Merge pull request #1777 from akohlmey/next_patch_release

Step version strings for next patch release

cmake/Modules/Documentation.cmake

@@ -9,9 +9,7 @@ if(BUILD_DOC)
 
   set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
-  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
-  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
   add_custom_command(
     OUTPUT docenv
@@ -28,25 +26,10 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
   )
 
-  set(RST_FILES "")
-  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
-  file(MAKE_DIRECTORY ${RST_DIR})
-  foreach(TXT_FILE ${DOC_SOURCES})
-    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
-    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
-    list(APPEND RST_FILES ${RST_FILE})
-    add_custom_command(
-      OUTPUT ${RST_FILE}
-      DEPENDS requirements.txt docenv ${TXT_FILE}
-      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
-    )
-  endforeach()
-
   add_custom_command(
     OUTPUT html
-    DEPENDS ${RST_FILES}
-    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
+    DEPENDS ${DOC_SOURCES} docenv requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
   )
 
   add_custom_target(

doc/.gitignore

@@ -6,3 +6,5 @@
 /LAMMPS.mobi
 /Manual.pdf
 /Developer.pdf
+/doctrees
+/docenv

doc/Makefile

@@ -1,12 +1,12 @@
 # Makefile for LAMMPS documentation
 
 SHELL         = /bin/bash
-SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
-BUILDDIR      = /tmp/lammps-docs-$(SHA1)
-RSTDIR        = $(BUILDDIR)/rst
+BUILDDIR      = ${CURDIR}
+RSTDIR        = $(BUILDDIR)/src
+TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
+ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
 PYTHON        = $(shell which python3)
 VIRTUALENV     = virtualenv
@@ -28,10 +28,10 @@ HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
-OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
+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 html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
 
 # ------------------------------------------
 
@@ -39,37 +39,36 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
 	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
 	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
-	@echo "  txt2html   build txt2html tool"
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees
 
 clean:
-	rm -rf $(RSTDIR) html old epub latex
+	rm -rf html epub latex
 	rm -rf spelling
 
 clean-spelling:
 	rm -rf spelling
 
+rst: clean $(OBJECTS) $(ANCHORCHECK)
+
 html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
-		doc_anchor_check src/*.txt ;\
-		env LC_ALL=C grep -n '[^ -~]' src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -89,8 +88,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
-		cp -r src/* $(RSTDIR)/ ;\
-        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
 		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		deactivate ;\
 	)
@@ -103,7 +101,6 @@ epub: $(OBJECTS)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
@@ -126,10 +123,9 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 	)
 	@(\
                 . $(VENV)/bin/activate ;\
-                cp -r src/* $(RSTDIR)/ ;\
                 sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
                 echo "############################################" ;\
-                doc_anchor_check src/*.txt ;\
+                rst_anchor_check src/*.rst ;\
                 echo "############################################" ;\
                 deactivate ;\
 	)
@@ -155,27 +151,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 	@rm -rf latex/USER/*/*.[sg]*
 	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
-old: utils/txt2html/txt2html.exe
-	@rm -rf old
-	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
-	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
-	  mv *.html ../old; \
-	  cp Eqs/*.jpg ../old/Eqs; \
-	  cp JPG/* ../old/JPG; \
-	  cp PDF/* ../old/PDF;
-	@(      set -e;\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../old/Developer.pdf; \
-		cd ../../old; \
-	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s ../src/lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		htmldoc --batch ../src/lammps.book;          \
-	)
-
-
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
 	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@@ -184,21 +159,16 @@ fetch:
 	@tar xzf lammps-doc.tar.gz
 	@rm -f lammps-doc.tar.gz
 
-txt2html: utils/txt2html/txt2html.exe
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.txt ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
-	g++ -O -Wall -o $@ $<
-
-$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
+$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
 	@(\
 		mkdir -p $(RSTDIR) ; \
 		. $(VENV)/bin/activate ;\

doc/README

@@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
-tools           tools and settings for building the documentation
+utils           utilities and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
 LAMMPS.epub     Manual in ePUB format
@@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
 code will not, unless you update your local repository).
 
 (b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
-HTML files already exist.  This requires various tools including
-Sphinx, which the build process will attempt to download and install
-on your system, if not already available.  See more details below.
-
-(c) You can genererate an older, simpler, less-fancy style of HTML
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
+html" or by "make pdf", respectively.  This requires various tools
+including the Python documentation processing tool Sphinx, which the
+build process will attempt to download and install on your system into
+a python virtual environment, if not already available.  The PDF file
+will require a working LaTeX installation with several add-on packages
+in addition to the Python/Sphinx setup.  See more details below.
 
 ----------------
 
@@ -46,11 +41,10 @@ Options:
 
 make html         # generate HTML in html dir using Sphinx
 make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
+                  #   in this dir via Sphinx and PDFLaTeX
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
-
+Same as for HTML plus a compatible LaTeX installation with
+support for PDFLaTeX. Also the following LaTeX packages need
+to be installed (e.g. from texlive):
+- amsmath
+- babel
+- cmap
+- fncychap
+- geometry
+- hyperref
+- hypcap
+- times
 ----------------
 
 Installing prerequisites for epub build
@@ -103,7 +106,11 @@ Installing prerequisites for epub build
 ## ePUB
 
 Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
+files as the HTML tree. The ePUB format conversion currently
+does not support processing mathematical expressions via MathJAX,
+so there will be limitations on some pages. For the time being
+until this is resolved, building and using the PDF format file
+is recommended instead.
 
 For converting the generated ePUB file to a mobi format file
 (for e-book readers like Kindle, that cannot read ePUB), you

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "30 October 2019" "2019-10-30"
+.TH LAMMPS "20 November 2019" "2019-11-20"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/.gitignore

@@ -0,0 +1,2 @@
+Eqs
+JPG

doc/src/Build.rst

@@ -0,0 +1,28 @@
+Build LAMMPS
+************
+
+LAMMPS can be built as an executable or library from source code via
+either traditional makefiles (which may require manual editing)
+for use with GNU make or gmake, or a build environment generated by CMake
+(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
+alternative you can download a package with pre-built executables
+as described on the :doc:`Install <Install>` doc page.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+   Build_development
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Build_basics.rst

@@ -0,0 +1,437 @@
+Basic build options
+===================
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+* :ref:`Serial vs parallel build <serial>`
+* :ref:`Choice of compiler and compile/link options <compile>`
+* :ref:`Build LAMMPS as an executable or a library <exe>`
+* :ref:`Build the LAMMPS documentation <doc>`
+* :ref:`Install LAMMPS after a build <install>`
+
+
+----------
+
+
+.. _serial:
+
+Serial vs parallel build
+-------------------------------------
+
+LAMMPS can be built to run in parallel using the ubiquitous `MPI (message-passing interface) <https://en.wikipedia.org/wiki/Message_Passing_Interface>`_
+library.  Or it can built to run on a single processor (serial)
+without MPI.  It can also be built with support for OpenMP threading
+(see more discussion below).
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+   -D BUILD_OMP=value        # yes or no (default)
+   -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value
+
+The executable created by CMake (after running make) is lmp\_name.  If
+the LAMMPS\_MACHINE variable is not specified, the executable is just
+lmp.  Using BUILD\_MPI=no will produce a serial executable.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+   make serial             # serial build, produces lmp_serial using Makefile/serial
+   make mybox          # uses Makefile.mybox to produce lmp_mybox
+
+Serial build (see src/MAKE/Makefile.serial):
+
+
+.. parsed-literal::
+
+   MPI_INC =       -I../STUBS
+   MPI_PATH =      -L../STUBS
+   MPI_LIB =       -lmpi_stubs
+
+For a parallel build, if MPI is installed on your system in the usual
+place (e.g. under /usr/local), you do not need to specify the 3
+variables MPI\_INC, MPI\_PATH, MPI\_LIB.  The MPI wrapper on the compiler
+(e.g. mpicxx, mpiCC) knows where to find the needed include and
+library files.  Failing this, these 3 variables can be used to specify
+where the mpi.h file (MPI\_INC), and the MPI library files (MPI\_PATH)
+are found, and the name of the library files (MPI\_LIB).
+
+For a serial build, you need to specify the 3 variables, as shown
+above.
+
+For a serial LAMMPS build, use the dummy MPI library provided in
+src/STUBS.  You also need to build the STUBS library for your platform
+before making LAMMPS itself.  A "make serial" build does this for.
+Otherwise, type "make mpi-stubs" from the src directory, or "make"
+from the src/STUBS dir.  If the build fails, you will need to edit the
+STUBS/Makefile for your platform.
+
+The file STUBS/mpi.c provides a CPU timer function called MPI\_Wtime()
+that calls gettimeofday() .  If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+
+**CMake and make info**\ :
+
+If you are installing MPI yourself, we recommend MPICH2 from Argonne
+National Laboratory or OpenMPI.  MPICH can be downloaded from the
+`Argonne MPI site <http://www.mcs.anl.gov/research/projects/mpich2/>`_.
+OpenMPI can be downloaded from the `OpenMPI site <http://www.open-mpi.org>`_.  Other MPI packages should also work.
+If you are running on a large parallel machine, your system admins or
+the vendor should have already installed a version of MPI, which is
+likely to be faster than a self-installed MPICH or OpenMPI, so find
+out how to build and link with it.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by
+the USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
+details. The USER-INTEL package also provides OpenMP support (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with the Intel compilers on top of that. Also, the KOKKOS package can
+be compiled for using OpenMP threading.
+
+However, there are a few commands in LAMMPS that have native OpenMP
+support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+USER-DPD packages.  In addition some packages support OpenMP threading
+indirectly through the libraries they interface to: e.g. LATTE and
+USER-COLVARS.  See the :doc:`Packages details <Packages_details>` doc
+page for more info on these packages and the doc pages for their
+respective commands for OpenMP threading info.
+
+For CMake, if you use BUILD\_OMP=yes, you can use these packages and
+turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the OMP\_NUM\_THREADS environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the CCFLAGS and LINKFLAGS
+variables in Makefile.machine need to include the compiler flag that
+enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
+compilers it is -qopenmp.  If you are using a different compiler,
+please refer to its documentation.
+
+.. _default-none-issues:
+
+**OpenMP Compiler compatibility info**\ : 
+
+Some compilers do not fully support the 'default(none)' directive
+and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
+semantics, which are incompatible with the OpenMP 3.1 directives used
+in LAMMPS (for maximal compatibility with compiler versions in use).
+In those case, all 'default(none)' directives (which aid in detecting
+incorrect and unwanted sharing) can be replaced with 'default(shared)'
+while dropping all 'shared()' directives. The script
+'src/USER-OMP/hack\_openmp\_for\_pgi\_gcc9.sh' can be used to automate
+this conversion.
+
+
+----------
+
+
+.. _compile:
+
+Choice of compiler and compile/link options
+---------------------------------------------------------
+
+The choice of compiler and compiler flags can be important for
+performance.  Vendor compilers can produce faster code than
+open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
+trying the `Intel C++ compiler <intel_>`_.
+
+.. _intel: https://software.intel.com/en-us/intel-compilers
+
+
+
+On parallel clusters or supercomputers which use "modules" for their
+compile/link environments, you can often access different compilers by
+simply loading the appropriate module before building LAMMPS.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+   -D CMAKE_C_COMPILER=name              # name of C compiler
+   -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
+
+   -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+   -D CMAKE_C_FLAGS=string               # flags to use with C compiler
+   -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any :doc:`accelerator packages <Speed_packages>` you have included in the build.
+
+You can tell CMake to look for a specific compiler with these variable
+settings.  Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags.  You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
+
+
+.. parsed-literal::
+
+   Building with GNU Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+   Building with Intel Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+   Building with LLVM/Clang Compilers:
+   cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+
+.. note::
+
+   When the cmake command completes, it prints info to the screen
+   as to which compilers it is using, and what flags will be used in the
+   compilation.  Note that if the top-level compiler is mpicxx, it is
+   simply a wrapper on a real compiler.  The underlying compiler info is
+   what will be listed in the CMake output.  You should check to insure
+   you are using the compiler and optimization flags are the ones you
+   want.
+
+**Makefile.machine settings**\ :
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+
+.. parsed-literal::
+
+   CC =            mpicxx
+   CCFLAGS =       -g -O3
+   LINK =          mpicxx
+   LINKFLAGS =     -g -O
+
+Serial build (see src/MAKE/Makefile.serial):
+
+
+.. parsed-literal::
+
+   CC =            g++
+   CCFLAGS =       -g -O3
+   LINK =          g++
+   LINKFLAGS =     -g -O
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  You should always use mpicxx or mpiCC for
+a parallel build, since these compiler wrappers will include
+a variety of settings appropriate for your MPI installation.
+
+.. note::
+
+   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>` included, they have specific
+   optimization flags that are either required or recommended for optimal
+   performance.  You need to include these in the CCFLAGS and LINKFLAGS
+   settings above.  For details, see the individual package doc pages
+   listed on the :doc:`Speed packages <Speed_packages>` doc page.  Or
+   examine these files in the src/MAKE/OPTIONS directory.  They
+   correspond to each of the 5 accelerator packages and their hardware
+   variants:
+
+
+.. parsed-literal::
+
+   Makefile.opt                   # OPT package
+   Makefile.omp                   # USER-OMP package
+   Makefile.intel_cpu             # USER-INTEL package for CPUs
+   Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+   Makefile.gpu                   # GPU package
+   Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+   Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+   Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP)
+
+
+----------
+
+
+.. _exe:
+
+Build LAMMPS as an executable or a library
+----------------------------------------------------
+
+LAMMPS can be built as either an executable or as a static or shared
+library.  The LAMMPS library can be called from another application or
+a scripting language.  See the :doc:`Howto couple <Howto_couple>` doc
+page for more info on coupling LAMMPS to other codes.  See the
+:doc:`Python <Python_head>` doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_EXE=value           # yes (default) or no
+   -D BUILD_LIB=value           # yes or no (default)
+   -D BUILD_SHARED_LIBS=value   # yes or no (default)
+   -D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                                # no default value
+
+Setting BUILD\_EXE=no will not produce an executable.  Setting
+BUILD\_LIB=yes will produce a static library named liblammps.a.
+Setting both BUILD\_LIB=yes and BUILD\_SHARED\_LIBS=yes will produce a
+shared library named liblammps.so. If LAMMPS\_LIB\_SUFFIX is set the generated
+libraries will be named liblammps\_name.a or liblammps\_name.so instead.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make machine               # build LAMMPS executable lmp_machine
+   make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+   make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so
+
+The two library builds also create generic soft links, named
+liblammps.a and liblammps.so, which point to the liblammps\_machine
+files.
+
+**CMake and make info**\ :
+
+Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries.  This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+the lib/packages directory, since they are always built as shared
+libraries using the -fPIC switch.  However, if a library like MPI or
+FFTW does not exist as a shared library, the shared library build will
+generate an error.  This means you will need to install a shared
+library version of the auxiliary library.  The build instructions for
+the library should tell you how to do this.
+
+As an example, here is how to build and install the `MPICH library <mpich_>`_, a popular open-source version of MPI, distributed by
+Argonne National Lab, as a shared library in the default
+/usr/local/lib location:
+
+.. _mpich: http://www-unix.mcs.anl.gov/mpi
+
+
+
+
+.. parsed-literal::
+
+   ./configure --enable-shared
+   make
+   make install
+
+You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib.  The end result
+should be the file /usr/local/lib/libmpich.so.
+
+
+----------
+
+
+.. _doc:
+
+Build the LAMMPS documentation
+----------------------------------------
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_DOC=value       # yes or no (default)
+
+This will create the HTML doc pages within the CMake build directory.
+The reason to do this is if you want to "install" LAMMPS on a system
+after the CMake build via "make install", and include the doc pages in
+the install.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/doc
+   make html       # html doc pages
+   make pdf        # single Manual.pdf file
+
+This will create a lammps/doc/html dir with the HTML doc pages so that
+you can browse them locally on your system.  Type "make" from the
+lammps/doc dir to see other options.
+
+.. note::
+
+   You can also download a tarball of the documentation for the
+   current LAMMPS version (HTML and PDF files), from the website
+   `download page <http://lammps.sandia.gov/download.html>`_.
+
+
+----------
+
+
+.. _tools:
+
+Build LAMMPS tools
+------------------------------
+
+Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
+using CMake or Make.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D BUILD_TOOLS=value       # yes or no (default)
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/tools
+   make all              # build all binaries of tools
+   make binary2txt       # build only binary2txt tool
+   make chain            # build only chain tool
+   make micelle2d        # build only micelle2d tool
+   make thermo_extract   # build only thermo_extract tool
+
+
+----------
+
+
+.. _install:
+
+Install LAMMPS after a build
+------------------------------------------
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user privileges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
+   make                        # perform make after CMake command
+   make install                # perform the installation into prefix
+
+**Traditional make**\ :
+
+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

