Merge pull request #1868 from akohlmey/next_patch_version

Step version strings for next patch release

.gitignore

@@ -26,6 +26,7 @@ vgcore.*
 .vagrant
 \#*#
 .#*
+.vscode
 
 .DS_Store
 .DS_Store?

cmake/CMakeLists.txt

@@ -739,7 +739,7 @@ if(PKG_KSPACE)
   else()
     message(STATUS "Using double precision FFTs")
   endif()
-  if(FFT_FFTW_THREADS)
+  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
     message(STATUS "Using threaded FFTs")
   else()
     message(STATUS "Using non-threaded FFTs")

cmake/Modules/Packages/KSPACE.cmake

@@ -22,7 +22,7 @@ if(PKG_KSPACE)
     include_directories(${${FFTW}_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
     if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
-      option(FFT_FFTW_THREADS "Use threaded FFT library" ON)
+      option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
     else()
       option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
     endif()
@@ -38,6 +38,10 @@ if(PKG_KSPACE)
   elseif(FFT STREQUAL "MKL")
     find_package(MKL REQUIRED)
     add_definitions(-DFFT_MKL)
+    option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
+    if(FFT_MKL_THREADS)
+      add_definitions(-DFFT_MKL_THREADS)
+    endif()
     include_directories(${MKL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
   else()

doc/Makefile

@@ -3,7 +3,6 @@
 SHELL         = /bin/bash
 BUILDDIR      = ${CURDIR}
 RSTDIR        = $(BUILDDIR)/src
-TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
@@ -28,8 +27,6 @@ HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
-OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
 .PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
 
@@ -61,9 +58,9 @@ clean:
 clean-spelling:
 	rm -rf spelling
 
-rst: clean $(OBJECTS) $(ANCHORCHECK)
+rst: clean $(ANCHORCHECK)
 
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
@@ -86,7 +83,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+spelling: utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
@@ -96,7 +93,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	)
 	@echo "Spell check finished."
 
-epub: $(OBJECTS)
+epub:
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
@@ -115,7 +112,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: $(OBJECTS) $(ANCHORCHECK)
+pdf: $(ANCHORCHECK)
 	@(\
 		cd src/Developer; \
 		pdflatex developer; \
@@ -167,7 +164,7 @@ fetch:
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		rst_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
 		deactivate ;\
 	)
 
@@ -180,14 +177,6 @@ style_check :
 
 # ------------------------------------------
 
-$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
-	@(\
-		mkdir -p $(RSTDIR) ; \
-		. $(VENV)/bin/activate ;\
-		txt2rst -v $< > $@ ;\
-		deactivate ;\
-	)
-
 $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "24 January 2020" "2020-01-24"
+.TH LAMMPS "4 February 2020" "2020-02-04"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build.rst

@@ -21,8 +21,3 @@ as described on the :doc:`Install <Install>` doc page.
    Build_extras
    Build_windows
    Build_development
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_basics.rst

@@ -430,8 +430,3 @@ you want to copy files to is protected.
 There is no "install" option in the src/Makefile for LAMMPS.  If you
 wish to do this you will need to first build LAMMPS, then manually
 copy the desired LAMMPS files to the appropriate system directories.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_cmake.rst

@@ -238,8 +238,3 @@ enough version, you can download the latest version at
 `https://cmake.org/download/ <https://cmake.org/download/>`_.
 Instructions on how to install it on various platforms can be found
 `on this page <https://cmake.org/install/>`_.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_development.rst

@@ -112,9 +112,3 @@ These reports require GCOVR to be installed. The easiest way to do this to insta
 .. parsed-literal::
 
    pip install git+https://github.com/gcovr/gcovr.git
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_extras.rst

@@ -177,7 +177,7 @@ KIM package
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>`
+use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
@@ -1414,8 +1414,3 @@ the settings are not valid for your system, check if one of the other
 lib/vtk/Makefile.lammps.\* files is compatible and copy it to
 Makefile.lammps.  If none of the provided files work, you will need to
 edit the Makefile.lammps file.  See lib/vtk/README for details.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_link.rst

@@ -84,8 +84,3 @@ See the sample codes in examples/COUPLE/simple for examples of C++ and
 C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the :doc:`Howto couple <Howto_couple>` doc page.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_make.rst

@@ -87,8 +87,3 @@ settings may become outdated:
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_package.rst

@@ -258,8 +258,3 @@ sub-directories with src files.
 
