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Tweaks to documentation to make it more consistent and machine-readable

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Karl Hammond
2022-08-19 19:25:15 -05:00
parent d32b303a82
commit de0b7bf737
12 changed files with 42 additions and 33 deletions
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doc/src/compute_modify.rst
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@ -20,7 +20,7 @@ Syntax
N = # of extra degrees of freedom to subtract
*extra* syntax is identical to *extra/dof*, will be disabled at some point
*dynamic/dof* value = *yes* or *no*
yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
yes/no = do or do not re-compute the number of degrees of freedom (dof) contributing to the temperature
*dynamic* syntax is identical to *dynamic/dof*, will be disabled at some point
Examples
@ -37,24 +37,27 @@ 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 velocities with zero total linear momentum. For compute
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 velocities with zero total linear momentum. For compute
temp/partial, if one or more velocity components are excluded, the
value used for *extra* is scaled accordingly. You can use a negative
number for the *extra* parameter if you need to add
degrees-of-freedom. See the :doc:`compute temp/asphere <compute_temp_asphere>` command for an 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
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, 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 <fix_evaporate>`), then this option should be used to
insure the temperature is correctly normalized.
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 <fix_evaporate>`), then this option should be used
to ensure the temperature is correctly normalized.
.. note::
@ -75,4 +78,4 @@ Default
"""""""
The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
dynamic/dof = no.
dynamic/dof = *no*.