Merge pull request #1881 from akohlmey/next_lammps_version

Update version string for next patch release

.github/CONTRIBUTING.md

@@ -68,12 +68,12 @@ How quickly your contribution will be integrated depends largely on how much eff
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
 
 * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI.
-* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
-* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.txt'.
+* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
 * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
 * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 

.gitignore

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

cmake/CMakeLists.txt

@@ -588,8 +588,9 @@ if(BUILD_TOOLS)
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
   # ninja-build currently does not support fortran. thus we skip building this tool
-  if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
+  if(CMAKE_GENERATOR STREQUAL "Ninja")
     message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
+  else()
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
@@ -738,4 +739,20 @@ if(PKG_KSPACE)
   else()
     message(STATUS "Using double precision FFTs")
   endif()
+  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+    message(STATUS "Using threaded FFTs")
+  else()
+    message(STATUS "Using non-threaded FFTs")
+  endif()
+  if(PKG_KOKKOS)
+    if(KOKKOS_ENABLE_CUDA)
+      if (${FFT} STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: cuFFT")
+      endif()
+    else()
+      message(STATUS "Kokkos FFT: ${FFT}")
+    endif()
+  endif()
 endif()

cmake/Modules/FindFFTW3.cmake

@@ -1,20 +1,22 @@
 # - Find fftw3
-# Find the native FFTW3 headers and libraries.
+# Find the native double precision FFTW3 headers and libraries.
 #
-#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
-#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
+#  FFTW3_INCLUDE_DIRS  - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES     - List of libraries when using fftw3.
+#  FFTW3_OMP_LIBRARIES - List of libraries when using fftw3.
+#  FFTW3_FOUND         - True if fftw3 found.
 #
 
 find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3 fftw3)
 find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
-
 find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
+find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
 
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
 set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
+set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
@@ -22,4 +24,4 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY FFTW3_OMP_LIBRARY)

cmake/Modules/FindFFTW3F.cmake

@@ -1,8 +1,8 @@
-# - Find fftw3f
-# Find the native FFTW3F headers and libraries.
+# Find the native single precision FFTW3 headers and libraries.
 #
 #  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
 #  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_OMP_LIBRARIES - List of libraries when using fftw3.
 #  FFTW3F_FOUND        - True if fftw3f found.
 #
 
@@ -10,11 +10,12 @@ find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3F fftw3f)
 find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
-
 find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
 
-set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
 set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
@@ -22,4 +23,4 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY)

cmake/Modules/Packages/KOKKOS.cmake

@@ -10,7 +10,7 @@ if(PKG_KOKKOS)
     set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
     set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
     add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-  
+
     set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                             ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                             ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
@@ -39,7 +39,15 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
   if(PKG_KSPACE)
-    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+    if(KOKKOS_ENABLE_CUDA)
+      if(NOT ${FFT} STREQUAL "KISS")
+        add_definitions(-DFFT_CUFFT)
+        list(APPEND LAMMPS_LINK_LIBS cufft)
+      endif()
+    endif()
   endif()
 
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")

cmake/Modules/Packages/KSPACE.cmake

@@ -21,9 +21,27 @@ if(PKG_KSPACE)
     add_definitions(-DFFT_FFTW3)
     include_directories(${${FFTW}_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+      option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
+    else()
+      option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
+    endif()
+
+    if(FFT_FFTW_THREADS)
+      if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+        add_definitions(-DFFT_FFTW_THREADS)
+        list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_OMP_LIBRARIES})
+      else()
+        message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
+      endif()
+    endif()
   elseif(FFT STREQUAL "MKL")
     find_package(MKL REQUIRED)
     add_definitions(-DFFT_MKL)
+    option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
+    if(FFT_MKL_THREADS)
+      add_definitions(-DFFT_MKL_THREADS)
+    endif()
     include_directories(${MKL_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
   else()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -49,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.3/plumed-src-2.5.3.tgz
-      URL_MD5 de30d6e7c2dcc0973298e24a6da24286
+      URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
+      URL_MD5 204d2edae58d9b10ba3ad460cad64191
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}

doc/Makefile

@@ -3,7 +3,6 @@
 SHELL         = /bin/bash
 BUILDDIR      = ${CURDIR}
 RSTDIR        = $(BUILDDIR)/src
-TXTDIR        = $(BUILDDIR)/txt
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
@@ -28,10 +27,8 @@ HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
-OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
 