 Type "make package-diff" to list all differences between pairs of
 files in both the src dir and a package dir.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_settings.rst

@@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
 | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
-| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
+| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
 | :ref:`Size of LAMMPS data types <size>`
 | :ref:`Read or write compressed files <gzip>`
 | :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
+| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
 | :ref:`Memory allocation alignment <align>`
 | :ref:`Workaround for long long integers <longlong>`
 | :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
@@ -72,7 +72,7 @@ FFT library
 ---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
-:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
@@ -106,6 +106,7 @@ to assist:
    -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
    -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
    -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
 **Makefile.machine settings**\ :
@@ -117,6 +118,7 @@ to assist:
                                  # default is KISS if not specified
    FFT_INC = -DFFT_SINGLE        # do not specify for double precision
    FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
    FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
 
 # default is FFT\_PACK\_ARRAY if not specified
@@ -129,12 +131,15 @@ to assist:
    FFT_LIB =       -lfftw3             # FFTW3 double precision
    FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
    FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
 As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
-make can find the FFT header and library files.  You must specify
-FFT\_LIB with the appropriate FFT libraries to include in the link.
+the compiler can find the FFT header and library files in its default search path.
+You must specify FFT\_LIB with the appropriate FFT libraries to include in the link.
 
 **CMake and make info**\ :
 
@@ -251,7 +256,7 @@ support 8-byte integers.  It allows for:
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
-:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+:doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Thus if you model a molecular system with
 more than 2 billion atoms, you need the "bigbig" setting.
@@ -357,7 +362,7 @@ Read or write compressed files
 
 If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
-:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 **CMake variables**\ :
 
@@ -488,8 +493,3 @@ e.g. to Python.
 .. parsed-literal::
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -104,8 +104,3 @@ Support for the Visual C++ compilers is currently not available. The
 CMake build system is capable of creating suitable a Visual Studio
 style build environment, but the LAMMPS code itself is not fully ported
 to support Visual C++. Volunteers to take on this task are welcome.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -136,4 +136,3 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`write_data <write_data>`
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
-

doc/src/Commands_bond.rst

@@ -131,7 +131,7 @@ OPT.
 Improper_style potentials
 =========================
 
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.

doc/src/Commands_category.rst

@@ -18,73 +18,73 @@ Setup simulation box:
 
 * :doc:`boundary <boundary>`,
 * :doc:`box <box>`,
-* :doc:`change\_box <change_box>`,
-* :doc:`create\_box <create_box>`,
+* :doc:`change_box <change_box>`,
+* :doc:`create_box <create_box>`,
 * :doc:`dimension <dimension>`,
 * :doc:`lattice <lattice>`,
 * :doc:`region <region>`
 
 Setup atoms:
 
-* :doc:`atom\_modify <atom_modify>`,
-* :doc:`atom\_style <atom_style>`,
+* :doc:`atom_modify <atom_modify>`,
+* :doc:`atom_style <atom_style>`,
 * :doc:`balance <balance>`,
-* :doc:`create\_atoms <create_atoms>`,
-* :doc:`create\_bonds <create_bonds>`,
-* :doc:`delete\_atoms <delete_atoms>`,
-* :doc:`delete\_bonds <delete_bonds>`,
-* :doc:`displace\_atoms <displace_atoms>`,
+* :doc:`create_atoms <create_atoms>`,
+* :doc:`create_bonds <create_bonds>`,
+* :doc:`delete_atoms <delete_atoms>`,
+* :doc:`delete_bonds <delete_bonds>`,
+* :doc:`displace_atoms <displace_atoms>`,
 * :doc:`group <group>`,
 * :doc:`mass <mass>`,
 * :doc:`molecule <molecule>`,
-* :doc:`read\_data <read_data>`,
-* :doc:`read\_dump <read_dump>`,
-* :doc:`read\_restart <read_restart>`,
+* :doc:`read_data <read_data>`,
+* :doc:`read_dump <read_dump>`,
+* :doc:`read_restart <read_restart>`,
 * :doc:`replicate <replicate>`,
 * :doc:`set <set>`,
 * :doc:`velocity <velocity>`
 
