From c68348911089149ebfedc3bd19eeac224c829df6 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 19:25:22 +0200 Subject: [PATCH 1/8] Added a valgrind section to Tools.rst. --- doc/src/Tools.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 1c16d370b9..121066bf99 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -97,6 +97,7 @@ Miscellaneous tools * :ref:`Offline build tool ` * :ref:`singularity/apptainer ` * :ref:`SWIG interface ` + * :ref:`valgrind ` * :ref:`vim ` ---------- @@ -1210,6 +1211,19 @@ included. See the README file for more information. ---------- +.. _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 From 30208f7173f60b16bcd73d6c0e412bae1f6c087f Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 19:32:56 +0200 Subject: [PATCH 2/8] Added a tinker section to Tools.rst. --- doc/src/Tools.rst | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 121066bf99..35853186d2 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -58,6 +58,7 @@ Pre-processing tools * :ref:`polybond ` * :ref:`stl_bin2txt ` * :ref:`tabulate ` + * :ref:`tinker ` Post-processing tools ===================== @@ -1211,6 +1212,20 @@ 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 From e52c739814d5b0c2000025cb008dc733bd03d211 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 19:35:47 +0200 Subject: [PATCH 3/8] There are actually 3 scripts in the amber2lmp folder. Is the 99 format version necessary? --- doc/src/Tools.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 35853186d2..ab5cb2aa9e 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -111,7 +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. From a91e534eabfec66bf83d759d68426e2c40059d06 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 19:57:48 +0200 Subject: [PATCH 4/8] Changed Germain Clavier's mail adress. --- doc/src/Tools.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index ab5cb2aa9e..f651e93e32 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -304,7 +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:: From 892d2dda96d75c5f960e9c69fd6e0adbf6c6318c Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 20:49:49 +0200 Subject: [PATCH 5/8] Added mention of the MatSci forum in the Errors_common introduction section after the section about mailing the devs. --- doc/src/Errors_common.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 7aca0f14fa..3229181d00 100644 --- a/doc/src/Errors_common.rst +++ b/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 `_. +the `developers `_ or create an new +topic on the dedicated `MatSci forum section `_. If you get an error message about an invalid command in your input script, you can determine what command is causing the problem by From cb03f45528db595668ae52d4910668aa9d868c04 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 21:16:54 +0200 Subject: [PATCH 6/8] Some typos --- doc/src/Errors_messages.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 2a146a9184..22070c8b16 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -1932,7 +1932,7 @@ Doc page with :doc:`WARNING messages ` 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 ` *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* -See the read_data command for info on using the "extra/bond/per/atom" -keyword to allow for additional bonds to be formed +*New bond exceeded bonds per atom in create\_bonds* + See the read_data command for info on using the "extra/bond/per/atom" + 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" From 29ee7191295bb8c324a2dfbc3a3ee03dd3b77a35 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 21:20:07 +0200 Subject: [PATCH 7/8] Formatting typo --- doc/src/Errors_warnings.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index d244818cc9..945c5b8cf7 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -233,7 +233,7 @@ Doc page with :doc:`ERROR 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. From 9ab921261211bcc5c3d17c2925e00fface1cce71 Mon Sep 17 00:00:00 2001 From: Germain Clavier Date: Wed, 14 Aug 2024 21:57:56 +0200 Subject: [PATCH 8/8] Changed docstring of lammps_create_atoms to avoid weird formatting in Manual.pdf --- src/library.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/library.cpp b/src/library.cpp index 9f77dad1c2..2ef65f430a 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -5450,7 +5450,7 @@ 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 *