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finish merge of develop

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Steve Plimpton
2022-08-29 17:07:49 -06:00
parent d67eed7e43 2f8c370645
commit 3e21738698
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doc/src/compute_modify.rst
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@ -37,8 +37,8 @@ Description
Modify one or more parameters of a previously defined compute. Not
all compute styles support all parameters.
The *extra/dof* or *extra* keyword refers to how many
degrees-of-freedom are subtracted (typically from 3N) as a normalizing
The *extra/dof* or *extra* keyword refers to how many degrees of
freedom are subtracted (typically from :math:`3N`) as a normalizing
factor in a temperature computation. Only computes that compute a
temperature use this option. The default is 2 or 3 for :doc:`2d or 3d
systems <dimension>` which is a correction factor for an ensemble of
@ -50,11 +50,11 @@ if one or more velocity components are excluded, the value used for
example.
The *dynamic/dof* or *dynamic* keyword determines whether the number
of atoms N in the compute group and their associated degrees of
freedom are re-computed each time a temperature is computed. Only
compute styles that calculate a temperature use this option. By
default, N and their DOF are assumed to be constant. If you are
adding atoms or molecules to the system (see the :doc:`fix pour
of atoms :math:`N` in the compute group and their associated degrees
of freedom (DOF) are re-computed each time a temperature is computed.
Only compute styles that calculate a temperature use this option. By
default, :math:`N` and their DOF are assumed to be constant. If you
are adding atoms or molecules to the system (see the :doc:`fix pour
<fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc
<fix_gcmc>` commands) or expect atoms or molecules to be lost
(e.g. due to exiting the simulation box or via :doc:`fix evaporate
@ -80,4 +80,4 @@ Default
"""""""
The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
dynamic/dof = no.
dynamic/dof = *no*.