Merge branch 'collected-small-changes' into next_patch_version

   * :doc:`manifoldforce <fix_manifoldforce>`

   * :doc:`meso/move <fix_meso_move>`

   * :doc:`momentum (k) <fix_momentum>`

   * :doc:`momentum/chunk <fix_momentum>`

   * :doc:`move <fix_move>`

   * :doc:`mscg <fix_mscg>`

   * :doc:`msst <fix_msst>`

* :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles

* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling

* :doc:`quartic <bond_quartic>` - breakable quartic bond

* :doc:`special <bond_special>` - enable special bond exclusions for 1-5 pairs and beyond

* :doc:`table <bond_table>` - tabulated by bond length

----------

* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization

* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion

* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms

* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms

* :doc:`move <fix_move>` - move atoms in a prescribed fashion

* :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models

* :doc:`msst <fix_msst>` - multi-scale shock technique (MSST) integration

fix momentum/kk command

=======================

fix momentum/chunk command

==========================

Syntax

""""""

* ID, group-ID are documented in :doc:`fix <fix>` command

* momentum = style name of this fix command

* N = adjust the momentum every this many timesteps

  one or more keyword/value pairs may be appended

* keyword = *linear* or *angular* or *rescale*

   fix ID group-ID momentum/chunk N chunkID keyword values ...

* ID, group-ID are documented in :doc:`fix <fix>` command

* momentum/chunk = style name of this fix command

* N = adjust the momentum per chunk every this many timesteps

* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command

  one or more keyword/value pairs may be appended

* keyword = *linear* or *angular* or *rescale*

       *linear* values = xflag yflag zflag

         xflag,yflag,zflag = 0/1 to exclude/include each dimension

       *angular* values = none

  .. parsed-literal::

       *rescale* values = none

Examples

   fix 1 all momentum 1 linear 1 1 0

   fix 1 all momentum 1 linear 1 1 1 rescale

   fix 1 all momentum 100 linear 1 1 1 angular

   fix 1 all momentum/chunk 100 molchunk linear 1 1 1 angular

Description

"""""""""""

Zero the linear and/or angular momentum of the group of atoms every N

timesteps by adjusting the velocities of the atoms.  One (or both) of

the *linear* or *angular* keywords must be specified.

Fix momentum zeroes the linear and/or angular momentum of the group of

atoms every N timesteps by adjusting the velocities of the atoms.

Fix momentum/chunk works equivalently, but operates on a per-chunk basis.

One (or both) of the *linear* or *angular* keywords **must** be specified.

If the *linear* keyword is used, the linear momentum is zeroed by

subtracting the center-of-mass velocity of the group from each atom.

This does not change the relative velocity of any pair of atoms.  One

or more dimensions can be excluded from this operation by setting the

corresponding flag to 0.

subtracting the center-of-mass velocity of the group or chunk from each

atom.  This does not change the relative velocity of any pair of atoms.

One or more dimensions can be excluded from this operation by setting

the corresponding flag to 0.

If the *angular* keyword is used, the angular momentum is zeroed by

subtracting a rotational component from each atom.

thermostatting).

The *rescale* keyword enables conserving the kinetic energy of the group

of atoms by rescaling the velocities after the momentum was removed.

or chunk of atoms by rescaling the velocities after the momentum was removed.

Note that the :doc:`velocity <velocity>` command can be used to create

initial velocities with zero aggregate linear and/or angular momentum.

**Restart, fix_modify, output, run start/stop, minimize info:**

No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options

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

by this fix for access by various :doc:`output commands <Howto_output>`.

No information about this fix is written to :doc:`binary restart files

<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are

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

this fix for access by various :doc:`output commands <Howto_output>`.

No parameter of this fix can be used with the *start/stop* keywords of

the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.

the :doc:`run <run>` command.  This fix is not invoked during

:doc:`energy minimization <minimize>`.

Restrictions

""""""""""""

 none

Fix momentum/chunk is part of the USER-MISC package.  It is only enabled

if LAMMPS was built with that package.  See the :doc:`Build package

<Build_package>` doc page for more info.

Related commands

""""""""""""""""

* ID, group-ID are documented in :doc:`fix <fix>` command

* style_name = *npt/cauchy*

* one or more keyword/value pairs may be appended

* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*

* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint*

  .. parsed-literal::

       *scaleyz* value = *yes* or *no* = scale yz with lz

       *scalexz* value = *yes* or *no* = scale xz with lz

       *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed

       *cauchystat* cauchystat values = alpha continue

         alpha = strength of Cauchy stress control parameter

         continue = *yes* or *no* = whether of not to continue from a previous run

       *alpha* value = strength of Cauchy stress control parameter

       *continue* value = *yes* or *no* = whether of not to continue from a previous run

       *fixedpoint* values = x y z

         x,y,z = perform barostat dilation/contraction around this point (distance units)

.. code-block:: LAMMPS

   fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0

   fix 1 water npt/cauchy temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 alpha 0.001

Description

"""""""""""

and if the tilt factor is not coupled to the barostat via keywords

*tri*\ , *yz*\ , *xz*\ , and *xy*\ .

Without the *cauchystat* keyword, the barostat algorithm

controls the Second-Piola Kirchhoff stress, which is a stress measure

referred to the unmodified (initial) simulation box.  If the box

deforms substantially during the equilibration, the difference between

the set values and the final true (Cauchy) stresses can be

considerable.

The *cauchystat* keyword modifies the barostat as per Miller et

The *alpha* keyword modifies the barostat as per Miller et

al. (Miller)_"#nc-Miller" so that the Cauchy stress is controlled.

*alpha* is the non-dimensional parameter, typically set to 0.001 or

0.01 that determines how aggressively the algorithm drives the system

Setting *alpha* to zero is not permitted.  To "turn off" the

cauchystat control and thus restore the equilibrium stress

fluctuations, two subsequent fixes should be used.  In the first, the

cauchystat flag is used and the simulation box equilibrates to the

correct shape for the desired stresses.  In the second, the *fix*

statement is identical except that the *cauchystat* keyword is removed

(along with related *alpha* and *continue* values). This restores the

original Parrinello-Rahman algorithm, but now with the correct simulation

box shape from the first fix.

fluctuations, two subsequent fixes should be used.  In the first, fix

npt/cauchy is used and the simulation box equilibrates to the

correct shape for the desired stresses.  In the second,

:doc:`fix npt <fix_nh>` is used instead which uses the

original Parrinello-Rahman algorithm, but now with the corrected

simulation box shape from using fix npt/cauchy.

This fix can be used with dynamic groups as defined by the

:doc:`group <group>` command.  Likewise it can be used with groups to