 # ------------------------------------------
 
@@ -46,6 +43,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
@@ -60,15 +58,16 @@ clean:
 clean-spelling:
 	rm -rf spelling
 
-rst: clean $(OBJECTS) $(ANCHORCHECK)
+rst: clean $(ANCHORCHECK)
 
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -76,15 +75,18 @@ html: $(OBJECTS) $(ANCHORCHECK)
 	@rm -rf html/_sources
 	@rm -rf html/PDF
 	@rm -rf html/USER
+	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
 	@cp -r src/USER html/USER
+	@mkdir -p html/JPG
+	@cp `grep -A2 '\.\. image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
 	@rm -rf html/USER/.[sg]*
 	@rm -rf html/USER/*/.[sg]*
 	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+spelling: utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
@@ -94,7 +96,7 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	)
 	@echo "Spell check finished."
 
-epub: $(OBJECTS)
+epub:
 	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
@@ -113,7 +115,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: $(OBJECTS) $(ANCHORCHECK)
+pdf: $(ANCHORCHECK)
 	@(\
 		cd src/Developer; \
 		pdflatex developer; \
@@ -122,24 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                rst_anchor_check src/*.rst ;\
-                echo "############################################" ;\
-                deactivate ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
@@ -162,20 +167,19 @@ fetch:
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		rst_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		deactivate ;\
+	)
+
+style_check :
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-$(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
-	@(\
-		mkdir -p $(RSTDIR) ; \
-		. $(VENV)/bin/activate ;\
-		txt2rst -v $< > $@ ;\
-		deactivate ;\
-	)
-
 $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi

doc/github-development-workflow.md

@@ -104,14 +104,17 @@ Here are some items to check:
   * every new command or style should have documentation. The names of
   source files (c++ and manual) should follow the name of the style.
   (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
-  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.rst`)
   * all new style names should be lower case, the must be no dashes,
   blanks, or underscores separating words, only forward slashes.
   * new style docs should be added to the "overview" files in
-  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
-  and `doc/src/lammps.book`
+  `doc/src/Commands_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
   * check whether manual cleanly translates with `make html` and `make pdf`
+  * if documentation is (still) provided as a .txt file, convert to .rst
+  and remove the .txt file. For files in doc/txt the conversion is automatic.
+  * remove all .txt files in `doc/txt` that are out of sync with their .rst counterparts in `doc/src`
   * check spelling of manual with `make spelling` in doc folder
+  * check style tables and command lists with `make style_check`
   * new source files in packages should be added to `src/.gitignore`
   * removed or renamed files in packages should be added to `src/Purge.list`
   * C++ source files should use C++ style include files for accessing
@@ -136,7 +139,7 @@ Here are some items to check:
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
   * indentation is 2 spaces per level
-  * there should be NO tabs and no trailing whitespace
+  * there should be NO tabs and no trailing whitespace (review the "checkstyle" test on pull requests)
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "9 January 2020" "2020-01-09"
+.TH LAMMPS "18 February 2020" "2020-02-18"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -11,13 +11,18 @@ or
 
 mpirun \-np 2
 .B lmp
-<input file> [OPTIONS] ...
+\-in <input file> [OPTIONS] ...
 
 or
 
 .B lmp
 \-r2data file.restart file.data
 
+or
+
+.B lmp
+\-h
+
 .SH DESCRIPTION
 .B LAMMPS
 is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
@@ -249,7 +254,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2019 Sandia Corporation
+© 2003--2020 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/src/Build.rst

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

doc/src/Build_basics.rst

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

doc/src/Build_cmake.rst

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

doc/src/Build_development.rst

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

doc/src/Build_extras.rst

@@ -177,7 +177,7 @@ KIM package
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>`
+use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
@@ -203,7 +203,7 @@ inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
-For using KIM web queries.
+For using OpenKIM web queries in LAMMPS.
 