@@ -0,0 +1,245 @@
+Build LAMMPS with CMake
+=======================
+
+This page is a short summary of how to use CMake to build LAMMPS.
+Details on CMake variables that enable specific LAMMPS build options
+are given on the pages linked to from the :doc:`Build <Build>` doc page.
+
+Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
+for how to use CMake to build LAMMPS.  If you are new to CMake it is a
+good place to start.
+
+
+----------
+
+
+Building LAMMPS with CMake is a two-step process.  First you use CMake
+to create a build environment in a new directory.  On Linux systems,
+this will be based on makefiles for use with make.  Then you use the
+make command to build LAMMPS, which uses the created
+Makefile(s). Example:
+
+
+.. parsed-literal::
+
+   cd lammps                        # change to the LAMMPS distribution directory
+   mkdir build; cd build            # create a new directory (folder) for build
+   cmake [options ...] ../cmake     # configuration with (command-line) cmake
+   make                             # compilation
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment.  By default
+this build environment will be created for "Unix Makefiles" on most
+platforms and particularly on Linux.  However, alternate build tools
+(e.g. Ninja) and support files for Integrated Development Environments
+(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+selected via the "-G" command line flag. For the rest of the documentation
+we will assume that the build environment is generated for makefiles
+and thus the make command will be used to compile and link LAMMPS as
+indicated above, producing (by default) an executable called "lmp" and
+a library called "liblammps.a" in the "build" folder.  When generating
+a build environment for the "Ninja" build tool, the build command would
+be "ninja" instead of "make".
+
+If your machine has multiple CPU cores (most do these days), using a
+command like "make -jN" (with N being the number of available local
+CPU cores) can be much faster.  If you plan to do development on
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
+ccache (= Compiler Cache) software may speed up repeated compilation
+even more.
+
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
+
+
+.. parsed-literal::
+
+   make install    # optional, copy LAMMPS executable & library elsewhere
+
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
+to ${HOME}/.local
+
+
+----------
+
+
+There are 3 variants of CMake: a command-line version (cmake), a text mode
+UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
+any of them interchangeably to configure and create the LAMMPS build
+environment.  On Linux all the versions produce a Makefile as their
+output.  See more details on each below.
+
+You can specify a variety of options with any of the 3 versions, which
+affect how the build is performed and what is included in the LAMMPS
+executable.  Links to pages explaining all the options are listed on
+the :doc:`Build <Build>` doc page.
+
+You must perform the CMake build system generation and compilation in
+a new directory you create.  It can be anywhere on your local machine.
+In these Build pages we assume that you are building in a directory
+called "lammps/build".  You can perform separate builds independently
+with different options, so long as you perform each of them in a
+separate directory you create.  All the auxiliary files created by one
+build process (executable, object files, log files, etc) are stored in
+this directory or sub-directories within it that CMake creates.
+
+.. note::
+
+   To perform a CMake build, no packages can be installed or a
+   build been previously attempted in the LAMMPS src directory by using
+   "make" commands to :doc:`perform a conventional LAMMPS build <Build_make>`.  CMake detects if this is the case and
+   generates an error, telling you to type "make no-all purge" in the src
+   directory to un-install all packages.  The purge removes all the \*.h
+   files auto-generated by make.
+
+You must have CMake version 2.8 or later on your system to build
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
+
+After the initial build, if you edit LAMMPS source files, or add your
+own new files to the source directory, you can just re-type make from
+your build directory and it will re-compile only the files that have
+changed.  If you want to change CMake options you can run cmake (or
+ccmake or cmake-gui) again from the same build directory and alter
+various options; see details below.  Or you can remove the entire build
+folder, recreate the directory and start over.
+
+
+----------
+
+
+**Command-line version of CMake**\ :
+
+
+.. parsed-literal::
+
+   cmake [options ...] /path/to/lammps/cmake  # build from any dir
+   cmake [options ...] ../cmake               # build from lammps/build
+
+The cmake command takes one required argument, which is the LAMMPS
+cmake directory which contains the CMakeLists.txt file.
+
+The argument can be preceeded or followed by various CMake
+command-line options.  Several useful ones are:
+
+
+.. parsed-literal::
+
+   -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
+   -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
+   -G output                     # style of output CMake generates
+   -DVARIABLE=value              # setting for a LAMMPS feature to enable
+   -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
+   -C path/to/preset/file        # load some CMake settings before configuring
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the :doc:`Build <Build>` doc page.
+All of these variable names are upper-case and their values are
+lower-case, e.g. -D LAMMPS\_SIZES=smallbig.  For boolean values, any of
+these forms can be used: yes/no, on/off, 1/0.
+
+On Unix/Linux machines, CMake generates a Makefile by default to
+perform the LAMMPS build.  Alternate forms of build info can be
+generated via the -G switch, e.g. Visual Studio on a Windows machine,
+Xcode on MacOS, or KDevelop on Linux.  Type "cmake --help" to see the
+"Generator" styles of output your system supports.
+
+.. note::
+
+   When CMake runs, it prints configuration info to the screen.
+   You should review this to verify all the features you requested were
+   enabled, including packages.  You can also see what compilers and
+   compile options will be used for the build.  Any errors in CMake
+   variable syntax will also be flagged, e.g. mis-typed variable names or
+   variable values.
+
+CMake creates a CMakeCache.txt file when it runs.  This stores all the
+settings, so that when running CMake again you can use the current
+folder '.' instead of the path to the LAMMPS cmake folder as the
+required argument to the CMake command. Either way the existing
+settings will be inherited unless the CMakeCache.txt file is removed.
+
+If you later want to change a setting you can rerun cmake in the build
+directory with different setting. Please note that some automatically
+detected variables will not change their value when you rerun cmake.
+In these cases it is usually better to first remove all the
+files/directories in the build directory, or start with a fresh build
+directory.
+
+
+----------
+
+
+**Curses version (terminal-style menu) of CMake**\ :
+
+
+.. parsed-literal::
+
+   ccmake ../cmake
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to type **c**\ , for the second you
+have to type **g**\ . You may need to type **c** multiple times, and may be
+required to edit some of the entries of CMake configuration variables
+in between.  Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
+more information.
+
+
+----------
+
+
+**GUI version of CMake**\ :
+
+
+.. parsed-literal::
+
+   cmake-gui ../cmake
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to click on the **Configure** button,
+for the second you have to click on the **Generate** button.  You may
+need to click on **Configure** multiple times, and may be required to
+edit some of the entries of CMake configuration variables in between.
+Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
+for more information.
+
+
+----------
+
+
+**Installing CMake**
+
+Check if your machine already has CMake installed:
+
+
+.. parsed-literal::
+
+   which cmake             # do you have it?
+   which cmake3            # version 3 may have this name
+   cmake --version         # what specific version you have
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+
+.. parsed-literal::
+
+   module list            # is a cmake module already loaded?
+   module avail           # is a cmake module available?
+   module load cmake3     # load cmake module with appropriate name
+
+Most Linux distributions offer pre-compiled cmake packages through
+their package management system. If you do not have CMake or a new
+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

@@ -0,0 +1,120 @@
+Development build options (CMake only)
+======================================
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+
+----------
+
+
+.. _compilation:
+
+Verify compilation flags
+------------------------------------------
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+
+.. parsed-literal::
+
+   -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+
+.. parsed-literal::
+
+   make VERBOSE=1
+
+
+----------
+
+
+.. _sanitizer:
+
+Address, Undefined Behavior, and Thread Sanitizer Support
+-------------------------------------------------------------------------
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
+code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
+language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+
+.. parsed-literal::
+
+   -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+
+
+----------
+
+
+.. _testing:
+
+Code Coverage and Testing
+---------------------------------------
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation.
+
+.. note::
+
+   this is incomplete and only represents a small subset of tests that we run
+
+
+.. parsed-literal::
+
+   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+   -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+
+.. parsed-literal::
+
+   make test
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+
+.. parsed-literal::
+
+   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+
+.. parsed-literal::
+
+   make test               # run tests first!
+   make gen_coverage_html  # generate coverage report in HTML format
+   make gen_coverage_xml   # generate coverage report in XML format
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+
+.. 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_link.rst

@@ -0,0 +1,91 @@
+Link LAMMPS as a library to another code
+========================================
+
+LAMMPS can be used as a library by another application, including
+Python scripts.  The files src/library.cpp and library.h define the
+C-style API for using LAMMPS as a library.  See the :doc:`Howto library <Howto_library>` doc page for a description of the
+interface and how to extend it for your needs.
+
+The :doc:`Build basics <Build_basics>` doc page explains how to build
+LAMMPS as either a shared or static library.  This results in one of
+these 2 files:
+
+liblammps.so      # shared library
+liblammps.a       # static library
+
+
+----------
+
+
+**Link with LAMMPS as a static library**\ :
+
+The calling application can link to LAMMPS as a static library with a
+link command like this:
+
+g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+
+The -L argument is the path to where the liblammps.a file is.  The
+-llammps argument is shorthand for the file liblammps.a.
+
+
+----------
+
+
+**Link with LAMMPS as a shared library**\ :
+
+If you wish to link to liblammps.so, the operating system finds shared
+libraries to load at run-time using the environment variable
+LD\_LIBRARY\_PATH.  To enable this you can do one of two things:
+
+(1) Copy the liblammps.so file to a location the system can find it,
+such as /usr/local/lib.  I.e. a directory already listed in your
+LD\_LIBRARY\_PATH variable.  You can type
+
+
+.. parsed-literal::
+
+   printenv LD_LIBRARY_PATH
+
+to see what directories are in that list.
+
+(2) Add the LAMMPS src directory (or the directory you perform CMake
+build in) to your LD\_LIBRARY\_PATH, so that the current version of the
+shared library is always available to programs that use it.
+
+For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+
+
+.. parsed-literal::
+
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+
+
+----------
+
+
+**Calling the LAMMPS library**\ :
+
+Either flavor of library (static or shared) allows one or more LAMMPS
+objects to be instantiated from the calling program.
+
+When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS\_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+
+When used from a C or Fortran program, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the :doc:`Python library <Python_library>` doc page for a
+description of the Python interface to LAMMPS, which wraps the C-style
+interface.
+
+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

@@ -0,0 +1,94 @@
+Build LAMMPS with make
+======================
+
+Building LAMMPS with traditional makefiles requires that you have a
+Makefile."machine" file appropriate for your system in the src/MAKE,
+src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+below).  It can include various options for customizing your LAMMPS
+build with a number of global compilation options and features.
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must install them first, as discussed on the :doc:`Build package <Build_package>` doc page.  If the packages require
+provided or external libraries, you must build those libraries before
+building LAMMPS.  Building :doc:`LAMMPS with CMake <Build_cmake>` can
+automate all of this for many types of machines, especially
+workstations, desktops and laptops, so we suggest you try it first.
+
+These commands perform a default LAMMPS build, producing the LAMMPS
+executable lmp\_serial or lmp\_mpi in lammps/src:
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make serial     # build a serial LAMMPS executable
+   make mpi        # build a parallel LAMMPS executable with MPI
+   make            # see a variety of make options
+
+This initial compilation can take a long time, since LAMMPS is a large
+project with many features. If your machine has multiple CPU cores
+(most do these days), using a command like "make -jN mpi" (with N =
+the number of available CPU cores) can be much faster.  If you plan to
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
+installation of the ccache (= Compiler Cache) software may speed up
+compilation even more.
+
+After the initial build, whenever you edit LAMMPS source files, or add
+or remove new files to the source directory (e.g. by installing or
+uninstalling packages), you must re-compile and relink the LAMMPS
+executable with the same "make" command.  This makefiles dependencies
+should insure that only the subset of files that need to be are
+re-compiled.
+
+.. note::
+
+   When you build LAMMPS for the first time, a long list of \*.d
+   files will be printed out rapidly.  This is not an error; it is the
+   Makefile doing its normal creation of dependencies.
+
+
+----------
+
+
+The lammps/src/MAKE tree contains all the Makefile.machine files
+included in the LAMMPS distribution.  Typing "make machine" uses
+Makefile.machine.  Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi.  Others are in these dirs:
+
+
+.. parsed-literal::
+
+   OPTIONS      # Makefiles which enable specific options
+   MACHINES     # Makefiles for specific machines
+   MINE         # customized Makefiles you create (you may need to create this folder)
+
+Typing "make" lists all the available Makefile.machine files.  A file
+with the same name can appear in multiple folders (not a good idea).
+The order the dirs are searched is as follows: src/MAKE/MINE,
+src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
+to a customized file you put in src/MAKE/MINE.
+
+Makefiles you may wish to try include these (some require a package
+first be installed).  Many of these include specific compiler flags
+for optimized performance.  Please note, however, that some of these
+customized machine Makefile are contributed by users.  Since both
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
+
+
+.. parsed-literal::
+
+   make mac             # build serial LAMMPS on a Mac
+   make mac_mpi         # build parallel LAMMPS on a Mac
+   make intel_cpu       # build with the USER-INTEL package optimized for CPUs
+   make knl             # build with the USER-INTEL package optimized for KNLs
+   make opt             # build with the OPT package optimized for CPUs
+   make omp             # build with the USER-OMP package optimized for OpenMP
+   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

@@ -0,0 +1,265 @@
+Include packages in build
+=========================
+
+In LAMMPS, a package is a group of files that enable a specific set of
+features.  For example, force fields for molecular systems or
+rigid-body constraints are in packages.  In the src directory, each
+package is a sub-directory with the package name in capital letters.
+
+An overview of packages is given on the :doc:`Packages <Packages>` doc
+page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` doc page.
+
+When building LAMMPS, you can choose to include or exclude each
+package.  In general there is no need to include a package if you
+never plan to use its features.
+
+If you get a run-time error that a LAMMPS command or style is
+"Unknown", it is often because the command is contained in a package,
+and your build did not include that package.  Running LAMMPS with the
+:doc:`-h command-line switch <Run_options>` will print all the included
+packages and commands for that executable.
+
+For the majority of packages, if you follow the single step below to
+include it, you can then build LAMMPS exactly the same as you would
+without any packages installed.  A few packages may require additional
+steps, as explained on the :doc:`Build extras <Build_extras>` doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D PKG_NAME=value          # yes or no (default)
+
+Examples:
+
+
+.. parsed-literal::
+
+   -D PKG_MANYBODY=yes
+   -D PKG_USER-INTEL=yes
+
+All standard and user packages are included the same way.  Note that
+USER packages have a hyphen between USER and the rest of the package
+name, not an underscore.
+
+See the shortcut section below for how to install many packages at
+once with CMake.
+
+.. note::
+
+   If you toggle back and forth between building with CMake vs
+   make, no packages in the src directory can be installed when you
+   invoke cmake.  CMake will give an error if that is not the case,
+   indicating how you can un-install all packages in the src dir.
+
+**Traditional make**\ :
+
+
+.. parsed-literal::
+
+   cd lammps/src
+   make ps                    # check which packages are currently installed
+   make yes-name              # install a package with name
+   make no-name               # un-install a package with name
+   make mpi                   # build LAMMPS with whatever packages are now installed
+
+Examples:
+
+
+.. parsed-literal::
+
+   make no-rigid
+   make yes-user-intel
+
+All standard and user packages are included the same way.
+
+See the shortcut section below for how to install many packages at
+once with make.
+
+.. note::
+
+   You must always re-build LAMMPS (via make) after installing or
+   un-installing a package, for the action to take effect.
+
+.. note::
+
+   You cannot install or un-install packages and build LAMMPS in a
+   single make command with multiple targets, e.g. make yes-colloid mpi.
+   This is because the make procedure creates a list of source files that
+   will be out-of-date for the build if the package configuration changes
+   within the same command.  You can include or exclude multiple packages
+   in a single make command, e.g. make yes-colloid no-manybody.
+
+**CMake and make info**\ :
+
+Any package can be included or excluded in a LAMMPS build, independent
+of all other packages.  However, some packages include files derived
+from files in other packages.  LAMMPS checks for this and does the
+right thing.  Individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
+dependent on that package are also excluded.
+
+When you download a LAMMPS tarball or download LAMMPS source files
+from the Git or SVN repositories, no packages are pre-installed in the
+src directory.
+
+.. note::
+
+   Prior to Aug 2018, if you downloaded a tarball, 3 packages
+   (KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
+   That is no longer the case, so that CMake will build as-is without the
+   need to un-install those packages.
+
+
+----------
+
+
+**CMake shortcuts for installing many packages**\ :
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing the variable cache using script files. These
+are regular CMake files which can manipulate and set variables, and
+can also contain control flow constructs.
+
+LAMMPS includes several of these files to define configuration
+"presets", similar to the options that exist for the Make based
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
+
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/all\_on.cmake  [OPTIONS] ../cmake | enable all packages                                       |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/all\_off.cmake [OPTIONS] ../cmake | disable all packages                                      |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/minimal.cmake [OPTIONS] ../cmake  | enable just a few core packages                           |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  | enable most common packages                               |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  | disable packages that do require extra libraries or tools |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  | change settings to use the Clang compilers by default     |
++-------------------------------------------------------------+-----------------------------------------------------------+
+| cmake -C ../cmake/presets/mingw.cmake [OPTIONS] ../cmake    | enable all packages compatible with MinGW compilers       |
++-------------------------------------------------------------+-----------------------------------------------------------+
+
+.. note::
+
+   Running cmake this way manipulates the variable cache in your
+   current build directory. You can combine multiple presets and options
+   in a single cmake run, or change settings incrementally by running
+   cmake with new flags.
+
+**Example:**
+
+
+.. parsed-literal::
+
+   # build LAMMPS with most commonly used packages, but then remove
+   # those requiring additional library or tools, but still enable
+   # GPU package and configure it for using CUDA. You can run.
+   mkdir build
+   cd build
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
+
+   # to add another package, say BODY to the previous configuration you can run:
+   cmake -D PKG_BODY=on .
+
+   # to reset the package selection from above to the default of no packages
+   # but leaving all other settings untouched. You can run:
+   cmake -C ../cmake/presets/no_all.cmake .
+
+
+----------
+
+
+**Make shortcuts for installing many packages**\ :
+
+The following commands are useful for managing package source files
+and their installation when building LAMMPS via traditional make.
+Just type "make" in lammps/src to see a one-line summary.
+
+These commands install/un-install sets of packages:
+
++-----------------------------------+-----------------------------------------------------+
+| make yes-all                      | install all packages                                |
++-----------------------------------+-----------------------------------------------------+
+| make no-all                       | un-install all packages                             |
++-----------------------------------+-----------------------------------------------------+
+| make yes-standard or make yes-std | install standard packages                           |
++-----------------------------------+-----------------------------------------------------+
+| make no-standard or make no-std   | un-install standard packages                        |
++-----------------------------------+-----------------------------------------------------+
+| make yes-user                     | install user packages                               |
++-----------------------------------+-----------------------------------------------------+
+| make no-user                      | un-install user packages                            |
++-----------------------------------+-----------------------------------------------------+
+| make yes-lib                      | install packages that require extra libraries       |
++-----------------------------------+-----------------------------------------------------+
+| make no-lib                       | un-install packages that require extra libraries    |
++-----------------------------------+-----------------------------------------------------+
+| make yes-ext                      | install packages that require external libraries    |
++-----------------------------------+-----------------------------------------------------+
+| make no-ext                       | un-install packages that require external libraries |
++-----------------------------------+-----------------------------------------------------+
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+.. note::
+
+   Installing or un-installing a package works by simply copying
+   files back and forth between the main src directory and
+   sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+   so that the files are included or excluded when LAMMPS is built.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or are
+:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
+site.
+
+Type "make package-status" or "make ps" to show which packages are
+currently installed.  For those that are installed, it will list any
+files that are different in the src directory and package
+sub-directory.
+
+Type "make package-installed" or "make pi" to show which packages are
+currently installed, without listing the status of packages that are
+not installed.
+
+Type "make package-update" or "make pu" to overwrite src files with
+files from the package sub-directories if the package is installed.
+It should be used after a :doc:`patch has been applied <Install_patch>`,
+since patches only update the files in the package sub-directory, but
+not the src files.
+
+Type "make package-overwrite" to overwrite files in the package
+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

