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initial implementation of minimizer support in fix shake/rattle

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Axel Kohlmeyer
2022-04-30 19:03:28 -04:00
parent 87b0939fe7
commit a7b6dc7b59
6 changed files with 249 additions and 166 deletions
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27
doc/src/fix_shake.rst
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@ -33,12 +33,14 @@ Syntax
*m* value = one or more mass values
* zero or more keyword/value pairs may be appended
* keyword = *mol*
* keyword = *mol* or *kbond*
.. parsed-literal::
*mol* value = template-ID
template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
*kbond* value = force constant
force constant = force constant used to apply a restraint force when used during minimization
Examples
""""""""
@ -152,17 +154,23 @@ for.
----------
The *mol* keyword should be used when other commands, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add molecules
The *mol* keyword should be used when other commands, such as :doc:`fix
deposit <fix_deposit>` or :doc:`fix pour <fix_pour>`, add molecules
on-the-fly during a simulation, and you wish to constrain the new
molecules via SHAKE. You specify a *template-ID* previously defined
using the :doc:`molecule <molecule>` command, which reads a file that
defines the molecule. You must use the same *template-ID* that the
command adding molecules uses. The coordinates, atom types, special
bond restrictions, and SHAKE info can be specified in the molecule
file. See the :doc:`molecule <molecule>` command for details. The only
bond restrictions, and SHAKE info can be specified in the molecule file.
See the :doc:`molecule <molecule>` command for details. The only
settings required to be in this file (by this command) are the SHAKE
info of atoms in the molecule.
The *kbond* keyword allows to set the restraint force constant when
fix shake or fix rattle are used during minimization. In that case
the constraint algorithms are **not** applied and restraint
forces are used instead to help maintaining the geometries.
----------
.. include:: accel_styles.rst
@ -205,8 +213,10 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
No global or per-atom quantities are stored by these fixes for access
by various :doc:`output commands <Howto_output>`. No parameter of
these fixes can be used with the *start/stop* keywords of the
:doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
:doc:`run <run>` command.
When used during minimization, the SHAKE or RATTLE algorithms are **not**
applied. Strong restraint forces are applied instead.
Restrictions
""""""""""""
@ -232,13 +242,14 @@ make a linear molecule rigid.
Related commands
""""""""""""""""
none
`fix rigid <fix_rigid>`, `fix ehex <fix_ehex>`,
`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
Default
"""""""
none
kbond = 1.0e6
----------