From 6b275e283c12d7b69b1cd9622c0cc84f1767e9e8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 13 May 2021 17:14:35 -0400 Subject: [PATCH 1/6] step version number for the next patch release --- doc/lammps.1 | 2 +- src/version.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/lammps.1 b/doc/lammps.1 index c10950643d..11438ac5c3 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,4 +1,4 @@ -.TH LAMMPS "8 April 2021" "2021-04-08" +.TH LAMMPS "14 May 2021" "2021-05-14" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. diff --git a/src/version.h b/src/version.h index d7839fcbfe..39344fdf55 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "8 Apr 2021" +#define LAMMPS_VERSION "14 May 2021" From c311574fe64ea3123ff0082a7b9a149f34a5b69f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 May 2021 23:50:38 -0400 Subject: [PATCH 2/6] add missing fix entry --- doc/src/fix.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 41c9732c62..d54594d5af 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -244,6 +244,7 @@ accelerated styles exist. * :doc:`lb/viscous ` - * :doc:`lineforce ` - constrain atoms to move in a line * :doc:`manifoldforce ` - restrain atoms to a manifold during minimization +* :doc:`mdi/engine ` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI) * :doc:`meso/move ` - move mesoscopic SPH/SDPD particles in a prescribed fashion * :doc:`momentum ` - zero the linear and/or angular momentum of a group of atoms * :doc:`momentum/chunk ` - zero the linear and/or angular momentum of a chunk of atoms From 9f4cca4981358b8ac21afff4dec0d3d0eefac46f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 May 2021 23:50:51 -0400 Subject: [PATCH 3/6] correct index entries --- doc/src/fix_mdi_engine.rst | 2 +- doc/src/mdi_engine.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_mdi_engine.rst b/doc/src/fix_mdi_engine.rst index a2f25780f5..76506f3e19 100644 --- a/doc/src/fix_mdi_engine.rst +++ b/doc/src/fix_mdi_engine.rst @@ -1,4 +1,4 @@ -.. index:: fix move +.. index:: fix mdi/engine fix mdi/engine command ====================== diff --git a/doc/src/mdi_engine.rst b/doc/src/mdi_engine.rst index 927a518f4e..b39999606d 100644 --- a/doc/src/mdi_engine.rst +++ b/doc/src/mdi_engine.rst @@ -1,4 +1,4 @@ -.. index:: mdi_engine +.. index:: mdi/engine mdi_engine command ================== From 59cc481108894df5a2f3e144847ed172d6ba2c63 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 May 2021 23:51:33 -0400 Subject: [PATCH 4/6] change config entry for post 3.5 sphinx versions and enable permalinks --- doc/utils/sphinx-config/conf.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index 17cb3c2395..baf472b9f9 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -241,7 +241,7 @@ html_show_sourcelink = False # Output file base name for HTML help builder. htmlhelp_basename = 'LAMMPSdoc' -html_add_permalinks = '' +html_permalinks = True if 'epub' in sys.argv: html_math_renderer = 'imgmath' From 492d82904f36ba4b767aaf3301e0ddbc88282d23 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 14 May 2021 23:51:43 -0400 Subject: [PATCH 5/6] add false positives --- doc/utils/sphinx-config/false_positives.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 7bbafaeafb..6133729b8a 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2850,6 +2850,8 @@ Runge runtime Rutuparna rx +rxnave +rxnsum ry rz Ryckaert From 7d40eb3cac62a047012a40a597eb914fce8afe5c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 15 May 2021 00:26:19 -0400 Subject: [PATCH 6/6] fix issue with commands docs not being kept separate from programmer guide --- doc/src/Manual.rst | 13 +++++++++---- doc/utils/sphinx-config/_static/css/lammps.css | 4 ++++ 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 9198f545bc..4c7e5fa8f5 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -89,10 +89,15 @@ Programmer Guide Modify Developer +***************** +Command Reference +***************** + +.. _command_reference: .. toctree:: - :caption: Index - :name: index - :hidden: + :name: reference + :maxdepth: 1 + :caption: Command Reference commands_list fixes @@ -118,7 +123,7 @@ Indices and tables .. admonition:: Web Browser Compatibility The HTML version of the manual makes use of advanced features present - int "modern" web browsers. This can lead to incompatibilities with older + in "modern" web browsers. This can lead to incompatibilities with older web browsers (released more than 4 years ago) and specific vendor browsers (e.g. Internet Explorer on Windows; Microsoft Edge works well though) where parts of the pages are not rendered as expected (e.g. the layout is diff --git a/doc/utils/sphinx-config/_static/css/lammps.css b/doc/utils/sphinx-config/_static/css/lammps.css index b69405365a..900054eeeb 100644 --- a/doc/utils/sphinx-config/_static/css/lammps.css +++ b/doc/utils/sphinx-config/_static/css/lammps.css @@ -35,6 +35,10 @@ hr { display: none; } +#command-reference.section h2 { + display: none; +} + .ui.tabular.menu .item { padding-right: 1em; padding-left: 1em;