 Force fields:
 
-* :doc:`angle\_coeff <angle_coeff>`,
-* :doc:`angle\_style <angle_style>`,
-* :doc:`bond\_coeff <bond_coeff>`,
-* :doc:`bond\_style <bond_style>`,
-* :doc:`bond\_write <bond_write>`,
+* :doc:`angle_coeff <angle_coeff>`,
+* :doc:`angle_style <angle_style>`,
+* :doc:`bond_coeff <bond_coeff>`,
+* :doc:`bond_style <bond_style>`,
+* :doc:`bond_write <bond_write>`,
 * :doc:`dielectric <dielectric>`,
-* :doc:`dihedral\_coeff <dihedral_coeff>`,
-* :doc:`dihedral\_style <dihedral_style>`,
-* :doc:`improper\_coeff <improper_coeff>`,
-* :doc:`improper\_style <improper_style>`,
-* :doc:`kspace\_modify <kspace_modify>`,
-* :doc:`kspace\_style <kspace_style>`,
-* :doc:`pair\_coeff <pair_coeff>`,
-* :doc:`pair\_modify <pair_modify>`,
-* :doc:`pair\_style <pair_style>`,
-* :doc:`pair\_write <pair_write>`,
-* :doc:`special\_bonds <special_bonds>`
+* :doc:`dihedral_coeff <dihedral_coeff>`,
+* :doc:`dihedral_style <dihedral_style>`,
+* :doc:`improper_coeff <improper_coeff>`,
+* :doc:`improper_style <improper_style>`,
+* :doc:`kspace_modify <kspace_modify>`,
+* :doc:`kspace_style <kspace_style>`,
+* :doc:`pair_coeff <pair_coeff>`,
+* :doc:`pair_modify <pair_modify>`,
+* :doc:`pair_style <pair_style>`,
+* :doc:`pair_write <pair_write>`,
+* :doc:`special_bonds <special_bonds>`
 
 Settings:
 
-* :doc:`comm\_modify <comm_modify>`,
-* :doc:`comm\_style <comm_style>`,
+* :doc:`comm_modify <comm_modify>`,
+* :doc:`comm_style <comm_style>`,
 * :doc:`info <info>`,
-* :doc:`min\_modify <min_modify>`,
-* :doc:`min\_style <min_style>`,
-* :doc:`neigh\_modify <neigh_modify>`,
+* :doc:`min_modify <min_modify>`,
+* :doc:`min_style <min_style>`,
+* :doc:`neigh_modify <neigh_modify>`,
 * :doc:`neighbor <neighbor>`,
 * :doc:`partition <partition>`,
-* :doc:`reset\_timestep <reset_timestep>`,
-* :doc:`run\_style <run_style>`,
+* :doc:`reset_timestep <reset_timestep>`,
+* :doc:`run_style <run_style>`,
 * :doc:`timer <timer>`,
 * :doc:`timestep <timestep>`
 
 Operations within timestepping (fixes) and diagnostics (computes):
 
 * :doc:`compute <compute>`,
-* :doc:`compute\_modify <compute_modify>`,
+* :doc:`compute_modify <compute_modify>`,
 * :doc:`fix <fix>`,
-* :doc:`fix\_modify <fix_modify>`,
+* :doc:`fix_modify <fix_modify>`,
 * :doc:`uncompute <uncompute>`,
 * :doc:`unfix <unfix>`
 
@@ -93,22 +93,22 @@ Output:
 * :doc:`dump image <dump_image>`,
 * :doc:`dump movie <dump_image>`,
 * :doc:`dump <dump>`,
-* :doc:`dump\_modify <dump_modify>`,
+* :doc:`dump_modify <dump_modify>`,
 * :doc:`restart <restart>`,
 * :doc:`thermo <thermo>`,
-* :doc:`thermo\_modify <thermo_modify>`,
-* :doc:`thermo\_style <thermo_style>`,
+* :doc:`thermo_modify <thermo_modify>`,
+* :doc:`thermo_style <thermo_style>`,
 * :doc:`undump <undump>`,
-* :doc:`write\_coeff <write_coeff>`,
-* :doc:`write\_data <write_data>`,
-* :doc:`write\_dump <write_dump>`,
-* :doc:`write\_restart <write_restart>`
+* :doc:`write_coeff <write_coeff>`,
+* :doc:`write_data <write_data>`,
+* :doc:`write_dump <write_dump>`,
+* :doc:`write_restart <write_restart>`
 
