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update docs and include suggestions

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This commit is contained in:
Axel Kohlmeyer
2022-06-10 11:07:50 -04:00
parent 1ee35bea61
commit c4a7610366
2 changed files with 33 additions and 24 deletions
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56
doc/src/fix_shake.rst
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@ -168,13 +168,17 @@ 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. How well the geometries
are maintained and how quickly a minimization will converge depends on
the magnitude of the force constant (kbond). If it is chosen too large
the minimization may converge slowly. The default is 1.0e6*k_B.
The *kbond* keyword sets 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
maintain the geometries similar to the constraints. How well the
geometries are maintained and how quickly a minimization converges,
depends on the force constant *kbond*: larger values will reduce the
deviation from the desired geometry, but can also lead to slower
convergence of the minimization or lead to instabilities depending on
the minimization algorithm requiring to reduce the value of
:doc:`timestep <timestep>`. The default value for *kbond* depends on
the :doc:`units <units>` setting and is 1.0e6*k_B.
----------
@ -190,7 +194,7 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
.. note::
The fix rattle command modifies forces and velocities and thus
The *fix rattle* command modifies forces and velocities and thus
should be defined after all other integration fixes in your input
script. If you define other fixes that modify velocities or forces
after fix rattle operates, then fix rattle will not take them into
@ -207,24 +211,28 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about these fixes is written to :doc:`binary restart
files <restart>`.
When used during minimization, the SHAKE or RATTLE algorithms are **not**
applied. Strong restraint forces are applied instead.
Fix *shake* and *rattle* behave differently during minimization and
during a molecular dynamics run.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
these fixes to add the contribution due to the added 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>`.
During minimization, the virial contribution is *NOT* available.
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.
No global or per-atom quantities are stored by these fixes for access by
various :doc:`output commands <Howto_output>` during a run. During
minimization, this fix computes a global scalar which is the energy of
the restraint forces applied insteat of the constraints. No parameter
of these fixes can be used with the *start/stop* keywords of the
:doc:`run <run>` command.
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.
Restrictions

1
doc/utils/sphinx-config/false_positives.txt
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@ -1609,6 +1609,7 @@ kb
kB
kbit
kbits
kbond
kcal
kcl
Kd