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Axel Kohlmeyer
2022-06-17 06:19:57 -04:00
parent 0ad45a0224
commit e66229dadb
1 changed files with 22 additions and 15 deletions
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37
doc/src/fix_shake.rst
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@ -216,23 +216,25 @@ during a molecular dynamics run.
When used during minimization, the SHAKE or RATTLE algorithms are
**not** applied. The constraints are replaced by restraint forces
instead. The energy due to restraint forces is included in the global
potential energy, but virial contributions from them are not included in
the global pressure. The restraint energy is also accessible as a
global scalar property of the fix.
instead. The energy and virial contributions due to the restraint
forces are tallied into global and per-atom accumulators. The total
restraint energy is also accessible as a global scalar property of the
fix.
During molecular dynamics runs, the fixes apply the requested
constraints. The :doc:`fix_modify <fix_modify>` *virial* option is in
this case supported by these fixes to add the contribution due to the
added constraint forces on atoms to both the global pressure and
per-atom stress of the system via the :doc:`compute pressure
<compute_pressure>` and :doc:`compute stress/atom <compute_stress_atom>`
commands. The former can be accessed by :doc:`thermodynamic output
<thermo_style>`. The default 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>`
during a run. No parameter of these fixes can be used with the
*start/stop* keywords of the :doc:`run <run>` command.
constraints.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by these
fixes to add the contribution due to the added constraint forces on
atoms to both the global pressure and per-atom stress of the system via
the :doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be accessed
by :doc:`thermodynamic output <thermo_style>`. The default 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>` during an MD run. No parameter of
these fixes can be used with the *start/stop* keywords of the :doc:`run
<run>` command.
Restrictions
@ -256,6 +258,11 @@ degrees (e.g. linear CO2 molecule). This causes numeric difficulties.
You can use :doc:`fix rigid or fix rigid/small <fix_rigid>` instead to
make a linear molecule rigid.
When used during minimization choosing a too large value of the *kbond*
can make minimization very inefficent and also cause stability problems
with some minimization algorithms. Sometimes those can be avoided by
reducing the :doc:`timestep <timestep>`.
Related commands
""""""""""""""""