 If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
 libcurl calls within the KIM web query display a lot of information about
@@ -350,10 +350,12 @@ For NVIDIA GPUs using CUDA:
    KOKKOS_DEVICES = Cuda
    KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU
                                     # archGPU = GPU from list above
+   FFT_INC = -DFFT_CUFFT            # enable use of cuFFT (optional)
+   FFT_LIB = -lcufft                # link to cuFFT library
 
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx.  The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
+For GPUs, you also need the following 2 lines in your Makefile.machine
+before the CC line is defined, in this case for use with OpenMPI mpicxx.
+The 2 lines define a nvcc wrapper compiler, which will use nvcc for
 compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
 files.
 
@@ -878,6 +880,9 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
+The USER-PLUMED package has been tested to work with Plumed versions
+2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
+with a different version of the Plumed kernel.
 
 
 PLUMED can be linked into MD codes in three different modes: static,
@@ -1412,8 +1417,3 @@ the settings are not valid for your system, check if one of the other
 lib/vtk/Makefile.lammps.\* files is compatible and copy it to
 Makefile.lammps.  If none of the provided files work, you will need to
 edit the Makefile.lammps file.  See lib/vtk/README for details.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_link.rst

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

doc/src/Build_make.rst

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

doc/src/Build_package.rst

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

doc/src/Build_settings.rst

@@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
 | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
-| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
+| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
 | :ref:`Size of LAMMPS data types <size>`
 | :ref:`Read or write compressed files <gzip>`
 | :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
+| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
 | :ref:`Memory allocation alignment <align>`
 | :ref:`Workaround for long long integers <longlong>`
 | :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
@@ -49,13 +49,19 @@ through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
 
    -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
 
-**Makefile.machine setting**\ :
+**Makefile.machine setting**\ to bypass the C++11 test and compile in C++98 mode:
 
 
 .. parsed-literal::
 
    LMP_INC = -DLAMMPS_CXX98
 
+**Makefile.machine setting**\ to enable the C++11 with older (but not too old) GNU c++ (e.g. on CentOS 7):
+
+
+.. parsed-literal::
+
+   CCFLAGS = -g -O3 -std=c++11
 
 ----------
 
@@ -66,7 +72,7 @@ FFT library
 ---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
-:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
@@ -86,15 +92,21 @@ LAMMPS can use them if they are available on your system.
    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:
+Usually these settings are all that is needed.  If FFTW3 is selected,
+then CMake will try to detect, if threaded FFTW libraries are available
+and enable them by default.  This setting is independent of whether
+OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
+used.  If CMake cannot detect the FFT library, you can set these variables
+to assist:
 
 
 .. parsed-literal::
 
    -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
    -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
    -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
 **Makefile.machine settings**\ :
@@ -105,6 +117,8 @@ the FFT library, you can set these variables:
    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_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
    FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
 
 # default is FFT\_PACK\_ARRAY if not specified
@@ -115,27 +129,34 @@ the FFT library, you can set these variables:
    FFT_INC =       -I/usr/local/include
    FFT_PATH =      -L/usr/local/lib
    FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
    FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
 As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
-make can find the FFT header and library files.  You must specify
-FFT\_LIB with the appropriate FFT libraries to include in the link.
+the compiler can find the FFT header and library files in its default search path.
+You must specify FFT\_LIB with the appropriate FFT libraries to include in the link.
 
 **CMake and make info**\ :
 
 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.
+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.
+to the screen at the end of a run when using the
+:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+doc page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
+:doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 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
@@ -166,7 +187,7 @@ 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
+library libfftw3f.a or libfftw3f.so.
 
 
 .. parsed-literal::
@@ -235,7 +256,7 @@ support 8-byte integers.  It allows for:
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
-:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+:doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Thus if you model a molecular system with
 more than 2 billion atoms, you need the "bigbig" setting.
@@ -341,7 +362,7 @@ Read or write compressed files
 
 If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
-:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 **CMake variables**\ :
 
@@ -472,8 +493,3 @@ e.g. to Python.
 .. parsed-literal::
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -17,9 +17,9 @@ 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.
+While portability to other platforms is desired, it is not always achieved.
 The LAMMPS developers strongly rely on LAMMPS users giving feedback and
-providing assistance in resolving portability issues. This particularly
+providing assistance in resolving portability issues. This is particularly
 true for compiling LAMMPS on Windows, since this platform has significant
 differences with some low-level functionality.
 