 Actions:
 
 * :doc:`minimize <minimize>`,
 * :doc:`neb <neb>`,
-* :doc:`neb\_spin <neb_spin>`,
+* :doc:`neb_spin <neb_spin>`,
 * :doc:`prd <prd>`,
 * :doc:`rerun <rerun>`,
 * :doc:`run <run>`,

doc/src/Commands_compute.rst

@@ -163,4 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`
-

doc/src/Commands_input.rst

@@ -45,7 +45,7 @@ belong to the group.
 (3) Sometimes command B will use values that can be set by command A.
 This means command A must precede command B in the input script if it
 is to have the desired effect.  For example, the
-:doc:`read\_data <read_data>` command initializes the system by setting
+:doc:`read_data <read_data>` command initializes the system by setting
 up the simulation box and assigning atoms to processors.  If default
 values are not desired, the :doc:`processors <processors>` and
 :doc:`boundary <boundary>` commands need to be used before read\_data to

doc/src/Commands_kspace.rst

@@ -14,7 +14,7 @@
 KSpace solvers
 ==============
 
-All LAMMPS :doc:`kspace\_style <kspace_style>` solvers.  Some styles have
+All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.

doc/src/Commands_removed.rst

@@ -57,11 +57,6 @@ restart2data tool
 
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read\_restart <read_restart>` and
-:doc:`write\_data <write_data>` can be used to the same effect.  For added
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For added
 convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_structure.rst

@@ -26,23 +26,23 @@ read-in from a file.
 The relevant commands are :doc:`units <units>`,
 :doc:`dimension <dimension>`, :doc:`newton <newton>`,
 :doc:`processors <processors>`, :doc:`boundary <boundary>`,
-:doc:`atom\_style <atom_style>`, :doc:`atom\_modify <atom_modify>`.
+:doc:`atom_style <atom_style>`, :doc:`atom_modify <atom_modify>`.
 
 If force-field parameters appear in the files that will be read, these
 commands tell LAMMPS what kinds of force fields are being used:
-:doc:`pair\_style <pair_style>`, :doc:`bond\_style <bond_style>`,
-:doc:`angle\_style <angle_style>`, :doc:`dihedral\_style <dihedral_style>`,
-:doc:`improper\_style <improper_style>`.
+:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`,
+:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
+:doc:`improper_style <improper_style>`.
 
 (2) Atom definition
 
 There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the :doc:`read\_data <read_data>` or
-:doc:`read\_restart <read_restart>` commands.  These files can contain
+or restart file via the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands.  These files can contain
 molecular topology information.  Or create atoms on a lattice (with no
 molecular topology), using these commands: :doc:`lattice <lattice>`,
-:doc:`region <region>`, :doc:`create\_box <create_box>`,
-:doc:`create\_atoms <create_atoms>`.  The entire set of atoms can be
+:doc:`region <region>`, :doc:`create_box <create_box>`,
+:doc:`create_atoms <create_atoms>`.  The entire set of atoms can be
 duplicated to make a larger simulation using the
 :doc:`replicate <replicate>` command.
 
@@ -53,25 +53,25 @@ can be specified: force field coefficients, simulation parameters,
 output options, etc.
 
 Force field coefficients are set by these commands (they can also be
-set in the read-in files): :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_coeff <bond_coeff>`, :doc:`angle\_coeff <angle_coeff>`,
-:doc:`dihedral\_coeff <dihedral_coeff>`,
-:doc:`improper\_coeff <improper_coeff>`,
-:doc:`kspace\_style <kspace_style>`, :doc:`dielectric <dielectric>`,
-:doc:`special\_bonds <special_bonds>`.
+set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
+:doc:`bond_coeff <bond_coeff>`, :doc:`angle_coeff <angle_coeff>`,
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`improper_coeff <improper_coeff>`,
+:doc:`kspace_style <kspace_style>`, :doc:`dielectric <dielectric>`,
+:doc:`special_bonds <special_bonds>`.
 
