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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
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@ -65,10 +65,13 @@ Examples
Description 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. These commands are variants of the Nose-Hoover fix styles :doc:`fix nvt
They apply temperature-grouped Nose-Hoover thermostat (TGNH) proposed by :ref:`(Son) <tgnh-Son>`. <fix_nh>` and :doc:`fix npt <fix_nh>` for thermalized Drude polarizable
When there are fast vibrational modes with frequencies close to Drude oscillators (e.g. double bonds or out-of-plane torsions), models. They apply temperature-grouped Nose-Hoover thermostat (TGNH)
this thermostat can provide better kinetic energy equipartition. 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, The difference between TGNH and the original Nose-Hoover thermostat is that,
TGNH separates the kinetic energy of the group into three contributions: 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 not. You must therefore use the :doc:`fix drude <fix_drude>` command to
specify the Drude status of each atom type. specify the Drude status of each atom type.
Because that TGNH thermostat thermalizes the molecular COM motion, Because the TGNH thermostat thermostats the molecular COM motion,
all atoms belong to the same molecule must be in the same group. 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. 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. 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
CUDA CUDA
CuH CuH
Cui
cuFFT cuFFT
Cummins Cummins
Curk Curk
@ -869,6 +870,7 @@ equilibrating
equilibration equilibration
Equilibria Equilibria
equilization equilization
equipartitioning
Ercolessi Ercolessi
Erdmann Erdmann
eradius eradius
@ -3071,9 +3073,11 @@ tex
tfac tfac
tfmc tfmc
tfMC tfMC
th tgnpt
tgnvt
Thakkar Thakkar
Thaokar Thaokar
th
thb thb
thei thei
Theodorou Theodorou
@ -3479,6 +3483,7 @@ Yc
ycm ycm
Yeh Yeh
yellowgreen yellowgreen
Yethiraj
yflag yflag
yhi yhi
yi yi