diff --git a/doc/src/fix_colvars.rst b/doc/src/fix_colvars.rst index 936fdaa83b..f62ae0e85a 100644 --- a/doc/src/fix_colvars.rst +++ b/doc/src/fix_colvars.rst @@ -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 ` 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 ` +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 ` 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 diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 5406c3ac79..7c43216a9a 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2903,6 +2903,7 @@ plumedfile pmb pmcmoves pme +pmf Pmolrotate Pmoltrans pN