 Various simulation parameters are set by these commands:
-:doc:`neighbor <neighbor>`, :doc:`neigh\_modify <neigh_modify>`,
+:doc:`neighbor <neighbor>`, :doc:`neigh_modify <neigh_modify>`,
 :doc:`group <group>`, :doc:`timestep <timestep>`,
-:doc:`reset\_timestep <reset_timestep>`, :doc:`run\_style <run_style>`,
-:doc:`min\_style <min_style>`, :doc:`min\_modify <min_modify>`.
+:doc:`reset_timestep <reset_timestep>`, :doc:`run_style <run_style>`,
+:doc:`min_style <min_style>`, :doc:`min_modify <min_modify>`.
 
 Fixes impose a variety of boundary conditions, time integration, and
 diagnostic options.  The :doc:`fix <fix>` command comes in many flavors.
 
 Various computations can be specified for execution during a
 simulation using the :doc:`compute <compute>`,
-:doc:`compute\_modify <compute_modify>`, and :doc:`variable <variable>`
+:doc:`compute_modify <compute_modify>`, and :doc:`variable <variable>`
 commands.
 
 Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,

doc/src/Eqs/angle_class2_p6.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

doc/src/Eqs/box.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-a &=& {\rm lx} \\
-b^2 &=&  {\rm ly}^2 +  {\rm xy}^2 \\
-c^2 &=&  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
-\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
-\cos{\beta} &=& \frac{\rm xz}{c} \\
-\cos{\gamma} &=& \frac{\rm xy}{b} \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/box_inverse.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-{\rm lx} &=& a \\
-{\rm xy} &=& b \cos{\gamma}  \\
-{\rm xz} &=& c \cos{\beta}\\
-{\rm ly}^2 &=&   b^2 - {\rm xy}^2 \\
-{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
-{\rm lz}^2 &=&  c^2 - {\rm xz}^2 - {\rm yz}^2 \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/dihedral_charmm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = K [ 1 + \cos (n \phi - d) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_class2.tex

@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
-  E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
-  E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
-  E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
-  & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
-  E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
-  & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
-  E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
-  E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/dihedral_cosine_shift_exp.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min} 
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_fourier.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{i=1,m} K_i  [ 1.0 + \cos ( n_i \phi - d_i ) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [ 1 + d  \cos (n \phi) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_helix.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + 
-      C [1 + \cos(\theta + \frac{\pi}{4})]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_multi_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{n=1,5} A_n  \cos^{n-1}(\phi)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_nharmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{n=1,n} A_n  \cos^{n-1}(\phi)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_opls.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] +
-      \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_quadratic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\phi - \phi_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/dihedral_spherical.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\pagestyle{empty}
-\begin{eqnarray*}
-E(\phi,\theta_1,\theta_2) & = &\sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2)\\
-\Phi_{i}(\phi)        & = &  u_i - \mathrm{cos}((\phi   - a_i)K_i) \\
-\Theta_{1i}(\theta_1) & = &  v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
-\Theta_{2i}(\theta_2) & = &  w_i - \mathrm{cos}((\theta_2-c_i)M_i)
-\end{eqnarray*}
-
-% Check using: http://quicklatex.com/  (24pt font)
-\pagestyle{empty}
-\end{document}
-

doc/src/Eqs/dihedral_table_cut.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-        f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
-        f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
-\end{eqnarray*}
-
-\end{document}
-

doc/src/Eqs/improper_class2.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_i + E_{aa} \\
-  E_i & = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\
-  E_{aa} & = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\
-  & & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\
-  & & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/improper_cossq.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)}
-$$
-
-\end{document}

doc/src/Eqs/improper_cvff.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K [1 + d  \cos (n \phi) ] 
-$$
-
-\end{document}

doc/src/Eqs/improper_dist-1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K_2 d^2 + K_4 d^4
-$$
-
-\end{document}

doc/src/Eqs/improper_distharm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (d - d_0)^2
-$$
-
-\end{document}

doc/src/Eqs/improper_fourier.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K [C_0 + C_1 \cos ( \omega) + C_2 \cos( 2 \omega) ] 
-$$
-
-\end{document}

doc/src/Eqs/improper_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\chi - \chi_0)^2
-$$
-
-\end{document}

