fix

poems"_fix_poems.html.

The default is {late}.  If there are other fixes that add forces to

individual atoms, then the rigid-body constraints will include these

forces when time-integrating the rigid bodies.  If {early} is

specified, then new fixes can be written that use or modify the

per-body force and torque, before time-integration of the rigid bodies

occurs.  Note however this has the side effect, that fixes such as

"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,

"fix spring"_fix_spring.html, which add forces to individual atoms

will have no effect on the motion of the rigid bodies if they are

specified in the input script after the fix rigid command.  LAMMPS

will give a warning if that is the case.

[Restrictions:] none

[Related commands:]

[Default:]

The option defaults are temp = ID defined by fix, press = ID defined

by fix, energy = no, virial = different for each fix style, respa = 0.

by fix, energy = no, virial = different for each fix style, respa = 0,

bodyforce = late.

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart

files"_restart.html.  None of the "fix_modify"_fix_modify.html options

are relevant to this fix.  No global or per-atom quantities are stored

by this fix for access by various "output

commands"_Section_howto.html#howto_15.  No parameter of this fix can

be used with the {start/stop} keywords of the "run"_run.html command.

This fix is not invoked during "energy minimization"_minimize.html.

files"_restart.html.  

The "fix_modify"_fix_modify.html {bodyforces} option is supported by

this fix style to set whether per-body forces and torques are computed

early or late in a timestep, i.e. at the post-force stage or at the

final-integrate stage, respectively.

No global or per-atom quantities are stored by this fix for access by

various "output commands"_Section_howto.html#howto_15.  No parameter

of this fix can be used with the {start/stop} keywords of the

"run"_run.html command.  This fix is not invoked during "energy

minimization"_minimize.html.

[Restrictions:]

NOTE: With the {rigid/small} styles, which require that {bodystyle} be

specified as {molecule} or {custom}, you can define a system that has

no rigid bodies initially.  This is useful when you are using the {mol}

keyword in conjunction with another fix that is adding rigid bodies

on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or

"fix pour"_fix_pour.html.

no rigid bodies initially.  This is useful when you are using the

{mol} keyword in conjunction with another fix that is adding rigid

bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html

or "fix pour"_fix_pour.html.

For bodystyle {single} the entire fix group of atoms is treated as one

rigid body.  This option is only allowed for the {rigid} styles.

NVT rigid fixes do not use any external compute to compute

instantaneous temperature.

The "fix_modify"_fix_modify.html {bodyforces} option is supported by

all rigid styles to set whether per-body forces and torques are

computed early or late in a timestep, i.e. at the post-force stage or

at the final-integrate stage or the timestep, respectively.

The 2 NVE rigid fixes compute a global scalar which can be accessed by

various "output commands"_Section_howto.html#howto_15.  The scalar

value calculated by these fixes is "intensive".  The scalar is the