Merge pull request #1387 from akohlmey/next-patch-release

Step version string for next patch release

.github/ISSUE_TEMPLATE/generic.md

@@ -0,0 +1,21 @@
+---
+name: Generic Issue
+about: For issues that do not fit any of the other categories
+title: "_Replace With a Descriptive Title_"
+labels: 
+assignees: ''
+
+---
+
+**Summary**
+
+_Please provide a clear and concise description of what this issue report is about._
+
+**LAMMPS Version and Platform**
+
+_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+
+**Details**
+
+_Please explain the issue in detail here_
+

.github/ISSUE_TEMPLATE/help_request.md

@@ -0,0 +1,15 @@
+---
+name: Request for Help
+about: "Don't post help requests here, email the lammps-users mailing list"
+title: ""
+labels: invalid
+assignees: ''
+
+---
+
+Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
+Instead send an e-mail to the lammps-users mailing list.
+
+This issue tracker is for tracking LAMMPS development related issues only.
+
+Thanks for your cooperation.

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,22 +4,19 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
 
 **Related Issues**
 
-__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
+_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
 
 **Licensing**
 
-By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under the GNU General Public License version 2.
-
-_Please complete the following statement by adding "yes" or "no":_
-My contribution may be re-licensed as LGPL (for use of LAMMPS as a library linked to proprietary software):
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
 
 **Implementation Notes**
 
@@ -27,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted_
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete

cmake/CMakeLists.txt

@@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
 
+find_package(Git)
+
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 # this is fast, so check for it all the time
 message(STATUS "Running check for auto-generated files from make-based build system")
 file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
+list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
 foreach(_SRC ${SRC_AUTOGEN_FILES})
   get_filename_component(FILENAME "${_SRC}" NAME)
   if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@@ -178,7 +180,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
   USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
   USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM USER-YAFF)
+  USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -201,6 +203,17 @@ endif()
 
 include_directories(${LAMMPS_SOURCE_DIR})
 
+
+if(PKG_USER-ADIOS)
+  # The search for ADIOS2 must come before MPI because
+  # it includes its own MPI search with the latest FindMPI.cmake
+  # script that defines the MPI::MPI_C target
+  enable_language(C)
+  find_package(ADIOS2 REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
+endif()
+
+
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -368,19 +381,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
 endif()
 
 if(PKG_PYTHON)
-  find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(BUILD_LIB AND BUILD_SHARED_LIBS)
-    if(NOT PYTHON_INSTDIR)
-      execute_process(COMMAND ${PYTHON_EXECUTABLE}
-        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    endif()
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  endif()
 endif()
 
 find_package(JPEG QUIET)
@@ -453,7 +457,7 @@ if(PKG_VORONOI)
     set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
 
     ExternalProject_Add(voro_build
-      URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
       URL_MD5 2338b824c3b7b25590e18e8df5d68af9
       CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
       )
@@ -600,8 +604,9 @@ if(PKG_USER-PLUMED)
 endif()
 
 if(PKG_USER-MOLFILE)
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
   target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
@@ -656,28 +661,40 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)
   if(DOWNLOAD_KIM)
-    message(STATUS "KIM-API v1 download requested - we will build our own")
+    message(STATUS "KIM-API download requested - we will build our own")
+    enable_language(C)
+    enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
-      URL_MD5 9f66efc128da33039e30659f36fc6d00
-      BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
+      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
       )
     ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
-    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM)
-    if(NOT KIM_FOUND)
-      message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+    find_package(KIM-API)
+    if(NOT KIM-API_FOUND)
+      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
     endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
-  include_directories(${KIM_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
 endif()
 
 if(PKG_MESSAGE)
@@ -1151,6 +1168,10 @@ if(PKG_GPU)
         message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
       endif()
       option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
 
       set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
@@ -1214,7 +1235,7 @@ if(PKG_GPU)
       add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
       target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
       target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
       if(CUDPP_OPT)
         target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
         target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -1308,6 +1329,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
 file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
 execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
 
