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fix spelling errors

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This commit is contained in:
Axel Kohlmeyer
2023-01-23 17:45:59 -05:00
parent 70012131b6
commit 8b897e1fed
2 changed files with 25 additions and 19 deletions
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2
doc/src/Errors_messages.rst
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@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
*Replacing a fix, but new style != old style*
A fix ID can be used a second time, but only if the style matches the
previous fix. In this case it is assumed you with to reset a fix's
previous fix. In this case it is assumed you want to reset a fix's
parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to.

42
doc/src/fix_rigid.rst
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@ -702,9 +702,10 @@ also accounted for by this fix.
----------
If your simulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If your simulation is a hybrid model with a mixture of rigid bodies and
non-rigid particles (e.g. solvent) there are several ways these rigid
fixes can be used in tandem with :doc:`fix nve <fix_nve>`, :doc:`fix nvt
<fix_nh>`, :doc:`fix npt <fix_nh>`, and :doc:`fix nph <fix_nh>`.
If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid
@ -713,13 +714,17 @@ particles.
If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid
bodies, and any thermostatting fix for the non-rigid particles (:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`). You can also use one of the
4 NVE rigid styles for the rigid bodies and thermostat them using :doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix langevin <fix_langevin>` to each rigid body effectively thermostats
its translational center-of-mass motion. Not sure how well it does at
bodies, and any thermostatting fix for the non-rigid particles
(:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`). You can also use one of the 4
NVE rigid styles for the rigid bodies and thermostat them using
:doc:`fix langevin <fix_langevin>` on the group that contains all the
particles in the rigid bodies. The net force added by :doc:`fix
langevin <fix_langevin>` to each rigid body effectively thermostats its
translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
If you with to perform NPT or NPH dynamics (barostatting), you cannot
If you wish to perform NPT or NPH dynamics (barostatting), you cannot
use both :doc:`fix npt <fix_nh>` and the NPT or NPH rigid styles. This
is because there can only be one fix which monitors the global
pressure and changes the simulation box dimensions. So you have 3
@ -727,27 +732,28 @@ choices:
* Use one of the 4 NPT or NPH styles for the rigid bodies. Use the
*dilate* all option so that it will dilate the positions of the
non-rigid particles as well. Use :doc:`fix nvt <fix_nh>` (or any other
thermostat) for the non-rigid particles.
*non-rigid particles as well. Use :doc:`fix nvt <fix_nh>` (or any
*other thermostat) for the non-rigid particles.
* Use :doc:`fix npt <fix_nh>` for the group of non-rigid particles. Use
the *dilate* all option so that it will dilate the center-of-mass
positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies.
* Use :doc:`fix press/berendsen <fix_press_berendsen>` to compute the
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies. Use :doc:`fix nvt <fix_nh>` (or any
other thermostat) for the non-rigid particles.
rigid styles for the rigid bodies. Use :doc:`fix nvt <fix_nh>` (or
any other thermostat) for the non-rigid particles.
In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the second and third options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give :doc:`fix npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure
and change the box dimensions, but not time integrate any particles.
The integration of the rigid bodies will be performed by fix
rigid/nvt.
You could even use the second and third options for a non-hybrid
simulation consisting of only rigid bodies, assuming you give :doc:`fix
npt <fix_nh>` an empty group, though it's an odd thing to do. The
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen
<fix_press_berendsen>`) will monitor the pressure and change the box
dimensions, but not time integrate any particles. The integration of
the rigid bodies will be performed by fix rigid/nvt.
----------