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fix up fix colvars docs

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This commit is contained in:
Axel Kohlmeyer
2024-08-07 16:04:26 -04:00
parent 6544861bd3
commit 6bc0cae2d4
2 changed files with 13 additions and 8 deletions
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20
doc/src/fix_colvars.rst
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@ -69,10 +69,11 @@ source tree.
----------
The only required argument to the fix is the name of the Colvars
configuration file. The contents of this file are independent from the MD
engine in which the Colvars library has been integrated, save for the units
that are specific to each engine. In LAMMPS, the units used by Colvars are
consistent with those specificed by the :doc:`units <units>` command.
configuration file. The contents of this file are independent from the
MD engine in which the Colvars library has been integrated, save for the
units that are specific to each engine. In LAMMPS, the units used by
Colvars are consistent with those specified by the :doc:`units <units>`
command.
.. versionadded:: Colvars_2023-06-04 The special value "*none*"
(lowercase) initializes an empty Colvars module, which
@ -153,6 +154,8 @@ For this reason, the "output" keyword is required for fix colvars.
Controlling Colvars via `fix_modify`
""""""""""""""""""""""""""""""""""""
.. versionadded:: Colvars_2023-06-04
The :doc:`fix_modify <fix_modify>` command may be used on "fix colvars" in
either one of two ways:
@ -177,10 +180,9 @@ either one of two ways:
fix_modify Colvars output equil2
(2) .. versionadded:: Colvars_2023-06-04 Call one of the scripting
functions provided by the Colvars module itself (a full list is available
in the Colvars doc). The arguments to these functions are provided as
strings and passed to Colvars.
(2) Call one of the scripting functions provided by the Colvars module
itself (a full list is available in the Colvars doc). The arguments
to these functions are provided as strings and passed to Colvars.
LAMMPS variables referenced by their string representation
"${variable}" will be expanded immediately. Note also that this
@ -229,7 +231,9 @@ Related commands
----------
.. _Fiorin:
**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys. 111, 3345 (2013) https://doi.org/10.1080/00268976.2013.813594
.. _Colvars_LAMMPS_doc:
https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html

1
doc/utils/sphinx-config/false_positives.txt
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@ -2903,6 +2903,7 @@ plumedfile
pmb
pmcmoves
pme
pmf
Pmolrotate
Pmoltrans
pN