doc/src/Eqs/improper_inversion_harmonic.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E = K \left(\theta - \theta_0\right)^2
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

doc/src/Eqs/improper_ring.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-   E & = &\frac{1}{6} K \left(\Delta_{ijl} + \Delta_{ijk} + \Delta_{kjl} \right)^6 \\
-   \Delta_{ijl} & = & \cos{\theta_{ijl} - \cos{\theta_0}} \\
-   \Delta_{ijk} & = & \cos{\theta_{ijk} - \cos{\theta_0}} \\
-   \Delta_{kjl} & = & \cos{\theta_{kjl} - \cos{\theta_0}}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/improper_sqdistharm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (d^2 - d_0^2)^2
-$$
-
-\end{document}

doc/src/Eqs/improper_umbrella.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E=\frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o
-$$
-
-$$
-E=K\left( 1-cos\omega\right)  \qquad \omega_0 = 0^o
-$$
-
-\end{document}

doc/src/Eqs/min_energy.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E(r_1,r_2, \ldots ,r_N) & = & \sum_{i,j} E_{\it pair}(r_i,r_j) + 
-                              \sum_{ij} E_{\it bond}(r_i,r_j) +
-                              \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\
-                           && \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) +
-                              \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) +
-                              \sum_i E_{\it fix}(r_i) 
-\end{eqnarray*}
-
-\end{document}
-

doc/src/Eqs/min_spin_damping.tex

@@ -1,13 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/min_spin_timestep.tex

@@ -1,14 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    {\Delta t}_{\rm max} = \frac{2\pi}{\kappa
-    \left|\vec{\omega}_{\rm max} \right|} 
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/neb_spin_angle.tex

@@ -1,15 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \omega_i^{\nu} = 
-    (\nu - 1) \Delta \omega_i
-    {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
-  , \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/neb_spin_k.tex

@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \vec{k}_i =  
-    \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I 
-    \times \vec{m}_i^F\right|} 
-    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
-  , \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/neb_spin_rodrigues_formula.tex

@@ -1,16 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    \vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
-    + (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
-    + (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
-    \vec{m}_i^{I})
-  , \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/norm_inf.tex

@@ -1,15 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    || \vec{F} ||_{inf} 
-    = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, 
-    |F_N^1|, |F_N^2|, |F_N^3|\right)
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/norm_max.tex

@@ -1,15 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    % \left| \left| \vec{F} \right| \right|_2 
-    || \vec{F} ||_{max} 
-    = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/norm_two.tex

@@ -1,15 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath, amssymb, graphics, setspace}
-
-\begin{document}
-\begin{varwidth}{50in}
-  \begin{equation}
-    % \left| \left| \vec{F} \right| \right|_2 
-    || \vec{F} ||_{2} 
-    = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N}
-    \nonumber
-  \end{equation}
-\end{varwidth}
-\end{document}

doc/src/Eqs/rotate.tex

@@ -1,26 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-\mathbf{x}
- &=& 
-\begin{pmatrix}
-\mathbf{a}  &
-\mathbf{b}  &
-\mathbf{c} 
-\end{pmatrix}
-\cdot 
- \frac{1}{V}
- \begin{pmatrix}
-\mathbf{B \times C}  \\
-\mathbf{C \times A}  \\
-\mathbf{A \times B} 
-\end{pmatrix}
-\cdot 
-\mathbf{X}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/transform.tex

@@ -1,27 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-\begin{pmatrix}
-\mathbf{a}  &
-\mathbf{b}  &
-\mathbf{c} 
-\end{pmatrix}
-& = &
-\begin{pmatrix}
-a_x & b_x & c_x \\
-0 & b_y & c_y \\
-0 & 0 & c_z \\
-\end{pmatrix} \\
-a_x &=& A \\
-b_x &=& \mathbf{B} \cdot \mathbf{\hat{A}} \quad = \quad B \cos{\gamma} \\
-b_y &=& |\mathbf{\hat{A}} \times \mathbf{B}| \quad = \quad B \sin{\gamma} \quad =  \quad  \sqrt{B^2 - {b_x}^2} \\
-c_x &=& \mathbf{C} \cdot \mathbf{\hat{A}} \quad = \quad C \cos{\beta} \\
-c_y &=& \mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})} \times \mathbf{\hat{A}} \quad = \quad \frac{\mathbf{B} \cdot \mathbf{C} - b_x c_x}{b_y} \\
-c_z &=& |\mathbf{C} \cdot \widehat{(\mathbf{A} \times \mathbf{B})}|\quad = \quad \sqrt{C^2 - {c_x}^2 - {c_y}^2} \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Errors.rst

