Merge pull request #2297 from akohlmey/more-fix-tests

* 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

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

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

This fix writes the locations of the initial per-chunk center of mass

coordinates to :doc:`binary restart files <restart>`.  See the

:doc:`read_restart <read_restart>` command for info on how to

re-specify a fix in an input script that reads a restart file, so that

the fix continues in an uninterrupted fashion.  Since this fix depends

on an instance of :doc:`compute chunk/atom <compute_chunk_atom>`

it will check when reading the restart if the chunk still exists and

will define the same number of chunks. The restart data is only applied

when the number of chunks matches. Otherwise the center of mass

coordinates are recomputed.

The :doc:`fix_modify <fix_modify>` *energy* option is supported by this

fix to add the energy stored in all the springs to the system's potential

**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>`.

This fix writes the currently used reference RG (:math:`R_{G0}`) to

:doc:`binary restart files <restart>`.  See the :doc:`read_restart

<read_restart>` command for info on how to re-specify a fix in an input

script that reads a restart file, so that the fix continues in an

uninterrupted fashion.

None of the :doc:`fix_modify <fix_modify>` options

are relevant to this fix.

This fix computes a global scalar which can be accessed by various

:doc:`output commands <Howto_output>`.  The scalar is the reference

radius of gyration :math:`R_{G0}` used by the fix.  energy change due to

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

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>`.

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

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

This fix writes the cumulative global energy change to :doc:`binary

restart files <restart>`.  See the :doc:`read_restart <read_restart>`

command for info on how to re-specify a fix in an input script that

reads a restart file, so that the fix continues in an uninterrupted

fashion.

The :doc:`fix_modify <fix_modify>` *temp* option is supported by this

fix.  You can use it to assign a temperature :doc:`compute <compute>`

The :doc:`fix_modify <fix_modify>` *energy* option is supported by this

fix to add the energy change implied by a velocity rescaling to the

system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.

system's potential energy as part of :doc:`thermodynamic output

<thermo_style>`.

This fix computes a global scalar which can be accessed by various

:doc:`output commands <Howto_output>`.  The scalar is the cumulative

  double mtk_term1,mtk_term2;         // Martyna-Tobias-Klein corrections

  double t_current,t_target;

  double t_current;

  double p_current[3],p_target[3];

  char *id_temp,*id_press;