+######################################
+# Generate lmpgitversion.h
+######################################
+add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
+  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
+  -DGIT_FOUND="${GIT_FOUND}"
+  -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
+  -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
+set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
+list(APPEND LAMMPS_DEPS gitversion)
+
 ###########################################
 # Actually add executable and lib to build
 ############################################
@@ -1354,6 +1387,7 @@ if(BUILD_EXE)
   endif()
 endif()
 
+
 ###############################################################################
 # Build documentation
 ###############################################################################
@@ -1428,6 +1462,49 @@ install(
   DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
 )
 
+###############################################################################
+# Install LAMMPS lib and python module into site-packages folder with
+# "install-python" target.  Behaves exactly like "make install-python" for
+# conventional build.  Only available, if a shared library is built.
+# This is primarily for people that only want to use the Python wrapper.
+###############################################################################
+if(BUILD_LIB AND BUILD_SHARED_LIBS)
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    add_custom_target(
+      install-python
+      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
+      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python
+      COMMENT "Installing LAMMPS Python module")
+  else()
+    add_custom_target(
+      install-python
+      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
+  endif()
+else()
+  add_custom_target(
+    install-python
+    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
+endif()
+
+###############################################################################
+# Add LAMMPS python module to "install" target. This is taylored for building
+# LAMMPS for package managers and with different prefix settings.
+# This requires either a shared library or that the PYTHON package is included.
+###############################################################################
+if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  endif()
+endif()
+
 ###############################################################################
 # Testing
 #

cmake/Modules/FindKIM-API.cmake.in

@@ -0,0 +1,50 @@
+#
+# CDDL HEADER START
+#
+# The contents of this file are subject to the terms of the Common Development
+# and Distribution License Version 1.0 (the "License").
+#
+# You can obtain a copy of the license at
+# http://www.opensource.org/licenses/CDDL-1.0.  See the License for the
+# specific language governing permissions and limitations under the License.
+#
+# When distributing Covered Code, include this CDDL HEADER in each file and
+# include the License file in a prominent location with the name LICENSE.CDDL.
+# If applicable, add the following below this CDDL HEADER, with the fields
+# enclosed by brackets "[]" replaced with your own identifying information:
+#
+# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
+#
+# CDDL HEADER END
+#
+
+#
+# Copyright (c) 2013--2019, Regents of the University of Minnesota.
+# All rights reserved.
+#
+# Contributors:
+#    Richard Berger
+#    Christoph Junghans
+#    Ryan S. Elliott
+#
+
+# - Find KIM-API
+#
+# sets standard pkg_check_modules variables plus:
+#
+# KIM-API-CMAKE_C_COMPILER
+# KIM-API-CMAKE_CXX_COMPILER
+# KIM-API-CMAKE_Fortran_COMPILER
+#
+find_package(PkgConfig REQUIRED)
+include(FindPackageHandleStandardArgs)
+
+pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)
+
+pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
+pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
+pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+
+# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

cmake/Modules/FindKIM.cmake

@@ -1,22 +0,0 @@
-# - Find kim
-# Find the native KIM headers and libraries.
-#
-#  KIM_INCLUDE_DIRS - where to find kim.h, etc.
-#  KIM_LIBRARIES    - List of libraries when using kim.
-#  KIM_FOUND        - True if kim found.
-#
-
-find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
-
-find_library(KIM_LIBRARY NAMES kim-api-v1)
-
-set(KIM_LIBRARIES ${KIM_LIBRARY})
-set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
-
-mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

cmake/Modules/StyleHeaderUtils.cmake

@@ -50,6 +50,7 @@ function(CreateStyleHeader path filename)
         list(REMOVE_AT ARGV 0 1)
         set(header_list)
         foreach(FNAME ${ARGV})
+            set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
             get_filename_component(FNAME ${FNAME} NAME)
             list(APPEND header_list ${FNAME})
         endforeach()
@@ -61,6 +62,7 @@ function(CreateStyleHeader path filename)
     message(STATUS "Generating ${filename}...")
     file(WRITE "${path}/${filename}.tmp" "${temp}" )
     execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+    set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
 endfunction(CreateStyleHeader)
 