@@ -0,0 +1,479 @@
+Optional build settings
+=======================
+
+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:`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:`Memory allocation alignment <align>`
+| :ref:`Workaround for long long integers <longlong>`
+| :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
+| 
+
+
+----------
+
+
+.. _cxx11:
+
+C++11 standard compliance test
+------------------------------------------
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to switch.  To determine the impact of requiring C++11,
+we have added a simple compliance test to the source code, that will cause
+the compilation to abort, if C++11 compliance is not available or enabled.
+To bypass this check, you need to change a setting in the makefile or
+when calling CMake.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D DISABLE_CXX11_REQUIREMENT=yes
+
+You can set additional C++ compiler flags (beyond those selected by CMake)
+through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
+
+
+.. parsed-literal::
+
+   -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_CXX98
+
+
+----------
+
+
+.. _fft:
+
+FFT library
+---------------------
+
+When the KSPACE package is included in a LAMMPS build, the
+: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.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+   -D FFT_SINGLE=value       # yes or no (default), no = double precision
+   -D FFT_PACK=value         # array (default) or pointer or memcpy
+
+.. note::
+
+   The values for the FFT variable must be in upper-case.  This is
+   an exception to the rule that all CMake variables can be specified
+   with lower-case values.
+
+Usually these settings are all that is needed.  If CMake cannot find
+the FFT library, you can set these variables:
+
+
+.. parsed-literal::
+
+   -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
+   -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D MKL_LIBRARIES=path
+
+**Makefile.machine settings**\ :
+
+
+.. parsed-literal::
+
+   FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                                 # default is KISS if not specified
+   FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+   FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+
+# default is FFT\_PACK\_ARRAY if not specified
+
+
+.. parsed-literal::
+
+   FFT_INC =       -I/usr/local/include
+   FFT_PATH =      -L/usr/local/lib
+   FFT_LIB =       -lfftw3             # FFTW3 double precision
+   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
+
+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.
+
+**CMake and make info**\ :
+
+The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+distribution.  It is portable across all platforms.  Depending on the
+size of the FFTs and the number of processors used, the other
+libraries listed here can be faster.
+
+However, note that long-range Coulombics are only a portion of the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly).  A breakdown of these timings is printed
+to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command.  The :doc:`Run output <Run_output>`
+doc page gives more details.
+
+FFTW is a fast, portable FFT library that should also work on any
+platform and can be faster than the KISS FFT library.  You can
+download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
+
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options.
+
+The Intel MKL math library is part of the Intel compiler suite.  It
+can be used with the Intel or GNU compiler (see FFT\_LIB setting above).
+
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication.  This cost can be reduced by
+performing single-precision FFTs instead of double precision.  Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats.  Double precision means they are 8-byte doubles.  Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the -DFFT\_SINGLE
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
+
+When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
+library a second time with support for single-precision.
+
+For FFTW3, do the following, which should produce the additional
+library libfftw3f.a
+
+
+.. parsed-literal::
+
+   make clean
+   ./configure --enable-single; make; make install
+
+Performing 3d FFTs requires communication to transpose the 3d FFT
+grid.  The data packing/unpacking for this can be done in one of 3
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT\_PACK syntax above.
+Depending on the machine, the size of the FFT grid, the number of
+processors used, one option may be slightly faster.  The default is
+ARRAY mode.
+
+
+----------
+
+
+.. _size:
+
+Size of LAMMPS data types
+------------------------------------
+
+LAMMPS has a few integer data types which can be defined as 4-byte or
+8-byte integers.  The default setting of "smallbig" is almost always
+adequate.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+
+# default is LAMMPS\_SMALLBIG if not specified
+**CMake and make info**\ :
+
+The default "smallbig" setting allows for simulations with:
+
+* total atom count = 2\^63 atoms (about 9e18)
+* total timesteps = 2\^63 (about 9e18)
+* atom IDs = 2\^31 (about 2 billion)
+* image flags = roll over at 512
+
+The "bigbig" setting increases the latter two limits.  It allows for:
+
+* total atom count = 2\^63 atoms (about 9e18)
+* total timesteps = 2\^63 (about 9e18)
+* atom IDs = 2\^63 (about 9e18)
+* image flags = roll over at about 1 million (2\^20)
+
+The "smallsmall" setting is only needed if your machine does not
+support 8-byte integers.  It allows for:
+
+* total atom count = 2\^31 atoms (about 2 billion)
+* total timesteps = 2\^31 (about 2 billion)
+* atom IDs = 2\^31 (about 2 billion)
+* image flags = roll over at 512 (2\^9)
+
+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
+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.
+
+Image flags store 3 values per atom which count the number of times an
+atom has moved through the periodic box in each dimension.  See the
+:doc:`dump <dump>` doc page for a discussion.  If an atom moves through
+the periodic box more than this limit, the value will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the :doc:`compute msd <compute_msd>` command, to be faulty.
+
+Note that the USER-ATC package and the USER-INTEL package are currently
+not compatible with the "bigbig" setting. Also, there are limitations
+when using the library interface. Some functions with known issues
+have been replaced by dummy calls printing a corresponding error rather
+than crashing randomly or corrupting data.
+
+Also note that the GPU package requires its lib/gpu library to be
+compiled with the same size setting, or the link will fail.  A CMake
+build does this automatically.  When building with make, the setting
+in whichever lib/gpu/Makefile is used must be the same as above.
+
+
+----------
+
+
+.. _graphics:
+
+Output of JPG, PNG, and movie files
+--------------------------------------------------
+
+The :doc:`dump image <dump_image>` command has options to output JPEG or
+PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
+outputs movie files in MPEG format.  Using these options requires the
+following settings:
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D WITH_JPEG=value      # yes or no
+                             # default = yes if CMake finds JPEG files, else no
+   -D WITH_PNG=value       # yes or no
+                             # default = yes if CMake finds PNG and ZLIB files, else no
+   -D WITH_FFMPEG=value    # yes or no
+                             # default = yes if CMake can find ffmpeg, else no
+
+Usually these settings are all that is needed.  If CMake cannot find
+the graphics header, library, executable files, you can set these
+variables:
+
+
+.. parsed-literal::
+
+   -D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
+   -D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
+   -D PNG_INCLUDE_DIR=path     # path to png.h header file
+   -D PNG_LIBRARIES=path       # path to libpng.a (.so) file
+   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
+   -D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable
+
+**Makefile.machine settings**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_JPEG
+   LMP_INC = -DLAMMPS_PNG
+   LMP_INC = -DLAMMPS_FFMPEG
+
+   JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+   JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+   JPG_LIB = -ljpeg -lpng -lz       # library names
+
+As with CMake, you do not need to set JPG\_INC or JPG\_PATH, if make can
+find the graphics header and library files.  You must specify JPG\_LIB
+with a list of graphics libraries to include in the link.  You must
+insure ffmpeg is in a directory where LAMMPS can find it at runtime,
+i.e. a dir in your PATH environment variable.
+
+**CMake and make info**\ :
+
+Using ffmpeg to output movie files requires that your machine
+supports the "popen" function in the standard runtime library.
+
+.. note::
+
+   On some clusters with high-speed networks, using the fork()
+   library calls (required by popen()) can interfere with the fast
+   communication library and lead to simulations using ffmpeg to hang or
+   crash.
+
+
+----------
+
+
+.. _gzip:
+
+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>`.
+
+**CMake variables**\ :
+
+
+.. parsed-literal::
+
+   -D WITH_GZIP=value       # yes or no
+                            # default is yes if CMake can find gzip, else no
+   -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_GZIP
+
+**CMake and make info**\ :
+
+This option requires that your machine supports the "popen()" function
+in the standard runtime library and that a gzip executable can be
+found by LAMMPS during a run.
+
+.. note::
+
+   On some clusters with high-speed networks, using the fork()
+   library calls (required by popen()) can interfere with the fast
+   communication library and lead to simulations using compressed output
+   or input to hang or crash. For selected operations, compressed file
+   I/O is also available using a compression library instead, which is
+   what the :ref:`COMPRESS package <PKG-COMPRESS>` enables.
+
+
+----------
+
+
+.. _align:
+
+Memory allocation alignment
+---------------------------------------
+
+This setting enables the use of the posix\_memalign() call instead of
+malloc() when LAMMPS allocates large chunks or memory.  This can make
+vector instructions on CPUs more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.
+On most current systems, the malloc() implementation returns
+pointers that are aligned to 16-byte boundaries. Using SSE vector
+instructions efficiently, however, requires memory blocks being
+aligned on 64-byte boundaries.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
+
+Use a LAMMPS\_MEMALIGN value of 0 to disable using posix\_memalign()
+and revert to using the malloc() C-library function instead.  When
+compiling LAMMPS for Windows systems, malloc() will always be used
+and this setting ignored.
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
+
+Do not set -DLAMMPS\_MEMALIGN, if you want to have memory allocated
+with the malloc() function call instead. -DLAMMPS\_MEMALIGN **cannot**
+be used on Windows, as it does use different function calls for
+allocating aligned memory, that are not compatible with how LAMMPS
+manages its dynamical memory.
+
+
+----------
+
+
+.. _longlong:
+
+Workaround for long long integers
+------------------------------------------------
+
+If your system or MPI version does not recognize "long long" data
+types, the following setting will be needed.  It converts "long long"
+to a "long" data type, which should be the desired 8-byte integer on
+those systems:
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
+
+
+----------
+
+
+.. _exceptions:
+
+Exception handling when using LAMMPS as a library
+------------------------------------------------------------------
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled LAMMPS errors do not kill the caller.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python.
+
+**CMake variable**\ :
+
+
+.. parsed-literal::
+
+   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. parsed-literal::
+
+   LMP_INC = -DLAMMPS_EXCEPTIONS
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -0,0 +1,111 @@
+Notes for building LAMMPS on Windows
+====================================
+
+* :ref:`General remarks <generic>`
+* :ref:`Running Linux on Windows <linux>`
+* :ref:`Using GNU GCC ported to Windows <gnu>`
+* :ref:`Using a cross-compiler <cross>`
+
+
+----------
+
+
+.. _generic:
+
+General remarks
+-----------------------------
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+.. _linux:
+
+Running Linux on Windows
+------------------------------------
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
+
+.. _gnu:
+
+Using GNU GCC ported to Windows
+-----------------------------------------
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. Using CMake for this mode of compilation
+is untested and not likely to work.
+
+When compiling for Windows do **not** set the -DLAMMPS\_MEMALIGN define
+in the LMP\_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS GitHub project.
+
+.. _cross:
+
+Using a cross-compiler
+----------------------------------
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines. A CMake preset
+selecting all packages compatible with this cross-compilation build
+is provided. You likely need to disable the GPU package unless you
+download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
+into your MinGW64 cross-compiler environment. The cross-compilation
+currently will only produce non-MPI serial binaries.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers.  We instead rely on the feedback of the users
+of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+.. _native:
+
+Native Visual C++ support
+--------------------------------------
+
+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.rst

@@ -0,0 +1,34 @@
+Commands
+********
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_input
+   Commands_parse
+   Commands_structure
+   Commands_category
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_all
+   Commands_fix
+   Commands_compute
+   Commands_pair
+   Commands_bond
+   Commands_kspace
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -0,0 +1,59 @@
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
++----------------------------------------+------------------------------------+------------------------------------------+
+
+General commands
+================
+
+An alphabetic list of all general LAMMPS commands.
+
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`angle\_coeff <angle_coeff>`       | :doc:`angle\_style <angle_style>`       | :doc:`atom\_modify <atom_modify>`       | :doc:`atom\_style <atom_style>`         | :doc:`balance <balance>`                    | :doc:`bond\_coeff <bond_coeff>`         |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`bond\_style <bond_style>`         | :doc:`bond\_write <bond_write>`         | :doc:`boundary <boundary>`              | :doc:`box <box>`                        | :doc:`change\_box <change_box>`             | :doc:`clear <clear>`                    |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`comm\_modify <comm_modify>`       | :doc:`comm\_style <comm_style>`         | :doc:`compute <compute>`                | :doc:`compute\_modify <compute_modify>` | :doc:`create\_atoms <create_atoms>`         | :doc:`create\_bonds <create_bonds>`     |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`create\_box <create_box>`         | :doc:`delete\_atoms <delete_atoms>`     | :doc:`delete\_bonds <delete_bonds>`     | :doc:`dielectric <dielectric>`          | :doc:`dihedral\_coeff <dihedral_coeff>`     | :doc:`dihedral\_style <dihedral_style>` |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`dimension <dimension>`            | :doc:`displace\_atoms <displace_atoms>` | :doc:`dump <dump>`                      | :doc:`dump adios <dump_adios>`          | :doc:`dump image <dump_image>`              | :doc:`dump movie <dump_image>`          |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`dump netcdf <dump_netcdf>`        | :doc:`dump netcdf/mpiio <dump_netcdf>`  | :doc:`dump vtk <dump_vtk>`              | :doc:`dump\_modify <dump_modify>`       | :doc:`dynamical\_matrix <dynamical_matrix>` | :doc:`echo <echo>`                      |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`fix <fix>`                        | :doc:`fix\_modify <fix_modify>`         | :doc:`group <group>`                    | :doc:`group2ndx <group2ndx>`            | :doc:`hyper <hyper>`                        | :doc:`if <if>`                          |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`info <info>`                      | :doc:`improper\_coeff <improper_coeff>` | :doc:`improper\_style <improper_style>` | :doc:`include <include>`                | :doc:`jump <jump>`                          | :doc:`kim\_init <kim_commands>`         |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`kim\_interactions <kim_commands>` | :doc:`kim\_query <kim_commands>`        | :doc:`kspace\_modify <kspace_modify>`   | :doc:`kspace\_style <kspace_style>`     | :doc:`label <label>`                        | :doc:`lattice <lattice>`                |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`log <log>`                        | :doc:`mass <mass>`                      | :doc:`message <message>`                | :doc:`minimize <minimize>`              | :doc:`min\_modify <min_modify>`             | :doc:`min\_style <min_style>`           |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`min\_style spin <min_spin>`       | :doc:`molecule <molecule>`              | :doc:`ndx2group <group2ndx>`            | :doc:`neb <neb>`                        | :doc:`neb/spin <neb_spin>`                  | :doc:`neigh\_modify <neigh_modify>`     |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`neighbor <neighbor>`              | :doc:`newton <newton>`                  | :doc:`next <next>`                      | :doc:`package <package>`                | :doc:`pair\_coeff <pair_coeff>`             | :doc:`pair\_modify <pair_modify>`       |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`pair\_style <pair_style>`         | :doc:`pair\_write <pair_write>`         | :doc:`partition <partition>`            | :doc:`prd <prd>`                        | :doc:`print <print>`                        | :doc:`processors <processors>`          |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`python <python>`                  | :doc:`quit <quit>`                      | :doc:`read\_data <read_data>`           | :doc:`read\_dump <read_dump>`           | :doc:`read\_restart <read_restart>`         | :doc:`region <region>`                  |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`replicate <replicate>`            | :doc:`rerun <rerun>`                    | :doc:`reset\_ids <reset_ids>`           | :doc:`reset\_timestep <reset_timestep>` | :doc:`restart <restart>`                    | :doc:`run <run>`                        |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`run\_style <run_style>`           | :doc:`server <server>`                  | :doc:`set <set>`                        | :doc:`shell <shell>`                    | :doc:`special\_bonds <special_bonds>`       | :doc:`suffix <suffix>`                  |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`tad <tad>`                        | :doc:`temper <temper>`                  | :doc:`temper/grem <temper_grem>`        | :doc:`temper/npt <temper_npt>`          | :doc:`thermo <thermo>`                      | :doc:`thermo\_modify <thermo_modify>`   |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`thermo\_style <thermo_style>`     | :doc:`third\_order <third_order>`       | :doc:`timer <timer>`                    | :doc:`timestep <timestep>`              | :doc:`uncompute <uncompute>`                | :doc:`undump <undump>`                  |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`unfix <unfix>`                    | :doc:`units <units>`                    | :doc:`variable <variable>`              | :doc:`velocity <velocity>`              | :doc:`write\_coeff <write_coeff>`           | :doc:`write\_data <write_data>`         |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+| :doc:`write\_dump <write_dump>`         | :doc:`write\_restart <write_restart>`   |                                         |                                         |                                             |                                         |
++-----------------------------------------+-----------------------------------------+-----------------------------------------+-----------------------------------------+---------------------------------------------+-----------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_bond.rst

@@ -0,0 +1,112 @@
+.. _bond:
+
+Bond\_style potentials
+=================================
+
+All LAMMPS :doc:`bond\_style <bond_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:`none <bond_none>`               | :doc:`zero <bond_zero>`                         | :doc:`hybrid <bond_hybrid>`                             |                                 |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+|                                       |                                                 |                                                         |                                 |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+| :doc:`class2 (ko) <bond_class2>`      | :doc:`fene (iko) <bond_fene>`                   | :doc:`fene/expand (o) <bond_fene_expand>`               | :doc:`gromos (o) <bond_gromos>` |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+| :doc:`harmonic (iko) <bond_harmonic>` | :doc:`harmonic/shift (o) <bond_harmonic_shift>` | :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>` | :doc:`mm3 <bond_mm3>`           |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+| :doc:`morse (o) <bond_morse>`         | :doc:`nonlinear (o) <bond_nonlinear>`           | :doc:`oxdna/fene <bond_oxdna>`                          | :doc:`oxdna2/fene <bond_oxdna>` |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+| :doc:`quartic (o) <bond_quartic>`     | :doc:`table (o) <bond_table>`                   |                                                         |                                 |
++---------------------------------------+-------------------------------------------------+---------------------------------------------------------+---------------------------------+
+
+
+----------
+
+
+.. _angle:
+
+Angle\_style potentials
+===================================
+
+All LAMMPS :doc:`angle\_style <angle_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:`none <angle_none>`                             | :doc:`zero <angle_zero>`                         | :doc:`hybrid <angle_hybrid>`                       |                                              |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+|                                                      |                                                  |                                                    |                                              |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+| :doc:`charmm (iko) <angle_charmm>`                   | :doc:`class2 (ko) <angle_class2>`                | :doc:`class2/p6 <angle_class2>`                    | :doc:`cosine (ko) <angle_cosine>`            |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+| :doc:`cosine/buck6d <angle_cosine_buck6d>`           | :doc:`cosine/delta (o) <angle_cosine_delta>`     | :doc:`cosine/periodic (o) <angle_cosine_periodic>` | :doc:`cosine/shift (o) <angle_cosine_shift>` |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+| :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>` | :doc:`cosine/squared (o) <angle_cosine_squared>` | :doc:`cross <angle_cross>`                         | :doc:`dipole (o) <angle_dipole>`             |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+| :doc:`fourier (o) <angle_fourier>`                   | :doc:`fourier/simple (o) <angle_fourier_simple>` | :doc:`harmonic (iko) <angle_harmonic>`             | :doc:`mm3 <angle_mm3>`                       |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+| :doc:`quartic (o) <angle_quartic>`                   | :doc:`sdk (o) <angle_sdk>`                       | :doc:`table (o) <angle_table>`                     |                                              |
++------------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------+
+
+
+----------
+
+
+.. _dihedral:
+
+Dihedral\_style potentials
+=========================================
+
+All LAMMPS :doc:`dihedral\_style <dihedral_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:`none <dihedral_none>`               | :doc:`zero <dihedral_zero>`               | :doc:`hybrid <dihedral_hybrid>`           |                                                         |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+|                                           |                                           |                                           |                                                         |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`charmm (iko) <dihedral_charmm>`     | :doc:`charmmfsw <dihedral_charmm>`        | :doc:`class2 (ko) <dihedral_class2>`      | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`fourier (io) <dihedral_fourier>`    | :doc:`harmonic (iko) <dihedral_harmonic>` | :doc:`helix (o) <dihedral_helix>`         | :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`     |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`opls (iko) <dihedral_opls>`         | :doc:`quadratic (o) <dihedral_quadratic>` | :doc:`spherical <dihedral_spherical>`                   |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`table (o) <dihedral_table>`         | :doc:`table/cut <dihedral_table_cut>`     |                                           |                                                         |
++-------------------------------------------+-------------------------------------------+-------------------------------------------+---------------------------------------------------------+
+
+
+----------
+
+
+.. _improper:
+
+Improper\_style potentials
+=========================================
+
+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:`none <improper_none>`          | :doc:`zero <improper_zero>`             | :doc:`hybrid <improper_hybrid>`           |                                                         |
++--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+|                                      |                                         |                                           |                                                         |
++--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`class2 (ko) <improper_class2>` | :doc:`cossq (o) <improper_cossq>`       | :doc:`cvff (io) <improper_cvff>`          | :doc:`distance <improper_distance>`                     |
++--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`distharm <improper_distharm>`  | :doc:`fourier (o) <improper_fourier>`   | :doc:`harmonic (iko) <improper_harmonic>` | :doc:`inversion/harmonic <improper_inversion_harmonic>` |
++--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+| :doc:`ring (o) <improper_ring>`      | :doc:`sqdistharm <improper_sqdistharm>` | :doc:`umbrella (o) <improper_umbrella>`   |                                                         |
++--------------------------------------+-----------------------------------------+-------------------------------------------+---------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_category.rst

@@ -0,0 +1,137 @@
+Commands by category
+====================
+
+This page lists most of the LAMMPS commands, grouped by category.  The
+:doc:`General commands <Commands_all>` doc page lists all general commands
+alphabetically.  Style options for entries like fix, compute, pair etc.
+have their own pages where they are listed alphabetically.
+
+Initialization:
+
+* :doc:`newton <newton>`,
+* :doc:`package <package>`,
+* :doc:`processors <processors>`,
+* :doc:`suffix <suffix>`,
+* :doc:`units <units>`
+
+Setup simulation box:
+
+* :doc:`boundary <boundary>`,
+* :doc:`box <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:`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:`group <group>`,
+* :doc:`mass <mass>`,
+* :doc:`molecule <molecule>`,
+* :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:`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>`
+
+Settings:
+
+* :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:`neighbor <neighbor>`,
+* :doc:`partition <partition>`,
+* :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:`fix <fix>`,
+* :doc:`fix\_modify <fix_modify>`,
+* :doc:`uncompute <uncompute>`,
+* :doc:`unfix <unfix>`
+
+Output:
+
+* :doc:`dump image <dump_image>`,
+* :doc:`dump movie <dump_image>`,
+* :doc:`dump <dump>`,
+* :doc:`dump\_modify <dump_modify>`,
+* :doc:`restart <restart>`,
+* :doc:`thermo <thermo>`,
+* :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>`
+
+Actions:
+
+* :doc:`minimize <minimize>`,
+* :doc:`neb <neb>`,
+* :doc:`neb\_spin <neb_spin>`,
+* :doc:`prd <prd>`,
+* :doc:`rerun <rerun>`,
+* :doc:`run <run>`,
+* :doc:`tad <tad>`,
+* :doc:`temper <temper>`
+
+Input script control:
+
+* :doc:`clear <clear>`,
+* :doc:`echo <echo>`,
+* :doc:`if <if>`,
+* :doc:`include <include>`,
+* :doc:`jump <jump>`,
+* :doc:`label <label>`,
+* :doc:`log <log>`,
+* :doc:`next <next>`,
+* :doc:`print <print>`,
+* :doc:`python <python>`,
+* :doc:`quit <quit>`,
+* :doc:`shell <shell>`,
+* :doc:`variable <variable>`
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_compute.rst

