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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* *Replacing a fix, but new style != old style*
A fix ID can be used a second time, but only if the style matches the 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 parameters. This error may mean you are mistakenly re-using a fix ID
when you do not intend to. 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 If your simulation is a hybrid model with a mixture of rigid bodies and
and non-rigid particles (e.g. solvent) there are several ways these non-rigid particles (e.g. solvent) there are several ways these rigid
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>`. 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 If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid 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 If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid 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 bodies, and any thermostatting fix for the non-rigid particles
4 NVE rigid styles for the rigid bodies and thermostat them using :doc:`fix langevin <fix_langevin>` on the group that contains all the (:doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`, :doc:`fix
particles in the rigid bodies. The net force added by :doc:`fix langevin <fix_langevin>` to each rigid body effectively thermostats temp/berendsen <fix_temp_berendsen>`). You can also use one of the 4
its translational center-of-mass motion. Not sure how well it does at 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. 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 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 is because there can only be one fix which monitors the global
pressure and changes the simulation box dimensions. So you have 3 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 * 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 *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 *non-rigid particles as well. Use :doc:`fix nvt <fix_nh>` (or any
thermostat) for the non-rigid particles. *other thermostat) for the non-rigid particles.
* Use :doc:`fix npt <fix_nh>` for the group of non-rigid particles. Use * 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 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 positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies. rigid styles for the rigid bodies.
* Use :doc:`fix press/berendsen <fix_press_berendsen>` to compute the * 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 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 rigid styles for the rigid bodies. Use :doc:`fix nvt <fix_nh>` (or
other thermostat) for the non-rigid particles. any other thermostat) for the non-rigid particles.
In all case, the rigid bodies and non-rigid particles both contribute 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 to the global pressure and the box is scaled the same by any of the
barostatting fixes. barostatting fixes.
You could even use the second and third options for a non-hybrid simulation You could even use the second and third options for a non-hybrid
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 simulation consisting of only rigid bodies, assuming you give :doc:`fix
barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen <fix_press_berendsen>`) will monitor the pressure npt <fix_nh>` an empty group, though it's an odd thing to do. The
and change the box dimensions, but not time integrate any particles. barostatting fixes (:doc:`fix npt <fix_nh>` and :doc:`fix press/berensen
The integration of the rigid bodies will be performed by fix <fix_press_berendsen>`) will monitor the pressure and change the box
rigid/nvt. dimensions, but not time integrate any particles. The integration of
the rigid bodies will be performed by fix rigid/nvt.
---------- ----------