ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update docs and include suggestions

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

56
doc/src/fix_shake.rst
View File

@ -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 settings required to be in this file (by this command) are the SHAKE
info of atoms in the molecule. info of atoms in the molecule.
The *kbond* keyword allows to set the restraint force constant when fix The *kbond* keyword sets the restraint force constant when fix shake or
shake or fix rattle are used during minimization. In that case the fix rattle are used during minimization. In that case the constraint
constraint algorithms are *not* applied and restraint forces are used algorithms are *not* applied and restraint forces are used instead to
instead to help maintaining the geometries. How well the geometries maintain the geometries similar to the constraints. How well the
are maintained and how quickly a minimization will converge depends on geometries are maintained and how quickly a minimization converges,
the magnitude of the force constant (kbond). If it is chosen too large depends on the force constant *kbond*: larger values will reduce the
the minimization may converge slowly. The default is 1.0e6*k_B. 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:: .. 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 should be defined after all other integration fixes in your input
script. If you define other fixes that modify velocities or forces script. If you define other fixes that modify velocities or forces
after fix rattle operates, then fix rattle will not take them into 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 No information about these fixes is written to :doc:`binary restart
files <restart>`. files <restart>`.
When used during minimization, the SHAKE or RATTLE algorithms are **not** Fix *shake* and *rattle* behave differently during minimization and
applied. Strong restraint forces are applied instead. during a molecular dynamics run.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by When used during minimization, the SHAKE or RATTLE algorithms are
these fixes to add the contribution due to the added forces on atoms **not** applied. The constraints are replaced by restraint forces
to both the global pressure and per-atom stress of the system via the instead. The energy due to restraint forces is included in the global
:doc:`compute pressure <compute_pressure>` and :doc:`compute potential energy, but virial contributions from them are not included in
stress/atom <compute_stress_atom>` commands. The former can be the global pressure. The restraint energy is also accessible as a
accessed by :doc:`thermodynamic output <thermo_style>`. The default global scalar property of the fix.
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
During minimization, the virial contribution is *NOT* available.
No global or per-atom quantities are stored by these fixes for access by During molecular dynamics runs, the fixes apply the requested
various :doc:`output commands <Howto_output>` during a run. During constraints. The :doc:`fix_modify <fix_modify>` *virial* option is in
minimization, this fix computes a global scalar which is the energy of this case supported by these fixes to add the contribution due to the
the restraint forces applied insteat of the constraints. No parameter added constraint forces on atoms to both the global pressure and
of these fixes can be used with the *start/stop* keywords of the per-atom stress of the system via the :doc:`compute pressure
:doc:`run <run>` command. <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 Restrictions

1
doc/utils/sphinx-config/false_positives.txt
View File

@ -1609,6 +1609,7 @@ kb
kB kB
kbit kbit
kbits kbits
kbond
kcal kcal
kcl kcl
Kd Kd