@@ -0,0 +1,70 @@
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
++----------------------------------------+------------------------------------+------------------------------------------+
+
+Compute commands
+================
+
+An alphabetic list of all LAMMPS :doc:`compute <compute>` 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:`ackland/atom <compute_ackland_atom>`                 | :doc:`adf <compute_adf>`                               | :doc:`aggregate/atom <compute_cluster_atom>`                     | :doc:`angle <compute_angle>`                                 | :doc:`angle/local <compute_angle_local>`                 | :doc:`angmom/chunk <compute_angmom_chunk>`                   |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`basal/atom <compute_basal_atom>`                     | :doc:`body/local <compute_body_local>`                 | :doc:`bond <compute_bond>`                                       | :doc:`bond/local <compute_bond_local>`                       | :doc:`centro/atom <compute_centro_atom>`                 | :doc:`centroid/stress/atom <compute_stress_atom>`            |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`chunk/atom <compute_chunk_atom>`                     | :doc:`chunk/spread/atom <compute_chunk_spread_atom>`   | :doc:`cluster/atom <compute_cluster_atom>`                       | :doc:`cna/atom <compute_cna_atom>`                           | :doc:`cnp/atom <compute_cnp_atom>`                       | :doc:`com <compute_com>`                                     |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`com/chunk <compute_com_chunk>`                       | :doc:`contact/atom <compute_contact_atom>`             | :doc:`coord/atom <compute_coord_atom>`                           | :doc:`damage/atom <compute_damage_atom>`                     | :doc:`dihedral <compute_dihedral>`                       | :doc:`dihedral/local <compute_dihedral_local>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`dilatation/atom <compute_dilatation_atom>`           | :doc:`dipole/chunk <compute_dipole_chunk>`             | :doc:`displace/atom <compute_displace_atom>`                     | :doc:`dpd <compute_dpd>`                                     | :doc:`dpd/atom <compute_dpd_atom>`                       | :doc:`edpd/temp/atom <compute_edpd_temp_atom>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`entropy/atom <compute_entropy_atom>`                 | :doc:`erotate/asphere <compute_erotate_asphere>`       | :doc:`erotate/rigid <compute_erotate_rigid>`                     | :doc:`erotate/sphere <compute_erotate_sphere>`               | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`fep <compute_fep>`                                   | :doc:`force/tally <compute_tally>`                     | :doc:`fragment/atom <compute_cluster_atom>`                      | :doc:`global/atom <compute_global_atom>`                     | :doc:`group/group <compute_group_group>`                 | :doc:`gyration <compute_gyration>`                           |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`gyration/chunk <compute_gyration_chunk>`             | :doc:`gyration/shape <compute_gyration_shape>`         | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`       | :doc:`heat/flux <compute_heat_flux>`                         | :doc:`heat/flux/tally <compute_tally>`                   | :doc:`hexorder/atom <compute_hexorder_atom>`                 |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`hma <compute_hma>`                                   | :doc:`improper <compute_improper>`                     | :doc:`improper/local <compute_improper_local>`                   | :doc:`inertia/chunk <compute_inertia_chunk>`                 | :doc:`ke <compute_ke>`                                   | :doc:`ke/atom <compute_ke_atom>`                             |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`ke/atom/eff <compute_ke_atom_eff>`                   | :doc:`ke/eff <compute_ke_eff>`                         | :doc:`ke/rigid <compute_ke_rigid>`                               | :doc:`meso/e/atom <compute_meso_e_atom>`                     | :doc:`meso/rho/atom <compute_meso_rho_atom>`             | :doc:`meso/t/atom <compute_meso_t_atom>`                     |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`momentum <compute_momentum>`                         | :doc:`msd <compute_msd>`                               | :doc:`msd/chunk <compute_msd_chunk>`                             | :doc:`msd/nongauss <compute_msd_nongauss>`                   | :doc:`omega/chunk <compute_omega_chunk>`                 | :doc:`orientorder/atom <compute_orientorder_atom>`           |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`pair <compute_pair>`                                 | :doc:`pair/local <compute_pair_local>`                 | :doc:`pe <compute_pe>`                                           | :doc:`pe/atom <compute_pe_atom>`                             | :doc:`pe/mol/tally <compute_tally>`                      | :doc:`pe/tally <compute_tally>`                              |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`plasticity/atom <compute_plasticity_atom>`           | :doc:`pressure <compute_pressure>`                     | :doc:`pressure/cylinder <compute_pressure_cylinder>`             | :doc:`pressure/uef <compute_pressure_uef>`                   | :doc:`property/atom <compute_property_atom>`             | :doc:`property/chunk <compute_property_chunk>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`property/local <compute_property_local>`             | :doc:`ptm/atom <compute_ptm_atom>`                     | :doc:`rdf <compute_rdf>`                                         | :doc:`reduce <compute_reduce>`                               | :doc:`reduce/chunk <compute_reduce_chunk>`               | :doc:`reduce/region <compute_reduce>`                        |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`rigid/local <compute_rigid_local>`                   | :doc:`saed <compute_saed>`                             | :doc:`slice <compute_slice>`                                     | :doc:`smd/contact/radius <compute_smd_contact_radius>`       | :doc:`smd/damage <compute_smd_damage>`                   | :doc:`smd/hourglass/error <compute_smd_hourglass_error>`     |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`smd/internal/energy <compute_smd_internal_energy>`   | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>`                             | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>`     | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>`                   |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>`       | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>`               | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>`       | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>`     | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>`     | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>`           | :doc:`smd/vol <compute_smd_vol>`                         | :doc:`sna/atom <compute_sna_atom>`                           |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`snad/atom <compute_sna_atom>`                        | :doc:`snav/atom <compute_sna_atom>`                    | :doc:`spin <compute_spin>`                                       | :doc:`stress/atom <compute_stress_atom>`                     | :doc:`stress/mop <compute_stress_mop>`                   | :doc:`stress/mop/profile <compute_stress_mop>`               |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`stress/tally <compute_tally>`                        | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`             | :doc:`temp (k) <compute_temp>`                                   | :doc:`temp/asphere <compute_temp_asphere>`                   | :doc:`temp/body <compute_temp_body>`                     | :doc:`temp/chunk <compute_temp_chunk>`                       |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`temp/com <compute_temp_com>`                         | :doc:`temp/cs <compute_temp_cs>`                       | :doc:`temp/deform <compute_temp_deform>`                         | :doc:`temp/deform/eff <compute_temp_deform_eff>`             | :doc:`temp/drude <compute_temp_drude>`                   | :doc:`temp/eff <compute_temp_eff>`                           |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`temp/partial <compute_temp_partial>`                 | :doc:`temp/profile <compute_temp_profile>`             | :doc:`temp/ramp <compute_temp_ramp>`                             | :doc:`temp/region <compute_temp_region>`                     | :doc:`temp/region/eff <compute_temp_region_eff>`         | :doc:`temp/rotate <compute_temp_rotate>`                     |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`temp/sphere <compute_temp_sphere>`                   | :doc:`temp/uef <compute_temp_uef>`                     | :doc:`ti <compute_ti>`                                           | :doc:`torque/chunk <compute_torque_chunk>`                   | :doc:`vacf <compute_vacf>`                               | :doc:`vcm/chunk <compute_vcm_chunk>`                         |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+| :doc:`voronoi/atom <compute_voronoi_atom>`                 | :doc:`xrd <compute_xrd>`                               |                                                                  |                                                              |                                                          |                                                              |
++------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_fix.rst

@@ -0,0 +1,94 @@
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
++----------------------------------------+------------------------------------+------------------------------------------+
+
+Fix commands
+============
+
+An alphabetic list of all LAMMPS :doc:`fix <fix>` 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:`adapt <fix_adapt>`                         | :doc:`adapt/fep <fix_adapt_fep>`                       | :doc:`addforce <fix_addforce>`                        | :doc:`addtorque <fix_addtorque>`                       | :doc:`append/atoms <fix_append_atoms>`                         | :doc:`atc <fix_atc>`                           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`atom/swap <fix_atom_swap>`                 | :doc:`ave/atom <fix_ave_atom>`                         | :doc:`ave/chunk <fix_ave_chunk>`                      | :doc:`ave/correlate <fix_ave_correlate>`               | :doc:`ave/correlate/long <fix_ave_correlate_long>`             | :doc:`ave/histo <fix_ave_histo>`               |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`ave/histo/weight <fix_ave_histo>`          | :doc:`ave/time <fix_ave_time>`                         | :doc:`aveforce <fix_aveforce>`                        | :doc:`balance <fix_balance>`                           | :doc:`bocs <fix_bocs>`                                         | :doc:`bond/break <fix_bond_break>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`bond/create <fix_bond_create>`             | :doc:`bond/react <fix_bond_react>`                     | :doc:`bond/swap <fix_bond_swap>`                      | :doc:`box/relax <fix_box_relax>`                       | :doc:`client/md <fix_client_md>`                               | :doc:`cmap <fix_cmap>`                         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`colvars <fix_colvars>`                     | :doc:`controller <fix_controller>`                     | :doc:`deform (k) <fix_deform>`                        | :doc:`deposit <fix_deposit>`                           | :doc:`dpd/energy (k) <fix_dpd_energy>`                         | :doc:`drag <fix_drag>`                         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`drude <fix_drude>`                         | :doc:`drude/transform/direct <fix_drude_transform>`    | :doc:`drude/transform/inverse <fix_drude_transform>`  | :doc:`dt/reset <fix_dt_reset>`                         | :doc:`edpd/source <fix_dpd_source>`                            | :doc:`efield <fix_efield>`                     |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`ehex <fix_ehex>`                           | :doc:`electron/stopping <fix_electron_stopping>`       | :doc:`enforce2d (k) <fix_enforce2d>`                  | :doc:`eos/cv <fix_eos_cv>`                             | :doc:`eos/table <fix_eos_table>`                               | :doc:`eos/table/rx (k) <fix_eos_table_rx>`     |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`evaporate <fix_evaporate>`                 | :doc:`external <fix_external>`                         | :doc:`ffl <fix_ffl>`                                  | :doc:`filter/corotate <fix_filter_corotate>`           | :doc:`flow/gauss <fix_flow_gauss>`                             | :doc:`freeze (k) <fix_freeze>`                 |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`gcmc <fix_gcmc>`                           | :doc:`gld <fix_gld>`                                   | :doc:`gle <fix_gle>`                                  | :doc:`gravity (ko) <fix_gravity>`                      | :doc:`grem <fix_grem>`                                         | :doc:`halt <fix_halt>`                         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`heat <fix_heat>`                           | :doc:`hyper/global <fix_hyper_global>`                 | :doc:`hyper/local <fix_hyper_local>`                  | :doc:`imd <fix_imd>`                                   | :doc:`indent <fix_indent>`                                     | :doc:`ipi <fix_ipi>`                           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`langevin (k) <fix_langevin>`               | :doc:`langevin/drude <fix_langevin_drude>`             | :doc:`langevin/eff <fix_langevin_eff>`                | :doc:`langevin/spin <fix_langevin_spin>`               | :doc:`latte <fix_latte>`                                       | :doc:`lb/fluid <fix_lb_fluid>`                 |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`lb/momentum <fix_lb_momentum>`             | :doc:`lb/pc <fix_lb_pc>`                               | :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`    | :doc:`lb/viscous <fix_lb_viscous>`                     | :doc:`lineforce <fix_lineforce>`                               | :doc:`manifoldforce <fix_manifoldforce>`       |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`meso <fix_meso>`                           | :doc:`meso/move <fix_meso_move>`                       | :doc:`meso/stationary <fix_meso_stationary>`          | :doc:`momentum (k) <fix_momentum>`                     | :doc:`move <fix_move>`                                         | :doc:`mscg <fix_mscg>`                         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`msst <fix_msst>`                           | :doc:`mvv/dpd <fix_mvv_dpd>`                           | :doc:`mvv/edpd <fix_mvv_dpd>`                         | :doc:`mvv/tdpd <fix_mvv_dpd>`                          | :doc:`neb <fix_neb>`                                           | :doc:`neb\_spin <fix_neb_spin>`                |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nph (ko) <fix_nh>`                         | :doc:`nph/asphere (o) <fix_nph_asphere>`               | :doc:`nph/body <fix_nph_body>`                        | :doc:`nph/eff <fix_nh_eff>`                            | :doc:`nph/sphere (o) <fix_nph_sphere>`                         | :doc:`nphug (o) <fix_nphug>`                   |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`npt (iko) <fix_nh>`                        | :doc:`npt/asphere (o) <fix_npt_asphere>`               | :doc:`npt/body <fix_npt_body>`                        | :doc:`npt/eff <fix_nh_eff>`                            | :doc:`npt/sphere (o) <fix_npt_sphere>`                         | :doc:`npt/uef <fix_nh_uef>`                    |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nve (iko) <fix_nve>`                       | :doc:`nve/asphere (i) <fix_nve_asphere>`               | :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`  | :doc:`nve/awpmd <fix_nve_awpmd>`                       | :doc:`nve/body <fix_nve_body>`                                 | :doc:`nve/dot <fix_nve_dot>`                   |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>` | :doc:`nve/eff <fix_nve_eff>`                           | :doc:`nve/limit <fix_nve_limit>`                      | :doc:`nve/line <fix_nve_line>`                         | :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`           | :doc:`nve/noforce <fix_nve_noforce>`           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nve/sphere (ko) <fix_nve_sphere>`          | :doc:`nve/spin <fix_nve_spin>`                         | :doc:`nve/tri <fix_nve_tri>`                          | :doc:`nvk <fix_nvk>`                                   | :doc:`nvt (iko) <fix_nh>`                                      | :doc:`nvt/asphere (o) <fix_nvt_asphere>`       |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nvt/body <fix_nvt_body>`                   | :doc:`nvt/eff <fix_nh_eff>`                            | :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`  | :doc:`nvt/sllod (io) <fix_nvt_sllod>`                  | :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`                       | :doc:`nvt/sphere (o) <fix_nvt_sphere>`         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`nvt/uef <fix_nh_uef>`                      | :doc:`oneway <fix_oneway>`                             | :doc:`orient/bcc <fix_orient>`                        | :doc:`orient/fcc <fix_orient>`                         | :doc:`phonon <fix_phonon>`                                     | :doc:`pimd <fix_pimd>`                         |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`planeforce <fix_planeforce>`               | :doc:`plumed <fix_plumed>`                             | :doc:`poems <fix_poems>`                              | :doc:`pour <fix_pour>`                                 | :doc:`precession/spin <fix_precession_spin>`                   | :doc:`press/berendsen <fix_press_berendsen>`   |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`print <fix_print>`                         | :doc:`property/atom (k) <fix_property_atom>`           | :doc:`python/invoke <fix_python_invoke>`              | :doc:`python/move <fix_python_move>`                   | :doc:`qbmsst <fix_qbmsst>`                                     | :doc:`qeq/comb (o) <fix_qeq_comb>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`qeq/dynamic <fix_qeq>`                     | :doc:`qeq/fire <fix_qeq>`                              | :doc:`qeq/point <fix_qeq>`                            | :doc:`qeq/reax (ko) <fix_qeq_reax>`                    | :doc:`qeq/shielded <fix_qeq>`                                  | :doc:`qeq/slater <fix_qeq>`                    |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`qmmm <fix_qmmm>`                           | :doc:`qtb <fix_qtb>`                                   | :doc:`rattle <fix_shake>`                             | :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`              | :doc:`reax/c/species (k) <fix_reaxc_species>`                  | :doc:`recenter <fix_recenter>`                 |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`restrain <fix_restrain>`                   | :doc:`rhok <fix_rhok>`                                 | :doc:`rigid (o) <fix_rigid>`                          | :doc:`rigid/meso <fix_rigid_meso>`                     | :doc:`rigid/nph (o) <fix_rigid>`                               | :doc:`rigid/nph/small <fix_rigid>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`rigid/npt (o) <fix_rigid>`                 | :doc:`rigid/npt/small <fix_rigid>`                     | :doc:`rigid/nve (o) <fix_rigid>`                      | :doc:`rigid/nve/small <fix_rigid>`                     | :doc:`rigid/nvt (o) <fix_rigid>`                               | :doc:`rigid/nvt/small <fix_rigid>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`rigid/small (o) <fix_rigid>`               | :doc:`rx (k) <fix_rx>`                                 | :doc:`saed/vtk <fix_saed_vtk>`                        | :doc:`setforce (k) <fix_setforce>`                     | :doc:`shake <fix_shake>`                                       | :doc:`shardlow (k) <fix_shardlow>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`smd <fix_smd>`                             | :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`              | :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` | :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`  | :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` | :doc:`smd/setvel <fix_smd_setvel>`             |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`smd/wall\_surface <fix_smd_wall_surface>`  | :doc:`spring <fix_spring>`                             | :doc:`spring/chunk <fix_spring_chunk>`                | :doc:`spring/rg <fix_spring_rg>`                       | :doc:`spring/self <fix_spring_self>`                           | :doc:`srd <fix_srd>`                           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`store/force <fix_store_force>`             | :doc:`store/state <fix_store_state>`                   | :doc:`tdpd/source <fix_dpd_source>`                   | :doc:`temp/berendsen <fix_temp_berendsen>`             | :doc:`temp/csld <fix_temp_csvr>`                               | :doc:`temp/csvr <fix_temp_csvr>`               |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`temp/rescale <fix_temp_rescale>`           | :doc:`temp/rescale/eff <fix_temp_rescale_eff>`         | :doc:`tfmc <fix_tfmc>`                                | :doc:`thermal/conductivity <fix_thermal_conductivity>` | :doc:`ti/spring <fix_ti_spring>`                               | :doc:`tmd <fix_tmd>`                           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`ttm <fix_ttm>`                             | :doc:`ttm/mod <fix_ttm>`                               | :doc:`tune/kspace <fix_tune_kspace>`                  | :doc:`vector <fix_vector>`                             | :doc:`viscosity <fix_viscosity>`                               | :doc:`viscous <fix_viscous>`                   |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`wall/body/polygon <fix_wall_body_polygon>` | :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` | :doc:`wall/colloid <fix_wall>`                        | :doc:`wall/ees <fix_wall_ees>`                         | :doc:`wall/gran <fix_wall_gran>`                               | :doc:`wall/gran/region <fix_wall_gran_region>` |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`wall/harmonic <fix_wall>`                  | :doc:`wall/lj1043 <fix_wall>`                          | :doc:`wall/lj126 <fix_wall>`                          | :doc:`wall/lj93 (k) <fix_wall>`                        | :doc:`wall/morse <fix_wall>`                                   | :doc:`wall/piston <fix_wall_piston>`           |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+| :doc:`wall/reflect (k) <fix_wall_reflect>`       | :doc:`wall/region <fix_wall_region>`                   | :doc:`wall/region/ees <fix_wall_ees>`                 | :doc:`wall/srd <fix_wall_srd>`                         |                                                                |                                                |
++--------------------------------------------------+--------------------------------------------------------+-------------------------------------------------------+--------------------------------------------------------+----------------------------------------------------------------+------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_input.rst

@@ -1,13 +1,5 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-LAMMPS input scripts :h3
+LAMMPS input scripts
+====================
 
 LAMMPS executes by reading commands from a input script (text file),
 one line at a time.  When the input script ends, LAMMPS exits.  Each
@@ -24,15 +16,21 @@ simulation with all the settings.  Rather, the input script is read
 one line at a time and each command takes effect when it is read.
 Thus this sequence of commands:
 
