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update spelling/grammar and false positives

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This commit is contained in:
Axel Kohlmeyer
2020-12-20 15:02:59 -05:00
parent 24e2166357
commit 800ff0f1c2
2 changed files with 15 additions and 7 deletions
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15
doc/src/fix_tgnh_drude.rst
View File

@ -65,10 +65,13 @@ Examples
Description
"""""""""""
These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt <fix_nh>` and :doc:`fix npt <fix_nh>` for thermalized Drude polarizable models.
They apply temperature-grouped Nose-Hoover thermostat (TGNH) proposed by :ref:`(Son) <tgnh-Son>`.
When there are fast vibrational modes with frequencies close to Drude oscillators (e.g. double bonds or out-of-plane torsions),
this thermostat can provide better kinetic energy equipartition.
These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt
<fix_nh>` and :doc:`fix npt <fix_nh>` for thermalized Drude polarizable
models. They apply temperature-grouped Nose-Hoover thermostat (TGNH)
proposed by :ref:`(Son) <tgnh-Son>`. When there are fast vibrational
modes with frequencies close to Drude oscillators (e.g. double bonds or
out-of-plane torsions), this thermostat can provide better kinetic
energy equipartitioning.
The difference between TGNH and the original Nose-Hoover thermostat is that,
TGNH separates the kinetic energy of the group into three contributions:
@ -108,8 +111,8 @@ Here :math:`N_\mathrm{mol}` and :math:`N_\mathrm{mol,sys}` are the numbers of mo
not. You must therefore use the :doc:`fix drude <fix_drude>` command to
specify the Drude status of each atom type.
Because that TGNH thermostat thermalizes the molecular COM motion,
all atoms belong to the same molecule must be in the same group.
Because the TGNH thermostat thermostats the molecular COM motion,
all atoms belonging to the same molecule must be in the same group.
That is, these fixes can not be applied to a subset of a molecule.
For this fix to act correctly, ghost atoms need to know their velocity.

7
doc/utils/sphinx-config/false_positives.txt
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@ -533,6 +533,7 @@ cuda
Cuda
CUDA
CuH
Cui
cuFFT
Cummins
Curk
@ -869,6 +870,7 @@ equilibrating
equilibration
Equilibria
equilization
equipartitioning
Ercolessi
Erdmann
eradius
@ -3071,9 +3073,11 @@ tex
tfac
tfmc
tfMC
th
tgnpt
tgnvt
Thakkar
Thaokar
th
thb
thei
Theodorou
@ -3479,6 +3483,7 @@ Yc
ycm
Yeh
yellowgreen
Yethiraj
yflag
yhi
yi