@@ -31,18 +31,20 @@ 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
+using cross-compilers).  If it is necessary for you 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>`
+consider using a virtual machine software and compile and run LAMMPS in
+a Linux virtual machine, or - if you have a recently updated Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows 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 and more). For more details on that, please
+see :doc:`this tutorial <Howto_bash>`
 
 .. _gnu:
 
-Using GNU GCC ported to Windows
+Using a GNU GCC ported to Windows
 -----------------------------------------
 
 One option for compiling LAMMPS on Windows natively, that has been known
@@ -83,13 +85,13 @@ 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
+is provided. You will 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
+Please keep in mind, though, that this only applies to **compiling** LAMMPS.
+Whether the resulting binaries do work correctly is not 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
@@ -104,8 +106,3 @@ Support for the Visual C++ compilers is currently not available. The
 CMake build system is capable of creating suitable a Visual Studio
 style build environment, but the LAMMPS code itself is not fully ported
 to support Visual C++. Volunteers to take on this task are welcome.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -25,102 +25,105 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
    * :doc:`bond_coeff <bond_coeff>`
-   * :doc:`bond\_style <bond_style>`
-   * :doc:`bond\_write <bond_write>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
    * :doc:`box <box>`
-   * :doc:`change\_box <change_box>`
+   * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
-   * :doc:`comm\_modify <comm_modify>`
-   * :doc:`comm\_style <comm_style>`
+   * :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:`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:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
    * :doc:`dimension <dimension>`
-   * :doc:`displace\_atoms <displace_atoms>`
+   * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
-   * :doc:`dump adios <dump_adios>`
+   * :doc:`dump atom/adios <dump_adios>`
+   * :doc:`dump custom/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:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
-   * :doc:`fix\_modify <fix_modify>`
+   * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`if <if>`
-   * :doc:`improper\_coeff <improper_coeff>`
-   * :doc:`improper\_style <improper_style>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
+   * :doc:`info <info>`
    * :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:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <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:`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:`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\_write <pair_write>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :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:`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:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
-   * :doc:`run\_style <run_style>`
+   * :doc:`run_style <run_style>`
    * :doc:`server <server>`
    * :doc:`set <set>`
    * :doc:`shell <shell>`
-   * :doc:`special\_bonds <special_bonds>`
+   * :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:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -129,7 +132,7 @@ An alphabetic list of all general LAMMPS commands.
    * :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>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`

doc/src/Commands_bond.rst

@@ -13,7 +13,7 @@
 
 .. _bond:
 
-bond_style potentials
+Bond_style potentials
 =====================
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
@@ -44,16 +44,13 @@ OPT.
    * :doc:`nonlinear (o) <bond_nonlinear>`
    * :doc:`oxdna/fene <bond_oxdna>`
    * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
    * :doc:`table (o) <bond_table>`
-   *
-   *
-
----
 
 .. _angle:
 
-angle_style potentials
+Angle_style potentials
 ======================
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
@@ -91,13 +88,10 @@ OPT.
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`sdk (o) <angle_sdk>`
    * :doc:`table (o) <angle_table>`
-   *
-
----
 
 .. _dihedral:
 
-dihedral_style potentials
+Dihedral_style potentials
 =========================
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
@@ -131,15 +125,13 @@ OPT.
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
    * :doc:`table/cut <dihedral_table_cut>`
-   *
-   *
 
 .. _improper:
 
-improper_style potentials
+Improper_style potentials
 =========================
 
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -166,4 +158,3 @@ OPT.
    * :doc:`ring (o) <improper_ring>`
    * :doc:`sqdistharm <improper_sqdistharm>`
    * :doc:`umbrella (o) <improper_umbrella>`
-   *

doc/src/Commands_category.rst

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

doc/src/Commands_compute.rst

@@ -163,6 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`
-   *
-   *
-   *

doc/src/Commands_fix.rst

@@ -105,16 +105,17 @@ OPT.
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
-   * :doc:`neb\_spin <fix_neb_spin>`
+   * :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:`nphug <fix_nphug>`
    * :doc:`npt (iko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
+   * :doc:`npt/cauchy <fix_npt_cauchy>`
    * :doc:`npt/eff <fix_nh_eff>`
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
@@ -155,6 +156,7 @@ OPT.
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
    * :doc:`print <fix_print>`
+   * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
    * :doc:`python/invoke <fix_python_invoke>`
    * :doc:`python/move <fix_python_move>`
@@ -188,15 +190,16 @@ OPT.
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <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/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:`smd/wall_surface <fix_smd_wall_surface>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
@@ -233,8 +236,7 @@ OPT.
    * :doc:`wall/morse <fix_wall>`
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
+   * :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
-   *
-   *