-timestep 0.5
-run      100
-run      100 :pre
+
+.. code-block:: LAMMPS
+
+   timestep 0.5
+   run      100
+   run      100
 
 does something different than this sequence:
 
-run      100
-timestep 0.5
-run      100 :pre
+
+.. code-block:: LAMMPS
+
+   run      100
+   timestep 0.5
+   run      100
 
 In the first case, the specified timestep (0.5 fs) is used for two
 simulations of 100 timesteps each.  In the 2nd case, the default
@@ -47,14 +45,18 @@ 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
-"read_data"_read_data.html 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 "processors"_processors.html and
-"boundary"_boundary.html commands need to be used before read_data to
+values are not desired, the :doc:`processors <processors>` and
+:doc:`boundary <boundary>` commands need to be used before read\_data to
 tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The "Errors"_Errors.html doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
 
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_kspace.rst

@@ -0,0 +1,28 @@
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
++----------------------------------------+------------------------------------+------------------------------------------+
+
+KSpace solvers
+==============
+
+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:`ewald (o) <kspace_style>`    | :doc:`ewald/disp <kspace_style>`     | :doc:`msm (o) <kspace_style>`       | :doc:`msm/cg (o) <kspace_style>`      |
++------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
+| :doc:`pppm (gok) <kspace_style>`   | :doc:`pppm/cg (o) <kspace_style>`    | :doc:`pppm/disp (i) <kspace_style>` | :doc:`pppm/disp/tip4p <kspace_style>` |
++------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
+| :doc:`pppm/stagger <kspace_style>` | :doc:`pppm/tip4p (o) <kspace_style>` | :doc:`scafacos <kspace_style>`      |                                       |
++------------------------------------+--------------------------------------+-------------------------------------+---------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_pair.rst

@@ -0,0 +1,136 @@
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`General commands <Commands_all>` | :doc:`Fix styles <Commands_fix>`   | :doc:`Compute styles <Commands_compute>` |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :doc:`Pair styles <Commands_pair>`     | :doc:`Bond styles <Commands_bond>` | :ref:`Angle styles <angle>`              |
++----------------------------------------+------------------------------------+------------------------------------------+
+| :ref:`Dihedral styles <dihedral>`      | :ref:`Improper styles <improper>`  | :doc:`KSpace styles <Commands_kspace>`   |
++----------------------------------------+------------------------------------+------------------------------------------+
+
+Pair\_style potentials
+======================
+
+All LAMMPS :doc:`pair\_style <pair_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:`none <pair_none>`                                      | :doc:`zero <pair_zero>`                                           | :doc:`hybrid (k) <pair_hybrid>`                     | :doc:`hybrid/overlay (k) <pair_hybrid>`                     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+|                                                              |                                                                   |                                                     |                                                             |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`adp (o) <pair_adp>`                                    | :doc:`agni (o) <pair_agni>`                                       | :doc:`airebo (io) <pair_airebo>`                    | :doc:`airebo/morse (io) <pair_airebo>`                      |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`atm <pair_atm>`                                        | :doc:`awpmd/cut <pair_awpmd>`                                     | :doc:`beck (go) <pair_beck>`                        | :doc:`body/nparticle <pair_body_nparticle>`                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`body/rounded/polygon <pair_body_rounded_polygon>`      | :doc:`body/rounded/polyhedron <pair_body_rounded_polyhedron>`     | :doc:`bop <pair_bop>`                               | :doc:`born (go) <pair_born>`                                |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`born/coul/dsf <pair_born>`                             | :doc:`born/coul/dsf/cs <pair_cs>`                                 | :doc:`born/coul/long (go) <pair_born>`              | :doc:`born/coul/long/cs (g) <pair_cs>`                      |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`born/coul/msm (o) <pair_born>`                         | :doc:`born/coul/wolf (go) <pair_born>`                            | :doc:`born/coul/wolf/cs (g) <pair_cs>`              | :doc:`brownian (o) <pair_brownian>`                         |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`brownian/poly (o) <pair_brownian>`                     | :doc:`buck (giko) <pair_buck>`                                    | :doc:`buck/coul/cut (giko) <pair_buck>`             | :doc:`buck/coul/long (giko) <pair_buck>`                    |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`buck/coul/long/cs <pair_cs>`                           | :doc:`buck/coul/msm (o) <pair_buck>`                              | :doc:`buck/long/coul/long (o) <pair_buck_long>`     | :doc:`buck/mdf <pair_mdf>`                                  |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`buck6d/coul/gauss/dsf <pair_buck6d_coul_gauss>`        | :doc:`buck6d/coul/gauss/long <pair_buck6d_coul_gauss>`            | :doc:`colloid (go) <pair_colloid>`                  | :doc:`comb (o) <pair_comb>`                                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`comb3 <pair_comb>`                                     | :doc:`cosine/squared <pair_cosine_squared>`                       | :doc:`coul/cut (gko) <pair_coul>`                   | :doc:`coul/cut/soft (o) <pair_fep_soft>`                    |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`coul/debye (gko) <pair_coul>`                          | :doc:`coul/diel (o) <pair_coul_diel>`                             | :doc:`coul/dsf (gko) <pair_coul>`                   | :doc:`coul/long (gko) <pair_coul>`                          |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`coul/long/cs (g) <pair_cs>`                            | :doc:`coul/long/soft (o) <pair_fep_soft>`                         | :doc:`coul/msm (o) <pair_coul>`                     | :doc:`coul/shield <pair_coul_shield>`                       |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`coul/streitz <pair_coul>`                              | :doc:`coul/wolf (ko) <pair_coul>`                                 | :doc:`coul/wolf/cs <pair_cs>`                       | :doc:`dpd (gio) <pair_dpd>`                                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`dpd/fdt <pair_dpd_fdt>`                                | :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`                          | :doc:`dpd/tstat (go) <pair_dpd>`                    | :doc:`dsmc <pair_dsmc>`                                     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`e3b <pair_e3b>`                                        | :doc:`drip <pair_drip>`                                           | :doc:`eam (gikot) <pair_eam>`                       | :doc:`eam/alloy (gikot) <pair_eam>`                         |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`eam/cd (o) <pair_eam>`                                 | :doc:`eam/cd/old (o) <pair_eam>`                                  | :doc:`eam/fs (gikot) <pair_eam>`                    | :doc:`edip (o) <pair_edip>`                                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`edip/multi <pair_edip>`                                | :doc:`edpd <pair_meso>`                                           | :doc:`eff/cut <pair_eff>`                           | :doc:`eim (o) <pair_eim>`                                   |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`exp6/rx (k) <pair_exp6_rx>`                            | :doc:`extep <pair_extep>`                                         | :doc:`gauss (go) <pair_gauss>`                      | :doc:`gauss/cut (o) <pair_gauss>`                           |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`gayberne (gio) <pair_gayberne>`                        | :doc:`gran/hertz/history (o) <pair_gran>`                         | :doc:`gran/hooke (o) <pair_gran>`                   | :doc:`gran/hooke/history (ko) <pair_gran>`                  |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`granular <pair_granular>`                              | :doc:`gw <pair_gw>`                                               | :doc:`gw/zbl <pair_gw>`                             | :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`          |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`        | :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`                   | :doc:`kim <pair_kim>`                               | :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`        | :doc:`lcbop <pair_lcbop>`                                         | :doc:`lebedeva/z <pair_lebedeva_z>`                 | :doc:`lennard/mdf <pair_mdf>`                               |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`line/lj <pair_line_lj>`                                | :doc:`list <pair_list>`                                           | :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`    | :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`    |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`             | :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`               | :doc:`lj/charmm/coul/msm (o) <pair_charmm>`         | :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`            |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/charmmfsw/coul/long <pair_charmm>`                  | :doc:`lj/class2 (gko) <pair_class2>`                              | :doc:`lj/class2/coul/cut (ko) <pair_class2>`        | :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`              |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/class2/coul/long (gko) <pair_class2>`               | :doc:`lj/class2/coul/long/soft <pair_fep_soft>`                   | :doc:`lj/class2/soft <pair_fep_soft>`               | :doc:`lj/cubic (go) <pair_lj_cubic>`                        |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/cut (gikot) <pair_lj>`                              | :doc:`lj/cut/coul/cut (gko) <pair_lj>`                            | :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`     | :doc:`lj/cut/coul/debye (gko) <pair_lj>`                    |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/cut/coul/dsf (gko) <pair_lj>`                       | :doc:`lj/cut/coul/long (gikot) <pair_lj>`                         | :doc:`lj/cut/coul/long/cs <pair_cs>`                | :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`            |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/cut/coul/msm (go) <pair_lj>`                        | :doc:`lj/cut/coul/wolf (o) <pair_lj>`                             | :doc:`lj/cut/dipole/cut (go) <pair_dipole>`         | :doc:`lj/cut/dipole/long (g) <pair_dipole>`                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/cut/dipole/sf (go) <pair_dipole>`                   | :doc:`lj/cut/soft (o) <pair_fep_soft>`                            | :doc:`lj/cut/thole/long (o) <pair_thole>`           | :doc:`lj/cut/tip4p/cut (o) <pair_lj>`                       |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/cut/tip4p/long (ot) <pair_lj>`                      | :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`                 | :doc:`lj/expand (gko) <pair_lj_expand>`             | :doc:`lj/expand/coul/long (g) <pair_lj_expand>`             |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/gromacs (gko) <pair_gromacs>`                       | :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`                | :doc:`lj/long/coul/long (iot) <pair_lj_long>`       | :doc:`lj/long/dipole/long <pair_dipole>`                    |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/long/tip4p/long (o) <pair_lj_long>`                 | :doc:`lj/mdf <pair_mdf>`                                          | :doc:`lj/sdk (gko) <pair_sdk>`                      | :doc:`lj/sdk/coul/long (go) <pair_sdk>`                     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/sdk/coul/msm (o) <pair_sdk>`                        | :doc:`lj/sf/dipole/sf (go) <pair_dipole>`                         | :doc:`lj/smooth (o) <pair_lj_smooth>`               | :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`         |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>` | :doc:`lj96/cut (go) <pair_lj96>`                                  | :doc:`local/density <pair_local_density>`           | :doc:`lubricate (o) <pair_lubricate>`                       |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`lubricate/poly (o) <pair_lubricate>`                   | :doc:`lubricateU <pair_lubricateU>`                               | :doc:`lubricateU/poly <pair_lubricateU>`            | :doc:`mdpd <pair_meso>`                                     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`mdpd/rhosum <pair_meso>`                               | :doc:`meam/c <pair_meamc>`                                        | :doc:`meam/spline (o) <pair_meam_spline>`           | :doc:`meam/sw/spline <pair_meam_sw_spline>`                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`mgpt <pair_mgpt>`                                      | :doc:`mie/cut (g) <pair_mie>`                                     | :doc:`momb <pair_momb>`                             | :doc:`morse (gkot) <pair_morse>`                            |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`morse/smooth/linear (o) <pair_morse>`                  | :doc:`morse/soft <pair_fep_soft>`                                 | :doc:`multi/lucy <pair_multi_lucy>`                 | :doc:`multi/lucy/rx (k) <pair_multi_lucy_rx>`               |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`nb3b/harmonic <pair_nb3b_harmonic>`                    | :doc:`nm/cut (o) <pair_nm>`                                       | :doc:`nm/cut/coul/cut (o) <pair_nm>`                | :doc:`nm/cut/coul/long (o) <pair_nm>`                       |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`oxdna/coaxstk <pair_oxdna>`                            | :doc:`oxdna/excv <pair_oxdna>`                                    | :doc:`oxdna/hbond <pair_oxdna>`                     | :doc:`oxdna/stk <pair_oxdna>`                               |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`oxdna/xstk <pair_oxdna>`                               | :doc:`oxdna2/coaxstk <pair_oxdna2>`                               | :doc:`oxdna2/dh <pair_oxdna2>`                      | :doc:`oxdna2/excv <pair_oxdna2>`                            |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`oxdna2/hbond <pair_oxdna2>`                            | :doc:`oxdna2/stk <pair_oxdna2>`                                   | :doc:`oxdna2/xstk <pair_oxdna2>`                    | :doc:`peri/eps <pair_peri>`                                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`peri/lps (o) <pair_peri>`                              | :doc:`peri/pmb (o) <pair_peri>`                                   | :doc:`peri/ves <pair_peri>`                         | :doc:`polymorphic <pair_polymorphic>`                       |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`python <pair_python>`                                  | :doc:`quip <pair_quip>`                                           | :doc:`reax/c (ko) <pair_reaxc>`                     | :doc:`rebo (io) <pair_airebo>`                              |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`resquared (go) <pair_resquared>`                       | :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | :doc:`smd/hertz <pair_smd_hertz>`                   | :doc:`smd/tlsph <pair_smd_tlsph>`                           |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`      | :doc:`smd/ulsph <pair_smd_ulsph>`                                 | :doc:`smtbq <pair_smtbq>`                           | :doc:`snap (k) <pair_snap>`                                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`snap (k) <pair_snap>`                                  | :doc:`soft (go) <pair_soft>`                                      | :doc:`sph/heatconduction <pair_sph_heatconduction>` | :doc:`sph/idealgas <pair_sph_idealgas>`                     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`sph/lj <pair_sph_lj>`                                  | :doc:`sph/rhosum <pair_sph_rhosum>`                               | :doc:`sph/taitwater <pair_sph_taitwater>`           | :doc:`sph/taitwater/morris <pair_sph_taitwater_morris>`     |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`spin/dipole/cut <pair_spin_dipole>`                    | :doc:`spin/dipole/long <pair_spin_dipole>`                        | :doc:`spin/dmi <pair_spin_dmi>`                     | :doc:`spin/exchange <pair_spin_exchange>`                   |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`spin/magelec <pair_spin_magelec>`                      | :doc:`spin/neel <pair_spin_neel>`                                 | :doc:`srp <pair_srp>`                               | :doc:`sw (giko) <pair_sw>`                                  |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`table (gko) <pair_table>`                              | :doc:`table/rx (k) <pair_table_rx>`                               | :doc:`tdpd <pair_meso>`                             | :doc:`tersoff (giko) <pair_tersoff>`                        |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`tersoff/mod (gko) <pair_tersoff_mod>`                  | :doc:`tersoff/mod/c (o) <pair_tersoff_mod>`                       | :doc:`tersoff/table (o) <pair_tersoff>`             | :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`thole <pair_thole>`                                    | :doc:`tip4p/cut (o) <pair_coul>`                                  | :doc:`tip4p/long (o) <pair_coul>`                   | :doc:`tip4p/long/soft (o) <pair_fep_soft>`                  |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`tri/lj <pair_tri_lj>`                                  | :doc:`ufm (got) <pair_ufm>`                                       | :doc:`vashishta (gko) <pair_vashishta>`             | :doc:`vashishta/table (o) <pair_vashishta>`                 |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+| :doc:`yukawa (gko) <pair_yukawa>`                            | :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`                  | :doc:`zbl (gko) <pair_zbl>`                         |                                                             |
++--------------------------------------------------------------+-------------------------------------------------------------------+-----------------------------------------------------+-------------------------------------------------------------+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_parse.rst

@@ -1,13 +1,5 @@
-"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
-Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-Parsing rules for input scripts :h3
+Parsing rules for input scripts
+===============================
 
 Each non-blank line in the input script is treated as a command.
 LAMMPS commands are case sensitive.  Command names are lower-case, as
@@ -30,6 +22,10 @@ comment after a trailing "&" character will prevent the command from
 continuing on the next line.  Also note that for multi-line commands a
 single leading "#" will comment out the entire command.
 
+.. code-block:: LAMMPS
+
+   # this is a comment
+
 (3) The line is searched repeatedly for $ characters, which indicate
 variables that are replaced with a text string.  See an exception in
 (6).
@@ -37,11 +33,11 @@ variables that are replaced with a text string.  See an exception in
 If the $ is followed by curly brackets, then the variable name is the
 text inside the curly brackets.  If no curly brackets follow the $,
 then the variable name is the single character immediately following
-the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+the $.  Thus ${myTemp} and $x refer to variable names "myTemp" and
 "x".
 
 How the variable is converted to a text string depends on what style
-of variable it is; see the "variable"_variable.html doc page for details.
+of variable it is; see the :doc:`variable <variable>` doc page for details.
 It can be a variable that stores multiple text strings, and return one
 of them.  The returned text string can be multiple "words" (space
 separated) which will then be interpreted as multiple arguments in the
@@ -50,17 +46,23 @@ will be evaluated and its numeric result returned as a string.
 
 As a special case, if the $ is followed by parenthesis, then the text
 inside the parenthesis is treated as an "immediate" variable and
-evaluated as an "equal-style variable"_variable.html.  This is a way
+evaluated as an :doc:`equal-style variable <variable>`.  This is a way
 to use numeric formulas in an input script without having to assign
 them to variable names.  For example, these 3 input script lines:
 
-variable X equal (xlo+xhi)/2+sqrt(v_area)
-region 1 block $X 2 INF INF EDGE EDGE
-variable X delete :pre
+
+.. code-block:: LAMMPS
+
+   variable X equal (xlo+xhi)/2+sqrt(v_area)
+   region 1 block $X 2 INF INF EDGE EDGE
+   variable X delete
 
 can be replaced by
 
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+.. code-block:: LAMMPS
+
+   region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
 
 so that you do not have to define (or discard) a temporary variable X.
 
@@ -73,21 +75,27 @@ specified a high-precision "%.20g" is used as the default.
 
 This can be useful for formatting print output to a desired precision:
 
-print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+.. code-block:: LAMMPS
+
+   print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
 
 Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
 
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
+
+.. code-block:: LAMMPS
+
+   variable        a equal 2
+   variable        b2 equal 4
+   print           "B2 = ${b$a}"
 
 Nor can you specify this $($x-1.0) for an immediate variable, but
-you could use $(v_x-1.0), since the latter is valid syntax for an
-"equal-style variable"_variable.html.
+you could use $(v\_x-1.0), since the latter is valid syntax for an
+:doc:`equal-style variable <variable>`.
 
-See the "variable"_variable.html command for more details of how
+See the :doc:`variable <variable>` command for more details of how
 strings are assigned to variables and evaluated, and how they can be
 used in input script commands.
 
@@ -108,29 +116,38 @@ multiple lines of an argument to retain their line breaks, the text
 can be enclosed in triple quotes, in which case "&" characters are not
 needed.  For example:
 
-print "Volume = $v"
-print 'Volume = $v'
-if "$\{steps\} > 1000" then quit
-variable a string "red green blue &
-                   purple orange cyan"
-print """
-System volume = $v
-System temperature = $t
-""" :pre
+
+.. code-block:: LAMMPS
+
+   print "Volume = $v"
+   print 'Volume = $v'
+   if "${steps} > 1000" then quit
+   variable a string "red green blue &
+                      purple orange cyan"
+   print """
+   System volume = $v
+   System temperature = $t
+   """
 
 In each case, the single, double, or triple quotes are removed when
 the single argument they enclose is stored internally.
 
-See the "dump modify format"_dump_modify.html, "print"_print.html,
-"if"_if.html, and "python"_python.html commands for examples.
+See the :doc:`dump modify format <dump_modify>`, :doc:`print <print>`,
+:doc:`if <if>`, and :doc:`python <python>` commands for examples.
 
 A "#" or "$" character that is between quotes will not be treated as a
 comment indicator in (2) or substituted for as a variable in (3).
 
