Merge branch 'doc-pdf-GClavier' of https://github.com/Bibobu/lammps into collected-small-fixes

doc/src/Errors_common.rst

@@ -39,7 +39,8 @@ figure out your physics or numerical mistakes, like choosing too big a
 timestep, specifying erroneous force field coefficients, or putting 2
 atoms on top of each other!  If you run into errors that LAMMPS
 does not catch that you think it should flag, please send an email to
-the `developers <https://www.lammps.org/authors.html>`_.
+the `developers <https://www.lammps.org/authors.html>`_ or create an new
+topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by

doc/src/Errors_messages.rst

@@ -1932,7 +1932,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Compute chunk/atom fix array is accessed out-of-range*
-   the index for the array is out of bounds.
+   The index for the array is out of bounds.
 
 *Compute chunk/atom fix does not calculate a per-atom array*
    Self-explanatory.
@@ -6073,9 +6073,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *New atom IDs exceed maximum allowed ID*
    See the setting for tagint in the src/lmptype.h file.
 
-*New bond exceeded bonds per atom in create_bonds*
+*New bond exceeded bonds per atom in create\_bonds*
-See the read_data command for info on using the "extra/bond/per/atom"
+   See the read_data command for info on using the "extra/bond/per/atom"
-keyword to allow for additional bonds to be formed
+   keyword to allow for additional bonds to be formed
 
 *New bond exceeded bonds per atom in fix bond/create*
    See the read_data command for info on using the "extra/bond/per/atom"

doc/src/Errors_warnings.rst

@@ -233,7 +233,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    style.
 
 *Fix langevin gjf using random gaussians is not implemented with kokkos*
-This will most likely cause errors in kinetic fluctuations.
+   This will most likely cause errors in kinetic fluctuations.
 
 *Fix property/atom mol or charge w/out ghost communication*
    A model typically needs these properties defined for ghost atoms.

doc/src/Tools.rst

@@ -58,6 +58,7 @@ Pre-processing tools
    * :ref:`polybond <polybond>`
    * :ref:`stl_bin2txt <stlconvert>`
    * :ref:`tabulate <tabulate>`
+   * :ref:`tinker <tinker>`
 
 Post-processing tools
 =====================
@@ -97,6 +98,7 @@ Miscellaneous tools
    * :ref:`Offline build tool <offline>`
    * :ref:`singularity/apptainer <singularity_tool>`
    * :ref:`SWIG interface <swig>`
+   * :ref:`valgrind <valgrind>`
    * :ref:`vim <vim>`
 
 ----------
@@ -109,7 +111,7 @@ Tool descriptions
 amber2lmp tool
 --------------------------
 
-The amber2lmp subdirectory contains two Python scripts for converting
+The amber2lmp subdirectory contains three Python scripts for converting
 files back-and-forth between the AMBER MD code and LAMMPS.  See the
 README file in amber2lmp for more information.
 
@@ -302,7 +304,7 @@ The parameters for Cr were taken from:
 Lin Z B, Johnson R A and Zhigilei L V, Phys. Rev. B 77 214108 (2008).
 
 The Python version of the tool was authored  by Germain Clavier
-(TU Eindhoven) g.m.g.c.clavier at tue.nl or germain.clavier at gmail.com
+(Unicaen) germain.clavier at unicaen.fr
 
 .. note::
 
@@ -1210,6 +1212,33 @@ included.  See the README file for more information.
 
 ----------
 
+.. _tinker:
+
+tinker tool
+--------------
+
+The ``tinker`` folder contains Python scripts scripts to convert Tinker input
+files to LAMMPS.
+
+See the README file for more information.
+
+Those scripts were written by Steve Plimpton sjplimp at gmail.com
+
+----------
+
+.. _valgrind:
+
+valgrind tool
+-------------
+
+The ``valgrind`` folder contains additional suppressions fur LAMMPS when using
+valgrind's memcheck tool to search for memory access violation and memory
+leaks. These suppressions are automatically invoked when running tests through
+CMake "ctest -T memcheck". See the provided README file to add these
+suppressions when running LAMMPS.
+
+----------
+
 .. _vim:
 
 vim tool

src/library.cpp

@@ -5428,7 +5428,7 @@ The function returns the number of atoms created or -1 on failure (e.g.,
 when called before as box has been created).
 
 Coordinates and velocities have to be given in a 1d-array in the order
-X(1),Y(1),Z(1),X(2),Y(2),Z(2),...,X(N),Y(N),Z(N).
+X(1), Y(1), Z(1), X(2), Y(2), Z(2), ..., X(N), Y(N), Z(N).
 
 \endverbatim
  *