doc/src/Commands_input.rst

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

doc/src/Commands_kspace.rst

@@ -14,7 +14,7 @@
 KSpace solvers
 ==============
 
-All LAMMPS :doc:`kspace\_style <kspace_style>` solvers.  Some styles have
+All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -24,13 +24,16 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
-   * :doc:`pppm (gok) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
-   * :doc:`pppm/disp (i) <kspace_style>`
-   * :doc:`pppm/disp/tip4p <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
-   *

doc/src/Commands_pair.rst

@@ -11,10 +11,10 @@
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
-Pair\_style potentials
+Pair_style potentials
 ======================
 
-All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have
+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.
@@ -146,7 +146,7 @@ OPT.
    * :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 (got) <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>`
@@ -162,7 +162,7 @@ OPT.
    * :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:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
    * :doc:`local/density <pair_local_density>`
    * :doc:`lubricate (o) <pair_lubricate>`
@@ -174,8 +174,10 @@ OPT.
    * :doc:`meam/c <pair_meamc>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
+   * :doc:`mesocnt <pair_mesocnt>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -197,10 +199,17 @@ OPT.
    * :doc:`oxdna2/hbond <pair_oxdna2>`
    * :doc:`oxdna2/stk <pair_oxdna2>`
    * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :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>`
@@ -209,7 +218,7 @@ OPT.
    * :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/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
@@ -248,5 +257,3 @@ OPT.
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`
-   *
-   *

doc/src/Commands_removed.rst

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

doc/src/Commands_structure.rst

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

doc/src/Eqs/angle_class2_p6.tex

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

doc/src/Eqs/box.tex

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

doc/src/Eqs/box_inverse.tex

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

doc/src/Eqs/centro_symmetry.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
-$$
-
-\end{document}

doc/src/Eqs/cna_cutoff1.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cna_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_cutoff.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cnp_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_eq.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} |^2
-$$
-
-\end{document}

doc/src/Eqs/compute_dpd.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ 
-   U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
-   U^{chem} = \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
-   U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\
-   \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/compute_fep_bar.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
-
-\end{document}

doc/src/Eqs/compute_fep_fdti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
-    A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
-  A(\lambda_i)}{\delta} \]
-
-\end{document}

doc/src/Eqs/compute_fep_fep.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
-- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
-      U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_lambda.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
-  \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_fep_ti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
-    U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
-    U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_u.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[  U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
-
-\end{document}

doc/src/Eqs/compute_fep_vol.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
-    \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
-\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
-
-\end{document}

doc/src/Eqs/compute_gyration.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
-$$
-
-\end{document}

doc/src/Eqs/compute_msd_nongauss.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
-$$
-
-\end{document}

doc/src/Eqs/compute_saed1.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  I=\frac{F^{*}F}{N}
-$$
-
-\end{document}
-

doc/src/Eqs/compute_saed2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-

doc/src/Eqs/compute_saed3.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
-$$
-\end{document}
-

doc/src/Eqs/compute_shape_parameters.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
- c = l_z - 0.5(l_y+l_x) \\
- b = l_y - l_x \\
- k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
-\end{eqnarray*}
-
-\end{document}
-

doc/src/Eqs/compute_sna_atom1.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom2.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom3.tex

@@ -1,16 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
-
-\begin{equation}
-B_{j_1,j_2,j}  = \\
-\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
-\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
-u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom4.tex

@@ -1,14 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\label{eqn:f_c}
-f_c(r)  & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
-& = & 0,  r > R_{ii'}
-\end{eqnarray*}
-
-
-\end{document}

doc/src/Eqs/compute_sna_atom5.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{equation}
-- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial {\bf r}_i}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom6.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{eqnarray*}
-- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_xrd1.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  I=Lp(\theta)\frac{F^{*}F}{N}
-$$
-
-\end{document}
-

doc/src/Eqs/compute_xrd2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd3.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)}
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd4.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  \frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2}
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd5.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} 
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
-$$
-\end{document}
-