-NOTE: If the argument is itself a command that requires a quoted
-argument (e.g. using a "print"_print.html command as part of an
-"if"_if.html or "run every"_run.html command), then single, double, or
-triple quotes can be nested in the usual manner.  See the doc pages
-for those commands for examples.  Only one of level of nesting is
-allowed, but that should be sufficient for most use cases.
+.. note::
 
+   If the argument is itself a command that requires a quoted
+   argument (e.g. using a :doc:`print <print>` command as part of an
+   :doc:`if <if>` or :doc:`run every <run>` command), then single, double, or
+   triple quotes can be nested in the usual manner.  See the doc pages
+   for those commands for examples.  Only one of level of nesting is
+   allowed, but that should be sufficient for most use cases.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Commands_removed.rst

@@ -0,0 +1,67 @@
+Removed commands and packages
+=============================
+
+This page lists LAMMPS commands and packages that have been removed from
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
+
+Fix ave/spatial and fix ave/spatial/sphere
+------------------------------------------
+
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
+and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
+Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
+
+MEAM package
+------------
+
+The MEAM package has been removed since it was superseded by the
+:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. The code in
+the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+which removes several restrictions (e.g. there can be multiple instances
+in hybrid pair styles) and allows for some optimizations leading
+to better performance.  The new pair style :doc:`meam/c <pair_meamc>` has
+the exact same syntax as the old "meam" pair style and thus pair style
+:doc:`meam <pair_meamc>` is an alias to the new style and backward
+compatibility of old inputs is preserved.
+
+REAX package
+------------
+
+The REAX package has been removed since it was superseded by the
+:ref:`USER-REAXC package <PKG-USER-REAXC>`.  The USER-REAXC
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via USER-OMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
+
+USER-CUDA package
+-----------------
+
+The USER-CUDA package had been removed, since it had been unmaintained
+for a long time and had known bugs and problems.  Significant parts of
+the design were transferred to the
+:ref:`KOKKOS package <PKG-KOKKOS>`, which has similar
+performance characteristics on Nvidia GPUs. Both, the KOKKOS
+and the :ref:`GPU package <PKG-GPU>` are maintained
+and allow running LAMMPS with GPU acceleration.
+
+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
+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

@@ -0,0 +1,91 @@
+Input script structure
+======================
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the :doc:`Examples <Examples>` doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+1. Initialization
+2. Atom definition
+3. Settings
+4. Run a simulation
+
+The last 2 parts can be repeated as many times as desired.  I.e. run a
+simulation, change some settings, run some more, etc.  Each of the 4
+parts is now described in more detail.  Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+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>`.
+
+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>`.
+
+(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
+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
+duplicated to make a larger simulation using the
+:doc:`replicate <replicate>` command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+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>`.
+
+Various simulation parameters are set by these commands:
+: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>`.
+
+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>`
+commands.
+
+Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,
+and :doc:`restart <restart>` commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the :doc:`run <run>`
+command.  Energy minimization (molecular statics) is performed using
+the :doc:`minimize <minimize>` command.  A parallel tempering
+(replica-exchange) simulation can be run using the
+:doc:`temper <temper>` command.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Eqs/angle_charmm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_class2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_a + E_{bb} + E_{ba} \\
-  E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
-  E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
-  E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/angle_cosine.tex

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

doc/src/Eqs/angle_cosine_buck6d.tex

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

doc/src/Eqs/angle_cosine_delta.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [1 - \cos(\theta - \theta_0)]
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_periodic.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]  
-$$
-
-\end{document}

doc/src/Eqs/angle_cosine_shift.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
-$$
-
-\end{document}

doc/src/Eqs/angle_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/angle_cosine_squared.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [\cos(\theta) - \cos(\theta_0)]^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_cross.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
-$$
-
-\end{document}

doc/src/Eqs/angle_dipole_couple.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
--\vec{T_j} & = & \vec{r_{ij}} \times \vec{F_i}\\
-\vec{F_j} & = & -\vec{F_i} \\
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/angle_dipole_gamma.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
-$$
-
-\end{document}

doc/src/Eqs/angle_dipole_potential.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (\cos\gamma - \cos\gamma_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_dipole_torque.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
-           \vec{r_{ij}} \times \vec{\mu_j}
-$$
-\end{document}

doc/src/Eqs/angle_fourier.tex

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

doc/src/Eqs/angle_fourier_simple.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K [ 1.0 + c \cos ( n \theta) ] 
-$$
-
-\end{document}

doc/src/Eqs/angle_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\theta - \theta_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/angle_mm3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
-$$
-
-\end{document}

doc/src/Eqs/angle_quartic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
-$$
-
-\end{document}

doc/src/Eqs/bond_class2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4 
-$$
-
-\end{document}

doc/src/Eqs/bond_fene.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = -0.5 K R_0^2  \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
-  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
-    \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}

doc/src/Eqs/bond_fene_expand.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = -0.5 K R_0^2
-  \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 
-  4 \epsilon \left[ \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - 
-      \Delta\right)}\right)^6 \right] + \epsilon
-$$
-
-\end{document}

doc/src/Eqs/bond_gromos.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$
-   E = K (r^2 - r_0^2)^2
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = K (r - r_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic_shift.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] 
-$$
-
-\end{document}

doc/src/Eqs/bond_harmonic_shift_cut.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right] 
-$$
-
-\end{document}

doc/src/Eqs/bond_mm3.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\thispagestyle{empty}
-$$
-  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
-$$
-
-\end{document}

doc/src/Eqs/bond_morse.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-%   E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2 
-   E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 
-$$
-
-\end{document}

doc/src/Eqs/bond_nonlinear.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
-$$
-
-\end{document}

doc/src/Eqs/bond_oxdna_fene.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$ 
-  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
-$$
-
-\end{document}

doc/src/Eqs/bond_quartic.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-  E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
-  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
-    \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}

doc/src/Errors.rst

@@ -0,0 +1,22 @@
+Errors
+******
+
+These doc pages describe the errors you can encounter when using
+LAMMPS.  The common problems include conceptual issues.  The messages
+and warnings doc pages give complete lists of all the messages the
+code may generate (except those generated by USER packages), with
+additional details for many of them.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Errors_common
+   Errors_bugs
+   Errors_messages
+   Errors_warnings
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Errors_bugs.rst

@@ -0,0 +1,32 @@
+Reporting bugs
+==============
+
+If you are confident that you have found a bug in LAMMPS, follow these
+steps.
+
+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 `mailing list <http://lammps.sandia.gov/mail.html>`_ to see if
+it has been discussed before.
+
+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
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Errors_common.rst

@@ -0,0 +1,128 @@
+Common problems
+===============
+
+If two LAMMPS runs do not produce the exact same answer on different
+machines or different numbers of processors, this is typically not a
+bug.  In theory you should get identical answers on any number of
+processors and on any machine.  In practice, numerical round-off can
+cause slight differences and eventual divergence of molecular dynamics
+phase space trajectories within a few 100s or few 1000s of timesteps.
+However, the statistical properties of the two runs (e.g. average
+energy or temperature) should still be the same.
+
+If the :doc:`velocity <velocity>` command is used to set initial atom
+velocities, a particular atom can be assigned a different velocity
+when the problem is run on a different number of processors or on
+different machines.  If this happens, the phase space trajectories of
+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
+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.
+
+Some commands use random number generators which may be setup to
+produce different random number streams on each processor and hence
+will produce different effects when run on different numbers of
+processors.  A commonly-used example is the :doc:`fix langevin <fix_langevin>` command for thermostatting.
+
+A LAMMPS simulation typically has two stages, setup and run.  Most
+LAMMPS errors are detected at setup time; others like a bond
+stretching too far may not occur until the middle of a run.
+
+LAMMPS tries to flag errors and print informative error messages so
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+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
+doesn't catch that you think it should flag, please send an email to
+the `developers <http://lammps.sandia.gov/authors.html>`_.
+
+If you get an error message about an invalid command in your input
+script, you can determine what command is causing the problem by
+looking in the log.lammps file or using the :doc:`echo command <echo>`
+to see it on the screen.  If you get an error like "Invalid ...
+style", with ... being fix, compute, pair, etc, it means that you
+mistyped the style name or that the command is part of an optional
+package which was not compiled into your executable.  The list of
+available styles in your executable can be listed by using :doc:`the -h command-line swith <Run_options>`.  The installation and
+compilation of optional packages is explained on the :doc:`Build packages <Build_package>` doc page.
+
+For a given command, LAMMPS expects certain arguments in a specified
+order.  If you mess this up, LAMMPS will often flag the error, but it
+may also simply read a bogus argument and assign a value that is
+valid, but not what you wanted.  E.g. trying to read the string "abc"
+as an integer value of 0.  Careful reading of the associated doc page
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+
+.. parsed-literal::
+
+   ERROR: Expected integer parameter instead of '1.0' in input script or data file
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax *v\_name* for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax $\ *name* is performed while
+reading the input and before parsing commands,
+
+.. note::
+
+   Using a variable reference (i.e. *v\_name*) is only allowed if
+   the documentation of the corresponding command explicitly says it is.
+   Otherwise, you will receive an error message of this kind:
+
+
+.. parsed-literal::
+
+   ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
+
+Generally, LAMMPS will print a message to the screen and logfile and
+exit gracefully when it encounters a fatal error.  Sometimes it will
+print a WARNING to the screen and logfile and continue on; you can
+decide if the WARNING is important or not.  A WARNING message that is
+generated in the middle of a run is only printed to the screen, not to
+the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
+crashes or hangs without spitting out an error message first then it
+could be a bug (see :doc:`this section <Errors_bugs>`) or one of the following
+cases:
+
+LAMMPS runs in the available memory a processor allows to be
+allocated.  Most reasonable MD runs are compute limited, not memory
+limited, so this shouldn't be a bottleneck on most platforms.  Almost
+all large memory allocations in the code are done via C-style malloc's
+which will generate an error message if you run out of memory.
+Smaller chunks of memory are allocated via C++ "new" statements.  If
+you are unlucky you could run out of memory just when one of these
+small requests is made, in which case the code will crash or hang (in
+parallel), since LAMMPS doesn't trap on those errors.
+
+Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+typically due to invalid physics and numerics that your simulation is
+computing.  If you see wild thermodynamic values or NaN values in your
+LAMMPS output, something is wrong with your simulation.  If you
+suspect this is happening, it is a good idea to print out
+thermodynamic info frequently (e.g. every timestep) via the
+:doc:`thermo <thermo>` so you can monitor what is happening.
+Visualizing the atom movement is also a good idea to insure your model
+is behaving as you expect.
+
+In parallel, one way LAMMPS can hang is due to how different MPI
+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