@@ -15,8 +15,3 @@ additional details for many of them.
    Errors_bugs
    Errors_messages
    Errors_warnings
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Errors_bugs.rst

@@ -1,32 +1,45 @@
 Reporting bugs
 ==============
 
-If you are confident that you have found a bug in LAMMPS, follow these
-steps.
+If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below:
 
-Check the `New features and bug fixes <http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site <lws_>`_ to see if the bug has already been reported or fixed or the
-`Unfixed bug <http://lammps.sandia.gov/unbug.html>`_ to see if a fix is
-pending.
+ * Check the `New features and bug fixes
+   <http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
+   <lws_>`_ to see if the bug has already been addressed in a patch.
+ * Check that your issue can be reproduced with the latest development
+   version of LAMMPS.
+ * Check the manual carefully to verify that the unexpected behavior you
+   are observing is indeed in conflict with the documentation
+ * Check the `GitHub Issue page <gip_>`_
+   if your issue has already been reported and if it is still open.
+ * Check the `GitHub Pull Requests page <https://github.com/lammps/pulls>`_
+   if there is already a fix for your bug pending.
+ * Check the `mailing list archives <http://lammps.sandia.gov/mail.html>`_
+   to see if the issue has been discussed before.
 
-Check the `mailing list <http://lammps.sandia.gov/mail.html>`_ to see if
-it has been discussed before.
+If none of these steps yields any useful information, please file
+a new bug report on the `GitHub Issue page <gip_>`_\ .
+The website will offer you to select a suitable template with explanations
+and then you should replace those explanations with the information
+that you can provide to reproduce your issue.
 
-If not, send an email to the mailing list describing the problem with
-any ideas you have as to what is causing it or where in the code the
-problem might be.  The developers will ask for more info if needed,
-such as an input script or data files.
-
-The most useful thing you can do to help us fix the bug is to isolate
-the problem.  Run it on the smallest number of atoms and fewest number
-of processors and with the simplest input script that reproduces the
-bug and try to identify what command or combination of commands is
-causing the problem.
-
-.. note::
-
-   this page needs to have GitHub issues info added
+The most useful thing you can do to help us verify and fix a bug is to
+isolate the problem.  Run it on the smallest number of atoms and fewest
+number of processors with the simplest input script that reproduces the
+bug.  Try to identify what command or combination of commands is
+causing the problem and upload the complete input deck as a tar or zip
+archive.  Please avoid using binary restart files unless the issue requires
+it.  In the latter case you should also include an input deck to quickly
+generate this restart from a data file or a simple additional input.
 
+You may also send an email to the LAMMPS mailing list at
+"lammps-users at lists.sourceforge.net" describing the problem with the
+same kind of information.  The mailing list can provide a faster response,
+especially if the bug reported is actually expected behavior.  But because
+of the high volume of the mailing list, it can happen that your e-mail
+is overlooked and then forgotten.  Issues on GitHub have to be explicitly
+closed, so that will *guarantee* that at least one LAMMPS developer will
+have looked at it.
 
 .. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html
+.. _gip: https://github.com/lammps/issues

doc/src/Errors_common.rst

@@ -18,7 +18,7 @@ the two simulations will rapidly diverge.  See the discussion of the
 *loop* option in the :doc:`velocity <velocity>` command for details and
 options that avoid this issue.
 
-Similarly, the :doc:`create\_atoms <create_atoms>` command generates a
+Similarly, the :doc:`create_atoms <create_atoms>` command generates a
 lattice of atoms.  For the same physical system, the ordering and
 numbering of atoms by atom ID may be different depending on the number
 of processors.
@@ -121,8 +121,3 @@ implementations handle buffering of messages.  If the code hangs
 without an error message, it may be that you need to specify an MPI
 setting or two (usually via an environment variable) to enable
 buffering or boost the sizes of messages that can be buffered.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html