doc/src/Errors_warnings.rst

@@ -0,0 +1,796 @@
+Warning messages
+================
+
+This is an alphabetic list of the WARNING messages LAMMPS prints out
+and the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  Warning messages
+also list the source file and line number where the warning was
+generated.  For example, a message like this:
+
+
+.. parsed-literal::
+
+   WARNING: Bond atom missing in box size check (domain.cpp:187)
+
+means that line #187 in the file src/domain.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+
+Note that warning messages from :doc:`user-contributed packages <Packages_user>` are not listed here.  If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
+
+Doc page with :doc:`ERROR messages <Errors_messages>`
+
+
+----------
+
+
+
+
+*Adjusting Coulombic cutoff for MSM, new cutoff = %g*
+   The adjust/cutoff command is turned on and the Coulombic cutoff has been
+   adjusted to match the user-specified accuracy.
+
+*Angle atoms missing at step %ld*
+   One or more of 3 atoms needed to compute a particular angle are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the angle has blown apart and an atom is
+   too far away.
+
+*Angle style in data file differs from currently defined angle style*
+   Self-explanatory.
+
+*Angles are defined but no angle style is set*
+   The topology contains angles, but there are no angle forces computed
+   since there was no angle\_style command.
+
+*Atom style in data file differs from currently defined atom style*
+   Self-explanatory.
+
+*Bond atom missing in box size check*
+   The 2nd atoms needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond atom missing in image check*
+   The 2nd atom in a particular bond is missing on this processor.
+   Typically this is because the pairwise cutoff is set too short or the
+   bond has blown apart and an atom is too far away.
+
+*Bond atoms missing at step %ld*
+   The 2nd atom needed to compute a particular bond is missing on this
+   processor.  Typically this is because the pairwise cutoff is set too
+   short or the bond has blown apart and an atom is too far away.
+
+*Bond style in data file differs from currently defined bond style*
+   Self-explanatory.
+
+*Bonds are defined but no bond style is set*
+   The topology contains bonds, but there are no bond forces computed
+   since there was no bond\_style command.
+
+*Bond/angle/dihedral extent > half of periodic box length*
+   This is a restriction because LAMMPS can be confused about which image
+   of an atom in the bonded interaction is the correct one to use.
+   "Extent" in this context means the maximum end-to-end length of the
+   bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
+   length, multiplying by the number of bonds in the interaction (e.g. 3
+   for a dihedral) and adding a small amount of stretch.
+
+*Bond/react: Atom affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the superimpose
+   file. This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
+*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
+   Self-explanatory.
+
+*Calling write\_dump before a full system init.*
+   The write\_dump command is used before the system has been fully
+   initialized as part of a 'run' or 'minimize' command. Not all dump
+   styles and features are fully supported at this point and thus the
+   command may fail or produce incomplete or incorrect output. Insert
+   a "run 0" command, if a full system init is required.
+
+*Cannot count rigid body degrees-of-freedom before bodies are fully initialized*
+   This means the temperature associated with the rigid bodies may be
+   incorrect on this timestep.
+
+*Cannot count rigid body degrees-of-freedom before bodies are initialized*
+   This means the temperature associated with the rigid bodies may be
+   incorrect on this timestep.
+
+*Cannot include log terms without 1/r terms; setting flagHI to 1*
+   Self-explanatory.
+
+*Cannot include log terms without 1/r terms; setting flagHI to 1.*
+   Self-explanatory.
+
+*Charges are set, but coulombic solver is not used*
+   Self-explanatory.
+
+*Charges did not converge at step %ld: %lg*
+   Self-explanatory.
+
+*Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost*
+   The communication cutoff defaults to the maximum of what is inferred from
+   pair and bond styles (will be zero, if none are defined) and what is specified
+   via :doc:`comm\_modify cutoff <comm_modify>` (defaults to 0.0).  If this results
+   to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+   incorrect periodic images of atoms in interaction lists.  To avoid, either use
+   :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm\_modify cutoff <comm_modify>`.
+
+*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
+   Self-explanatory.
+
+*Compute cna/atom cutoff may be too large to find ghost atom neighbors*
+   The neighbor cutoff used may not encompass enough ghost atoms
+   to perform this operation correctly.
+
+*Computing temperature of portions of rigid bodies*
+   The group defined by the temperature compute does not encompass all
+   the atoms in one or more rigid bodies, so the change in
+   degrees-of-freedom for the atoms in those partial rigid bodies will
+   not be accounted for.
+
+*Create\_bonds max distance > minimum neighbor cutoff*
+   This means atom pairs for some atom types may not be in the neighbor
+   list and thus no bond can be created between them.
+
+*Delete\_atoms cutoff > minimum neighbor cutoff*
+   This means atom pairs for some atom types may not be in the neighbor
+   list and thus an atom in that pair cannot be deleted.
+
+*Dihedral atoms missing at step %ld*
+   One or more of 4 atoms needed to compute a particular dihedral are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the dihedral has blown apart and an atom is
+   too far away.
+
+*Dihedral problem*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Dihedral problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Dihedral style in data file differs from currently defined dihedral style*
+   Self-explanatory.
+
+*Dihedrals are defined but no dihedral style is set*
+   The topology contains dihedrals, but there are no dihedral forces computed
+   since there was no dihedral\_style command.
+
+*Dump dcd/xtc timestamp may be wrong with fix dt/reset*
+   If the fix changes the timestep, the dump dcd file will not
+   reflect the change.
+
+*Energy due to X extra global DOFs will be included in minimizer energies*
+   When using fixes like box/relax, the potential energy used by the minimizer
+   is augmented by an additional energy provided by the fix. Thus the printed
+   converged energy may be different from the total potential energy.
+
+*Estimated error in splitting of dispersion coeffs is %g*
+   Error is greater than 0.0001 percent.
+
+*Ewald/disp Newton solver failed, using old method to estimate g\_ewald*
+   Self-explanatory. Choosing a different cutoff value may help.
+
+*FENE bond too long*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*FENE bond too long: %ld %d %d %g*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*FENE bond too long: %ld %g*
+   A FENE bond has stretched dangerously far.  It's interaction strength
+   will be truncated to attempt to prevent the bond from blowing up.
+
+*Fix SRD walls overlap but fix srd overlap not set*
+   You likely want to set this in your input script.
+
+*Fix bond/swap will ignore defined angles*
+   See the doc page for fix bond/swap for more info on this
+   restriction.
+
+*Fix deposit near setting < possible overlap separation %g*
+   This test is performed for finite size particles with a diameter, not
+   for point particles.  The near setting is smaller than the particle
+   diameter which can lead to overlaps.
+
+*Fix evaporate may delete atom with non-zero molecule ID*
+   This is probably an error, since you should not delete only one atom
+   of a molecule.
+
+*Fix gcmc using full\_energy option*
+   Fix gcmc has automatically turned on the full\_energy option since it
+   is required for systems like the one specified by the user. User input
+   included one or more of the following: kspace, triclinic, a hybrid
+   pair style, an eam pair style, or no "single" function for the pair
+   style.
+
+*Fix langevin gjf using random gaussians is not implemented with kokkos*
+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.
+
+*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
+   Self-explanatory.
+
+*Fix qeq has non-zero lower Taper radius cutoff*
+   Absolute value must be <= 0.01.
+
+*Fix qeq has very low Taper radius cutoff*
+   Value should typically be >= 5.0.
+
+*Fix qeq/dynamic tolerance may be too small for damped dynamics*
+   Self-explanatory.
+
+*Fix qeq/fire tolerance may be too small for damped fires*
+   Self-explanatory.
+
+*Fix rattle should come after all other integration fixes*
+   This fix is designed to work after all other integration fixes change
+   atom positions.  Thus it should be the last integration fix specified.
+   If not, it will not satisfy the desired constraints as well as it
+   otherwise would.
+
+*Fix recenter should come after all other integration fixes*
+   Other fixes may change the position of the center-of-mass, so
+   fix recenter should come last.
+
+*Fix srd SRD moves may trigger frequent reneighboring*
+   This is because the SRD particles may move long distances.
+
+*Fix srd grid size > 1/4 of big particle diameter*
+   This may cause accuracy problems.
+
+*Fix srd particle moved outside valid domain*
+   This may indicate a problem with your simulation parameters.
+
+*Fix srd particles may move > big particle diameter*
+   This may cause accuracy problems.
+
+*Fix srd viscosity < 0.0 due to low SRD density*
+   This may cause accuracy problems.
+
+*Fixes cannot send data in Kokkos communication, switching to classic communication*
+   This is current restriction with Kokkos.
+
+*For better accuracy use 'pair\_modify table 0'*
+   The user-specified force accuracy cannot be achieved unless the table
+   feature is disabled by using 'pair\_modify table 0'.
+
+*Geometric mixing assumed for 1/r\^6 coefficients*
+   Self-explanatory.
+
+*Group for fix\_modify temp != fix group*
+   The fix\_modify command is specifying a temperature computation that
+   computes a temperature on a different group of atoms than the fix
+   itself operates on.  This is probably not what you want to do.
+
+*H matrix size has been exceeded: m\_fill=%d H.m=%d\n*
+   This is the size of the matrix.
+
+*Ignoring unknown or incorrect info command flag*
+   Self-explanatory.  An unknown argument was given to the info command.
+   Compare your input with the documentation.
+
+*Improper atoms missing at step %ld*
+   One or more of 4 atoms needed to compute a particular improper are
+   missing on this processor.  Typically this is because the pairwise
+   cutoff is set too short or the improper has blown apart and an atom is
+   too far away.
+
+*Improper problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed improper atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Improper style in data file differs from currently defined improper style*
+   Self-explanatory.
+
+*Impropers are defined but no improper style is set*
+   The topology contains impropers, but there are no improper forces computed
+   since there was no improper\_style command.
+
+*Inconsistent image flags*
+   The image flags for a pair on bonded atoms appear to be inconsistent.
+   Inconsistent means that when the coordinates of the two atoms are
+   unwrapped using the image flags, the two atoms are far apart.
+   Specifically they are further apart than half a periodic box length.
+   Or they are more than a box length apart in a non-periodic dimension.
+   This is usually due to the initial data file not having correct image
+   flags for the 2 atoms in a bond that straddles a periodic boundary.
+   They should be different by 1 in that case.  This is a warning because
+   inconsistent image flags will not cause problems for dynamics or most
+   LAMMPS simulations.  However they can cause problems when such atoms
+   are used with the fix rigid or replicate commands.  Note that if you
+   have an infinite periodic crystal with bonds then it is impossible to
+   have fully consistent image flags, since some bonds will cross
+   periodic boundaries and connect two atoms with the same image
+   flag.
+
+*Increasing communication cutoff for GPU style*
+   The pair style has increased the communication cutoff to be consistent with
+   the communication cutoff requirements for this pair style when run on the GPU.
+
+*KIM Model does not provide 'energy'; Potential energy will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'forces'; Forces will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
+   Self-explanatory.
+
+*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
+   Self-explanatory.
+
+*Kspace\_modify slab param < 2.0 may cause unphysical behavior*
+   The kspace\_modify slab parameter should be larger to insure periodic
+   grids padded with empty space do not overlap.
+
+*Less insertions than requested*
+   The fix pour command was unsuccessful at finding open space
+   for as many particles as it tried to insert.
+
+*Library error in lammps\_gather\_atoms*
+   This library function cannot be used if atom IDs are not defined
+   or are not consecutively numbered.
+
+*Library error in lammps\_scatter\_atoms*
+   This library function cannot be used if atom IDs are not defined or
+   are not consecutively numbered, or if no atom map is defined.  See the
+   atom\_modify command for details about atom maps.
+
+*Likewise 1-2 special neighbor interactions != 1.0*
+   The topology contains bonds, but there is no bond style defined
+   and a 1-2 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the bond style.
+
+*Likewise 1-3 special neighbor interactions != 1.0*
+   The topology contains angles, but there is no angle style defined
+   and a 1-3 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the angle style.
+
+*Likewise 1-4 special neighbor interactions != 1.0*
+   The topology contains dihedrals, but there is no dihedral style defined
+   and a 1-4 special neighbor scaling factor was not 1.0. This
+   means that pair style interactions may have scaled or missing
+   pairs in the neighbor list in expectation of interactions for
+   those pairs being computed from the dihedral style.
+
+*Lost atoms via change\_box: original %ld current %ld*
+   The command options you have used caused atoms to be lost.
+
+*Lost atoms via displace\_atoms: original %ld current %ld*
+   The command options you have used caused atoms to be lost.
+
+*Lost atoms: original %ld current %ld*
+   Lost atoms are checked for each time thermo output is done.  See the
+   thermo\_modify lost command for options.  Lost atoms usually indicate
+   bad dynamics, e.g. atoms have been blown far out of the simulation
+   box, or moved further than one processor's sub-domain away before
+   reneighboring.
+
+*MSM mesh too small, increasing to 2 points in each direction*
+   Self-explanatory.
+
+*Mismatch between velocity and compute groups*
+   The temperature computation used by the velocity command will not be
+   on the same group of atoms that velocities are being set for.
+
+*Mixing forced for lj coefficients*
+   Self-explanatory.
+
+*Molecule attributes do not match system attributes*
+   An attribute is specified (e.g. diameter, charge) that is
+   not defined for the specified atom style.
+
+*Molecule has bond topology but no special bond settings*
+   This means the bonded atoms will not be excluded in pair-wise
+   interactions.
+
+*Molecule template for create\_atoms has multiple molecules*
+   The create\_atoms command will only create molecules of a single type,
+   i.e. the first molecule in the template.
+
+*Molecule template for fix gcmc has multiple molecules*
+   The fix gcmc command will only create molecules of a single type,
+   i.e. the first molecule in the template.
+
+*Molecule template for fix shake has multiple molecules*
+   The fix shake command will only recognize molecules of a single
+   type, i.e. the first molecule in the template.
+
+*More than one compute centro/atom*
+   It is not efficient to use compute centro/atom more than once.
+
+*More than one compute cluster/atom*
+   It is not efficient to use compute cluster/atom  more than once.
+
+*More than one compute cna/atom defined*
+   It is not efficient to use compute cna/atom  more than once.
+
+*More than one compute contact/atom*
+   It is not efficient to use compute contact/atom more than once.
+
+*More than one compute coord/atom*
+   It is not efficient to use compute coord/atom more than once.
+
+*More than one compute damage/atom*
+   It is not efficient to use compute ke/atom more than once.
+
+*More than one compute dilatation/atom*
+   Self-explanatory.
+
+*More than one compute erotate/sphere/atom*
+   It is not efficient to use compute erorate/sphere/atom more than once.
+
+*More than one compute hexorder/atom*
+   It is not efficient to use compute hexorder/atom more than once.
+
+*More than one compute ke/atom*
+   It is not efficient to use compute ke/atom more than once.
+
+*More than one compute orientorder/atom*
+   It is not efficient to use compute orientorder/atom more than once.
+
+*More than one compute plasticity/atom*
+   Self-explanatory.
+
+*More than one compute sna/atom*
+   Self-explanatory.
+
+*More than one compute snad/atom*
+   Self-explanatory.
+
+*More than one compute snav/atom*
+   Self-explanatory.
+
+*More than one fix poems*
+   It is not efficient to use fix poems more than once.
+
+*More than one fix rigid*
+   It is not efficient to use fix rigid more than once.
+
+*Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
+   This is because excluding specific pair interactions also excludes
+   them from long-range interactions which may not be the desired effect.
+   The special\_bonds command handles this consistently by insuring
+   excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
+   consistently by both the short-range pair style and the long-range
+   solver.  This is not done for exclusions of charged atom pairs via the
+   neigh\_modify exclude command.
+
+*New thermo\_style command, previous thermo\_modify settings will be lost*
+   If a thermo\_style command is used after a thermo\_modify command, the
+   settings changed by the thermo\_modify command will be reset to their
+   default values.  This is because the thermo\_modify command acts on
+   the currently defined thermo style, and a thermo\_style command creates
+   a new style.
+
+*No Kspace calculation with verlet/split*
+   The 2nd partition performs a kspace calculation so the kspace\_style
+   command must be used.
+
+*No automatic unit conversion to XTC file format conventions possible for units lj*
+   This means no scaling will be performed.
+
+*No fixes defined, atoms won't move*
+   If you are not using a fix like nve, nvt, npt then atom velocities and
+   coordinates will not be updated during timestepping.
+
+*No joints between rigid bodies, use fix rigid instead*
+   The bodies defined by fix poems are not connected by joints.  POEMS
+   will integrate the body motion, but it would be more efficient to use
+   fix rigid.
+
+*Not using real units with pair reax*
+   This is most likely an error, unless you have created your own ReaxFF
+   parameter file in a different set of units.
+
+*Number of MSM mesh points changed to be a multiple of 2*
+   MSM requires that the number of grid points in each direction be a multiple
+   of two and the number of grid points in one or more directions have been
+   adjusted to meet this requirement.
+
+*OMP\_NUM\_THREADS environment is not set.*
+   This environment variable must be set appropriately to use the
+   USER-OMP package.
+
+*One or more atoms are time integrated more than once*
+   This is probably an error since you typically do not want to
+   advance the positions or velocities of an atom more than once
+   per timestep.
+
+*One or more chunks do not contain all atoms in molecule*
+   This may not be what you intended.
+
+*One or more dynamic groups may not be updated at correct point in timestep*
+   If there are other fixes that act immediately after the initial stage
+   of time integration within a timestep (i.e. after atoms move), then
+   the command that sets up the dynamic group should appear after those
+   fixes.  This will insure that dynamic group assignments are made
+   after all atoms have moved.
+
+*One or more respa levels compute no forces*
+   This is computationally inefficient.
+
+*Pair COMB charge %.10f with force %.10f hit max barrier*
+   Something is possibly wrong with your model.
+
+*Pair COMB charge %.10f with force %.10f hit min barrier*
+   Something is possibly wrong with your model.
+
+*Pair brownian needs newton pair on for momentum conservation*
+   Self-explanatory.
+
+*Pair dpd needs newton pair on for momentum conservation*
+   Self-explanatory.
+
+*Pair dsmc: num\_of\_collisions > number\_of\_A*
+   Collision model in DSMC is breaking down.
+
+*Pair dsmc: num\_of\_collisions > number\_of\_B*
+   Collision model in DSMC is breaking down.
+
+*Pair style in data file differs from currently defined pair style*
+   Self-explanatory.
+
+*Pair style restartinfo set but has no restart support*
+   This pair style has a bug, where it does not support reading and
+   writing information to a restart file, but does not set the member
+   variable "restartinfo" to 0 as required in that case.
+
+*Particle deposition was unsuccessful*
+   The fix deposit command was not able to insert as many atoms as
+   needed.  The requested volume fraction may be too high, or other atoms
+   may be in the insertion region.
+
+*Proc sub-domain size < neighbor skin, could lead to lost atoms*
+   The decomposition of the physical domain (likely due to load
+   balancing) has led to a processor's sub-domain being smaller than the
+   neighbor skin in one or more dimensions.  Since reneighboring is
+   triggered by atoms moving the skin distance, this may lead to lost
+   atoms, if an atom moves all the way across a neighboring processor's
+   sub-domain before reneighboring is triggered.
+
+*Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor*
+   This may lead to a larger grid than desired.  See the kspace\_modify overlap
+   command to prevent changing of the PPPM order.
+
+*Replacing a fix, but new group != old group*
+   The ID and style of a fix match for a fix you are changing with a fix
+   command, but the new group you are specifying does not match the old
+   group.
+
+*Replicating in a non-periodic dimension*
+   The parameters for a replicate command will cause a non-periodic
+   dimension to be replicated; this may cause unwanted behavior.
+
+*Resetting reneighboring criteria during PRD*
+   A PRD simulation requires that neigh\_modify settings be delay = 0,
+   every = 1, check = yes.  Since these settings were not in place,
+   LAMMPS changed them and will restore them to their original values
+   after the PRD simulation.
+
+*Resetting reneighboring criteria during TAD*
+   A TAD simulation requires that neigh\_modify settings be delay = 0,
+   every = 1, check = yes.  Since these settings were not in place,
+   LAMMPS changed them and will restore them to their original values
+   after the PRD simulation.
+
+*Resetting reneighboring criteria during minimization*
+   Minimization requires that neigh\_modify settings be delay = 0, every =
+   1, check = yes.  Since these settings were not in place, LAMMPS
+   changed them and will restore them to their original values after the
+   minimization.
+
+*Restart file used different # of processors*
+   The restart file was written out by a LAMMPS simulation running on a
+   different number of processors.  Due to round-off, the trajectories of
+   your restarted simulation may diverge a little more quickly than if
+   you ran on the same # of processors.
+
+*Restart file used different 3d processor grid*
+   The restart file was written out by a LAMMPS simulation running on a
+   different 3d grid of processors.  Due to round-off, the trajectories
+   of your restarted simulation may diverge a little more quickly than if
+   you ran on the same # of processors.
+
+*Restart file used different boundary settings, using restart file values*
+   Your input script cannot change these restart file settings.
+
+*Restart file used different newton bond setting, using restart file value*
+   The restart file value will override the setting in the input script.
+
+*Restart file used different newton pair setting, using input script value*
+   The input script value will override the setting in the restart file.
+
+*Restrain problem: %d %ld %d %d %d %d*
+   Conformation of the 4 listed dihedral atoms is extreme; you may want
+   to check your simulation geometry.
+
+*Running PRD with only one replica*
+   This is allowed, but you will get no parallel speed-up.
+
+*SRD bin shifting turned on due to small lamda*
+   This is done to try to preserve accuracy.
+
+*SRD bin size for fix srd differs from user request*
+   Fix SRD had to adjust the bin size to fit the simulation box.  See the
+   cubic keyword if you want this message to be an error vs warning.
+
+*SRD bins for fix srd are not cubic enough*
+   The bin shape is not within tolerance of cubic.  See the cubic
+   keyword if you want this message to be an error vs warning.
+
+*SRD particle %d started inside big particle %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*SRD particle %d started inside wall %d on step %ld bounce %d*
+   See the inside keyword if you want this message to be an error vs
+   warning.
+
+*Shake determinant < 0.0*
+   The determinant of the quadratic equation being solved for a single
+   cluster specified by the fix shake command is numerically suspect.  LAMMPS
+   will set it to 0.0 and continue.
+
+*Shell command '%s' failed with error '%s'*
+   Self-explanatory.
+
+*Shell command returned with non-zero status*
+   This may indicate the shell command did not operate as expected.
+
+*Should not allow rigid bodies to bounce off reflecting walls*
+   LAMMPS allows this, but their dynamics are not computed correctly.
+
+*Should not use fix nve/limit with fix shake or fix rattle*
+   This will lead to invalid constraint forces in the SHAKE/RATTLE
+   computation.
+
+*Simulations might be very slow because of large number of structure factors*
+   Self-explanatory.
+
+*Slab correction not needed for MSM*
+   Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
+
+*System is not charge neutral, net charge = %g*
+   The total charge on all atoms on the system is not 0.0.
+   For some KSpace solvers this is only a warning.
+
+*Table inner cutoff >= outer cutoff*
+   You specified an inner cutoff for a Coulombic table that is longer
+   than the global cutoff.  Probably not what you wanted.
+
+*Temperature for MSST is not for group all*
+   User-assigned temperature to MSST fix does not compute temperature for
+   all atoms.  Since MSST computes a global pressure, the kinetic energy
+   contribution from the temperature is assumed to also be for all atoms.
+   Thus the pressure used by MSST could be inaccurate.
+
+*Temperature for NPT is not for group all*
+   User-assigned temperature to NPT fix does not compute temperature for
+   all atoms.  Since NPT computes a global pressure, the kinetic energy
+   contribution from the temperature is assumed to also be for all atoms.
+   Thus the pressure used by NPT could be inaccurate.
+
+*Temperature for fix modify is not for group all*
+   The temperature compute is being used with a pressure calculation
+   which does operate on group all, so this may be inconsistent.
+
+*Temperature for thermo pressure is not for group all*
+   User-assigned temperature to thermo via the thermo\_modify command does
+   not compute temperature for all atoms.  Since thermo computes a global
+   pressure, the kinetic energy contribution from the temperature is
+   assumed to also be for all atoms.  Thus the pressure printed by thermo
+   could be inaccurate.
+
+*The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015*
+   Self-explanatory.
+
+*The minimizer does not re-orient dipoles when using fix efield*
+   This means that only the atom coordinates will be minimized,
+   not the orientation of the dipoles.
+
+*Too many common neighbors in CNA %d times*
+   More than the maximum # of neighbors was found multiple times.  This
+   was unexpected.
+
+*Too many inner timesteps in fix ttm*
+   Self-explanatory.
+
+*Too many neighbors in CNA for %d atoms*
+   More than the maximum # of neighbors was found multiple times.  This
+   was unexpected.
+
+*Triclinic box skew is large*
+   The displacement in a skewed direction is normally required to be less
+   than half the box length in that dimension.  E.g. the xy tilt must be
+   between -half and +half of the x box length.  You have relaxed the
+   constraint using the box tilt command, but the warning means that a
+   LAMMPS simulation may be inefficient as a result.
+
+*Use special bonds = 0,1,1 with bond style fene*
+   Most FENE models need this setting for the special\_bonds command.
+
+*Use special bonds = 0,1,1 with bond style fene/expand*
+   Most FENE models need this setting for the special\_bonds command.
+
+*Using a many-body potential with bonds/angles/dihedrals and special\_bond exclusions*
+   This is likely not what you want to do.  The exclusion settings will
+   eliminate neighbors in the neighbor list, which the many-body potential
+   needs to calculated its terms correctly.
+
+*Using compute temp/deform with inconsistent fix deform remap option*
+   Fix nvt/sllod assumes deforming atoms have a velocity profile provided
+   by "remap v" or "remap none" as a fix deform option.
+
+*Using compute temp/deform with no fix deform defined*
+   This is probably an error, since it makes little sense to use
+   compute temp/deform in this case.
+
+*Using fix srd with box deformation but no SRD thermostat*
+   The deformation will heat the SRD particles so this can
+   be dangerous.
+
+*Using kspace solver on system with no charge*
+   Self-explanatory.
+
+*Using largest cut-off for lj/long/dipole/long long long*
+   Self-explanatory.
+
+*Using largest cutoff for buck/long/coul/long*
+   Self-explanatory.
+
+*Using largest cutoff for lj/long/coul/long*
+   Self-explanatory.
+
+*Using largest cutoff for pair\_style lj/long/tip4p/long*
+   Self-explanatory.
+
+*Using package gpu without any pair style defined*
+   Self-explanatory.
+
+*Using pair potential shift with pair\_modify compute no*
+   The shift effects will thus not be computed.
+
+*Using pair tail corrections with nonperiodic system*
+   This is probably a bogus thing to do, since tail corrections are
+   computed by integrating the density of a periodic system out to
+   infinity.
+
+*Using pair tail corrections with pair\_modify compute no*
+   The tail corrections will thus not be computed.
+
+*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c*
+   Self-explanatory.
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Examples.rst

@@ -0,0 +1,235 @@
+Example scripts
+===============
+
+The LAMMPS distribution includes an examples sub-directory with many
+sample problems.  Many are 2d models that run quickly and are
+straightforward to visualize, requiring at most a couple of minutes to
+run on a desktop machine.  Each problem has an input script (in.\*) and
+produces a log file (log.\*) when it runs.  Some use a data file
+(data.\*) of initial coordinates as additional input.  A few sample log
+file run on different machines and different numbers of processors are
+included in the directories to compare your answers to.  E.g. a log
+file like log.date.crack.foo.P means the "crack" example was run on P
+processors of machine "foo" on that date (i.e. with that version of
+LAMMPS).
+
+Many of the input files have commented-out lines for creating dump
+files and image files.
+
+If you uncomment the :doc:`dump <dump>` command in the input script, a
+text dump file will be produced, which can be animated by various
+`visualization programs <http://lammps.sandia.gov/viz.html>`_.
+
+If you uncomment the :doc:`dump image <dump>` command in the input
+script, and assuming you have built LAMMPS with a JPG library, JPG
+snapshot images will be produced when the simulation runs.  They can
+be quickly post-processed into a movie using commands described on the
+:doc:`dump image <dump_image>` doc page.
+
+Animations of many of the examples can be viewed on the Movies section
+of the `LAMMPS web site <lws_>`_.
+
+There are two kinds of sub-directories in the examples dir.  Lowercase
+dirs contain one or a few simple, quick-to-run problems.  Uppercase
+dirs contain up to several complex scripts that illustrate a
+particular kind of simulation method or model.  Some of these run for
+longer times, e.g. to measure a particular quantity.
+
+Lists of both kinds of directories are given below.
+
+
+----------
+
+
+Lowercase directories
+---------------------
+
++-------------+------------------------------------------------------------------+
+| accelerate  | run with various acceleration options (OpenMP, GPU, Phi)         |
++-------------+------------------------------------------------------------------+
+| airebo      | polyethylene with AIREBO potential                               |
++-------------+------------------------------------------------------------------+
+| atm         | Axilrod-Teller-Muto potential example                            |
++-------------+------------------------------------------------------------------+
+| balance     | dynamic load balancing, 2d system                                |
++-------------+------------------------------------------------------------------+
+| body        | body particles, 2d system                                        |
++-------------+------------------------------------------------------------------+
+| cmap        | CMAP 5-body contributions to CHARMM force field                  |
++-------------+------------------------------------------------------------------+
+| colloid     | big colloid particles in a small particle solvent, 2d system     |
++-------------+------------------------------------------------------------------+
+| comb        | models using the COMB potential                                  |
++-------------+------------------------------------------------------------------+
+| controller  | use of fix controller as a thermostat                            |
++-------------+------------------------------------------------------------------+
+| coreshell   | core/shell model using CORESHELL package                         |
++-------------+------------------------------------------------------------------+
+| crack       | crack propagation in a 2d solid                                  |
++-------------+------------------------------------------------------------------+
+| deposit     | deposit atoms and molecules on a surface                         |
++-------------+------------------------------------------------------------------+
+| dipole      | point dipolar particles, 2d system                               |
++-------------+------------------------------------------------------------------+
+| dreiding    | methanol via Dreiding FF                                         |
++-------------+------------------------------------------------------------------+
+| eim         | NaCl using the EIM potential                                     |
++-------------+------------------------------------------------------------------+
+| ellipse     | ellipsoidal particles in spherical solvent, 2d system            |
++-------------+------------------------------------------------------------------+
+| flow        | Couette and Poiseuille flow in a 2d channel                      |
++-------------+------------------------------------------------------------------+
+| friction    | frictional contact of spherical asperities between 2d surfaces   |
++-------------+------------------------------------------------------------------+
+| gcmc        | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command      |
++-------------+------------------------------------------------------------------+
+| granregion  | use of fix wall/region/gran as boundary on granular particles    |
++-------------+------------------------------------------------------------------+
+| hugoniostat | Hugoniostat shock dynamics                                       |
++-------------+------------------------------------------------------------------+
+| hyper       | global and local hyperdynamics of diffusion on Pt surface        |
++-------------+------------------------------------------------------------------+
+| indent      | spherical indenter into a 2d solid                               |
++-------------+------------------------------------------------------------------+
+| kim         | use of potentials from the `OpenKIM Repository <openkim_>`_      |
++-------------+------------------------------------------------------------------+
+| latte       | examples for using fix latte for DFTB via the LATTE library      |
++-------------+------------------------------------------------------------------+
+| meam        | MEAM test for SiC and shear (same as shear examples)             |
++-------------+------------------------------------------------------------------+
+| melt        | rapid melt of 3d LJ system                                       |
++-------------+------------------------------------------------------------------+
+| message     | demos for LAMMPS client/server coupling with the MESSAGE package |
++-------------+------------------------------------------------------------------+
+| micelle     | self-assembly of small lipid-like molecules into 2d bilayers     |
++-------------+------------------------------------------------------------------+
+| min         | energy minimization of 2d LJ melt                                |
++-------------+------------------------------------------------------------------+
+| mscg        | parameterize a multi-scale coarse-graining (MSCG) model          |
++-------------+------------------------------------------------------------------+
+| msst        | MSST shock dynamics                                              |
++-------------+------------------------------------------------------------------+
+| nb3b        | use of non-bonded 3-body harmonic pair style                     |
++-------------+------------------------------------------------------------------+
+| neb         | nudged elastic band (NEB) calculation for barrier finding        |
++-------------+------------------------------------------------------------------+
+| nemd        | non-equilibrium MD of 2d sheared system                          |
++-------------+------------------------------------------------------------------+
+| obstacle    | flow around two voids in a 2d channel                            |
++-------------+------------------------------------------------------------------+
+| peptide     | dynamics of a small solvated peptide chain (5-mer)               |
++-------------+------------------------------------------------------------------+
+| peri        | Peridynamic model of cylinder impacted by indenter               |
++-------------+------------------------------------------------------------------+
+| pour        | pouring of granular particles into a 3d box, then chute flow     |
++-------------+------------------------------------------------------------------+
+| prd         | parallel replica dynamics of vacancy diffusion in bulk Si        |
++-------------+------------------------------------------------------------------+
+| python      | using embedded Python in a LAMMPS input script                   |
++-------------+------------------------------------------------------------------+
+| qeq         | use of the QEQ package for charge equilibration                  |
++-------------+------------------------------------------------------------------+
+| rdf-adf     | computing radial and angle distribution functions for water      |
++-------------+------------------------------------------------------------------+
+| reax        | RDX and TATB models using the ReaxFF                             |
++-------------+------------------------------------------------------------------+
+| rigid       | rigid bodies modeled as independent or coupled                   |
++-------------+------------------------------------------------------------------+
+| shear       | sideways shear applied to 2d solid, with and without a void      |
++-------------+------------------------------------------------------------------+
+| snap        | NVE dynamics for BCC tantalum crystal using SNAP potential       |
++-------------+------------------------------------------------------------------+
+| srd         | stochastic rotation dynamics (SRD) particles as solvent          |
++-------------+------------------------------------------------------------------+
+| streitz     | use of Streitz/Mintmire potential with charge equilibration      |
++-------------+------------------------------------------------------------------+
+| tad         | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
++-------------+------------------------------------------------------------------+
+| threebody   | regression test input for a variety of manybody potentials       |
++-------------+------------------------------------------------------------------+
+| vashishta   | use of the Vashishta potential                                   |
++-------------+------------------------------------------------------------------+
+| voronoi     | Voronoi tesselation via compute voronoi/atom command             |
++-------------+------------------------------------------------------------------+
+
+Here is how you can run and visualize one of the sample problems:
+
+
+.. parsed-literal::
+
+   cd indent
+   cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+   lmp_linux -in in.indent            # run the problem
+
+Running the simulation produces the files *dump.indent* and
+*log.lammps*\ .  You can visualize the dump file of snapshots with a
+variety of 3rd-party tools highlighted on the
+`Visualization <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
+web site.
+
+If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
+script a series of JPG images will be produced by the run (assuming
+you built LAMMPS with JPG support; see the
+:doc:`Build\_settings <Build_settings>` doc page for details).  These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools.  See the
+:doc:`dump image <dump_image>` doc page for more details.  E.g. this
+Imagemagick command would create a GIF file suitable for viewing in a
+browser.
+
+
+.. parsed-literal::
+
+   % convert -loop 1 \*.jpg foo.gif
+
+
+----------
+
+
+Uppercase directories
+---------------------
+
++------------+--------------------------------------------------------------------------------------------------+
+| ASPHERE    | various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc |
++------------+--------------------------------------------------------------------------------------------------+
+| COUPLE     | examples of how to use LAMMPS as a library                                                       |
++------------+--------------------------------------------------------------------------------------------------+
+| DIFFUSE    | compute diffusion coefficients via several methods                                               |
++------------+--------------------------------------------------------------------------------------------------+
+| ELASTIC    | compute elastic constants at zero temperature                                                    |
++------------+--------------------------------------------------------------------------------------------------+
+| ELASTIC\_T | compute elastic constants at finite temperature                                                  |
++------------+--------------------------------------------------------------------------------------------------+
+| HEAT       | compute thermal conductivity for LJ and water via fix ehex                                       |
++------------+--------------------------------------------------------------------------------------------------+
+| KAPPA      | compute thermal conductivity via several methods                                                 |
++------------+--------------------------------------------------------------------------------------------------+
+| MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
++------------+--------------------------------------------------------------------------------------------------+
+| SPIN       | examples for features of the SPIN package                                                        |
++------------+--------------------------------------------------------------------------------------------------+
+| UNITS      | examples that run the same simulation in lj, real, metal units                                   |
++------------+--------------------------------------------------------------------------------------------------+
+| USER       | examples for USER packages and USER-contributed commands                                         |
++------------+--------------------------------------------------------------------------------------------------+
+| VISCOSITY  | compute viscosity via several methods                                                            |
++------------+--------------------------------------------------------------------------------------------------+
+
+Nearly all of these directories have README files which give more
+details on how to understand and use their contents.
+
+The USER directory has a large number of sub-directories which
+correspond by name to a USER package.  They contain scripts that
+illustrate how to use the command(s) provided in that package.  Many
+of the sub-directories have their own README files which give further
+instructions.  See the :doc:`Packages\_details <Packages_details>` doc
+page for more info on specific USER packages.
+
+.. _openkim: https://openkim.org
+
+
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Howto.rst

@@ -0,0 +1,106 @@
+Howto discussions
+*****************
+
+These doc pages describe how to perform various tasks with LAMMPS,
+both for users and developers.  The
+`glossary <http://lammps.sandia.gov>`_ website page also lists MD
+terminology with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the examples dir of the LAMMPS
+distribution and highlighted on the :doc:`Examples <Examples>` doc page
+also show how to setup and run various kinds of simulations.
+
+Tutorials howto
+===============
+
+
+.. toctree::
+   :name: tutorials
+   :maxdepth: 1
+
+   Howto_github
+   Howto_pylammps
+   Howto_bash
+
+General howto
+=============
+
+
+.. toctree::
+   :name: general_howto
+   :maxdepth: 1
+
+   Howto_restart
+   Howto_viz
+   Howto_multiple
+   Howto_replica
+   Howto_library
+   Howto_couple
+   Howto_client_server
+
+Settings howto
+==============
+
+
+.. toctree::
+   :name: settings
+   :maxdepth: 1
+
+   Howto_2d
+   Howto_triclinic
+   Howto_thermostat
+   Howto_barostat
+   Howto_walls
+   Howto_nemd
+   Howto_dispersion
+
+Analysis howto
+==============
+
+
+.. toctree::
+   :name: analysis
+   :maxdepth: 1
+
+   Howto_output
+   Howto_chunk
+   Howto_temperature
+   Howto_elastic
+   Howto_kappa
+   Howto_viscosity
+   Howto_diffusion
+
+Force fields howto
+==================
+
+
+.. toctree::
+   :name: force
+   :maxdepth: 1
+
+   Howto_bioFF
+   Howto_tip3p
+   Howto_tip4p
+   Howto_spc
+
+Packages howto
+==============
+
+
+.. toctree::
+   :name: packages
+   :maxdepth: 1
+
+   Howto_spherical
+   Howto_granular
+   Howto_body
+   Howto_polarizable
+   Howto_coreshell
+   Howto_drude
+   Howto_drude2
+   Howto_manifold
+   Howto_spins
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Howto_2d.rst

@@ -0,0 +1,48 @@
+2d simulations
+==============
+
+Use the :doc:`dimension <dimension>` command to specify a 2d simulation.
+
+Make the simulation box periodic in z via the :doc:`boundary <boundary>`
+command.  This is the default.
+
+If using the :doc:`create box <create_box>` command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create\_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+
+
+.. parsed-literal::
+
+   :doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25
+
+If using the :doc:`read data <read_data>` command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create\_box command settings just described.  For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+
+Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep.  The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+
+Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+
+.. note::
+
+   Some models in LAMMPS treat particles as finite-size spheres, as
+   opposed to point particles.  See the :doc:`atom\_style sphere <atom_style>` and :doc:`fix nve/sphere <fix_nve_sphere>`
+   commands for details.  By default, for 2d simulations, such particles
+   will still be modeled as 3d spheres, not 2d discs (circles), meaning
+   their moment of inertia will be that of a sphere.  If you wish to
+   model them as 2d discs, see the :doc:`set density/disc <set>` command
+   and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
+   :doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
+   commands.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Howto_barostat.rst

@@ -0,0 +1,68 @@
+Barostats
+=========
+
+Barostatting means controlling the pressure in an MD simulation.
+:doc:`Thermostatting <Howto_thermostat>` means controlling the
+temperature of the particles.  Since the pressure includes a kinetic
+component due to particle velocities, both these operations require
+calculation of the temperature.  Typically a target temperature (T)
+and/or pressure (P) is specified by the user, and the thermostat or
+barostat attempts to equilibrate the system to the requested T and/or
+P.
+
+Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Two
+barostatting methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+* :doc:`fix npt <fix_nh>`
+* :doc:`fix npt/sphere <fix_npt_sphere>`
+* :doc:`fix npt/asphere <fix_npt_asphere>`
+* :doc:`fix nph <fix_nh>`
+* :doc:`fix press/berendsen <fix_press_berendsen>`
+
+The :doc:`fix npt <fix_nh>` commands include a Nose-Hoover thermostat
+and barostat.  :doc:`Fix nph <fix_nh>` is just a Nose/Hoover barostat;
+it does no thermostatting.  Both :doc:`fix nph <fix_nh>` and :doc:`fix press/berendsen <fix_press_berendsen>` can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the :doc:`thermostats <Howto_thermostat>`, :doc:`fix npt <fix_nh>`
+and :doc:`fix nph <fix_nh>` only use translational motion of the
+particles in computing T and P and performing thermo/barostatting.
+:doc:`Fix npt/sphere <fix_npt_sphere>` and :doc:`fix npt/asphere <fix_npt_asphere>` thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the :doc:`compute pressure <compute_pressure>` compute to calculate a current
+pressure.  By default, this compute is created with a simple :doc:`compute temp <compute_temp>` (see the last argument of the :doc:`compute pressure <compute_pressure>` command), which is used to calculated
+the kinetic component of the pressure.  The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic component which contributes to the current
+pressure.  See the doc pages for the individual fixes and for the
+:doc:`fix\_modify <fix_modify>` command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+
+.. note::
+
+   As with the thermostats, the Nose/Hoover methods (:doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`) perform time integration.
+   :doc:`Fix press/berendsen <fix_press_berendsen>` does NOT, so it should
+   be used with one of the constant NVE fixes or with one of the NVT
+   fixes.
+
+Thermodynamic output, which can be setup via the
+:doc:`thermo\_style <thermo_style>` command, often includes pressure
+values.  As explained on the doc page for the
+:doc:`thermo\_style <thermo_style>` command, the default pressure is
+setup by the thermo command itself.  It is NOT the pressure associated
+with any barostatting fix you have defined or with any compute you
+have defined that calculates a pressure.  The doc pages for the
+barostatting fixes explain the ID of the pressure compute they create.
+Thus if you want to view these pressures, you need to specify them
+explicitly via the :doc:`thermo\_style custom <thermo_style>` command.
+Or you can use the :doc:`thermo\_modify <thermo_modify>` command to
+re-define what pressure compute is used for default thermodynamic
+output.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html

doc/src/Howto_bash.rst

@@ -0,0 +1,291 @@
+Using LAMMPS with Bash on Windows
+=================================
+
+**written by Richard Berger**
+
+
+----------
+
+
+Starting with Windows 10 you can install Linux tools directly in Windows. This
+allows you to compile LAMMPS following the same procedure as on a real Ubuntu
+Linux installation. Software can be easily installed using the package manager
+via apt-get and all files are accessible in both the Windows Explorer and your
+Linux shell (bash). This avoids switching to a different operating system or
+installing a virtual machine. Everything runs on Windows.
+
+Installing Bash on Windows
+--------------------------
+
+Prerequisites
+^^^^^^^^^^^^^
+
+* Windows 10 (64bit only)
+* Latest updates installed
+
+Enable developer mode
+^^^^^^^^^^^^^^^^^^^^^
+
+You enable this feature by first opening Windows Settings and enabling
+Developer mode. Go to the Windows settings and search for "developer". This
+will allow you to install software which comes from outside of the Windows
+Store.  You might be prompted to reboot your compute. Please do so.
+
+.. image:: JPG/bow_tutorial_01_small.png
+   :target: JPG/bow_tutorial_01.png
+
+.. image:: JPG/bow_tutorial_02_small.png
+   :target: JPG/bow_tutorial_02.png
+
+.. image:: JPG/bow_tutorial_03_small.png
+   :target: JPG/bow_tutorial_03.png
+
+Install Windows Subsystem for Linux
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Next you must ensure that the Window Subsystem for Linux is installed. Again,
+search for "enable windows features" in the Settings dialog. This opens a
+dialog with a list of features you can install. Add a checkmark to Windows
+Subsystem for Linux (Beta) and press OK.
+
+.. image:: JPG/bow_tutorial_04_small.png
+   :target: JPG/bow_tutorial_04.png
+
+.. image:: JPG/bow_tutorial_05.png
+   :target: JPG/bow_tutorial_05.png
+
+Install Bash for Windows
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+After installation completes, type "bash" in the Windows Start menu search.
+Select the first found option. This will launch a command-line window which
+will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
+enter. This will then download Ubuntu for Windows.
+
+.. image:: JPG/bow_tutorial_06.png
+
+.. image:: JPG/bow_tutorial_07.png
+
+During installation, you will be asked for a new password. This will be used
+for installing new software and running commands with sudo.
+
+.. image:: JPG/bow_tutorial_08.png
+
+Type exit to close the command-line window.
+
+Go to the Start menu and type "bash" again. This time you will see a "Bash on
+Ubuntu on Windows" Icon. Start this program.
+
+.. image:: JPG/bow_tutorial_09.png
+
+Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
+
+.. image:: JPG/bow_tutorial_10.png
+
+
+----------
+
+
+Compiling LAMMPS in Bash on Windows
+-----------------------------------
+
+The installation of LAMMPS in this environment is identical to working inside
+of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
+
+Installing prerequisite packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+First upgrade all existing packages using
+
+
+.. parsed-literal::
+
+   sudo apt update
+   sudo apt upgrade -y
+
+Next install the following packages, which include compilers and libraries
+needed for various LAMMPS features:
+
+
+.. parsed-literal::
+
+   sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
+
+Files in Ubuntu on Windows
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
+user home directory /home/\ **username**\ . You can access your Windows user directory
+using the /mnt/c/Users/\ **username** folder.
+
+Download LAMMPS
+^^^^^^^^^^^^^^^
+
+Obtain a copy of the LAMMPS code and go into it using "cd"
+
+Option 1: Downloading LAMMPS tarball using wget
+"""""""""""""""""""""""""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
+   tar xvzf lammps-stable.tar.gz
+   cd lammps-31Mar17
+
+Option 2: Obtaining LAMMPS code from GitHub
+"""""""""""""""""""""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   git clone https://github.com/lammps/lammps.git
+   cd lammps
+
+Compiling LAMMPS
+^^^^^^^^^^^^^^^^
+
+At this point you can compile LAMMPS like on Ubuntu Linux.
+
+Compiling serial version
+""""""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   cd src/
+   make -j 4 serial
+
+This will create an executable called lmp\_serial in the src/ directory
+
+Compiling MPI version
+"""""""""""""""""""""
+
+
+.. parsed-literal::
+
+   cd src/
+   make -j 4 mpi
+
+This will create an executable called lmp\_mpi in the src/ directory
+
+
+----------
+
+
+Finally, please note the absolute path of your src folder. You can get this using
+
+
+.. parsed-literal::
+
+   pwd
+
+or
+
+
+.. parsed-literal::
+
+   echo $PWD
+
+To run any examples you need the location of the executable. For now, let us
+save this location in a temporary variable
+
+
+.. parsed-literal::
+
+   LAMMPS_DIR=$PWD
+
+
+----------
+
+
+Running an example script
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Once compiled you can execute some of the LAMMPS examples. Switch into the
+examples/melt folder
+
+
+.. parsed-literal::
+
+   cd ../examples/melt
+
+The full path of the serial executable is $LAMMPS\_DIR/lmp\_serial, while the mpi
+version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either
+version as follows:
+
+
+.. parsed-literal::
+
+   $LAMMPS_DIR/lmp_serial -in in.melt
+
+or
+
+
+.. parsed-literal::
+
+   mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
+
+Note the use of our variable $LAMMPS\_DIR, which expands into the full path of
+the LAMMPS src folder we saved earlier.
+
+Adding your executable directory to your PATH
+"""""""""""""""""""""""""""""""""""""""""""""
+
+You can avoid having to type the full path of your LAMMPS binary by adding its
+parent folder to the PATH environment variable as follows:
+
+
+.. parsed-literal::
+
+   export PATH=$LAMMPS_DIR:$PATH
+
+Input scripts can then be run like this:
+
+
+.. parsed-literal::
+
+   lmp_serial -in in.melt
+
+or
+
+
+.. parsed-literal::
+
+   mpirun -np 4 lmp_mpi -in in.melt
+
+However, this PATH variable will not persist if you close your bash window.
+To persist this setting edit the $HOME/.bashrc file using your favorite editor
+and add this line
+
+
+.. parsed-literal::
+
+   export PATH=/full/path/to/your/lammps/src:$PATH
+
+**Example:**
+
+For an executable lmp\_serial with a full path
+
+
+.. parsed-literal::
+
+   /home/richard/lammps/src/lmp_serial
+
+the PATH variable should be
+
+
+.. parsed-literal::
+
+   export PATH=/home/richard/lammps/src:$PATH
+
+.. note::
+
+   This should give you a jump start when trying to run LAMMPS on Windows.
+   To become effective in this environment I encourage you to look into Linux
+   tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Commands_all.html