 function(GenerateStyleHeader path property style)

cmake/Modules/generate_lmpgitversion.cmake

@@ -0,0 +1,30 @@
+set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
+set(temp_git_commit "(unknown)")
+set(temp_git_branch "(unknown)")
+set(temp_git_describe "(unknown)")
+set(temp_git_info "false")
+if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+  set(temp_git_info "true")
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+    OUTPUT_VARIABLE temp_git_commit
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+    OUTPUT_VARIABLE temp_git_branch
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+    OUTPUT_VARIABLE temp_git_describe
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+
+set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
+set(temp "${temp}#endif\n\n")
+
+message(STATUS "Generating lmpgitversion.h...")
+file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

cmake/README.md

@@ -1503,6 +1503,16 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>CUDA_MPS_SUPPORT</code> (CUDA only)</td>
+  <td>Enable tweaks for running with Nvidia CUDA Multi-process services daemon</td>
+  <td>
+  <dl>
+    <dt><code>on</code></dt>
+    <dt><code>off</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BIN2C</code> (CUDA only)</td>
   <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

doc/.gitignore

@@ -1,3 +1,4 @@
+/old
 /html
 /latex
 /spelling

doc/Makefile

@@ -39,7 +39,7 @@ 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 in old 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)"
@@ -56,7 +56,7 @@ clean-all: clean
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html old epub
+	rm -rf $(RSTDIR) html old epub latex
 	rm -rf spelling
 
 clean-spelling:
@@ -115,21 +115,44 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: utils/txt2html/txt2html.exe
+pdf: $(OBJECTS) $(ANCHORCHECK)
 	@(\
-		set -e; \
 		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
-		cd ..; \
-		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		rm *.html; \
+		cd ../../; \
 	)
+	@(\
+                . $(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 ;\
+                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 ../;
+	@rm -rf latex/_sources
+	@rm -rf latex/PDF
+	@rm -rf latex/USER
+	@cp -r src/PDF latex/PDF
+	@cp -r src/USER latex/USER
+	@rm -rf latex/PDF/.[sg]*
+	@rm -rf latex/USER/.[sg]*
+	@rm -rf latex/USER/*/.[sg]*
+	@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
@@ -139,6 +162,18 @@ old: utils/txt2html/txt2html.exe
 	  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
@@ -176,7 +211,7 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx; \
+		pip install Sphinx==1.7.6; \
 		deactivate;\
 	)
 

doc/src/Build_basics.txt

@@ -116,6 +116,18 @@ 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.
 
+[OpenMP Compiler compatibility info]: :link(default-none-issues)
+
+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.
+
 :line
 
 Choice of compiler and compile/link options :h4,link(compile)

doc/src/Build_extras.txt

@@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
 "POEMS"_#poems,
 "PYTHON"_#python,
 "VORONOI"_#voronoi,
+"USER-ADIOS"_#user-adios,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
@@ -81,17 +82,19 @@ which GPU hardware to build for.
 
 [CMake build]:
 
--D GPU_API=value      # value = opencl (default) or cuda
--D GPU_PREC=value     # precision setting
-                      # value = double or mixed (default) or single
--D OCL_TUNE=value     # hardware choice for GPU_API=opencl
-                      # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
--D GPU_ARCH=value     # primary GPU hardware choice for GPU_API=cuda
-                      # value = sm_XX, see below
-                      # default is Cuda-compiler dependent, but typically sm_20
--D CUDPP_OPT=value    # optimization setting for GPU_API=cuda
-                      # enables CUDA Performance Primitives Optimizations
-                      # yes (default) or no :pre
+-D GPU_API=value          # value = opencl (default) or cuda
+-D GPU_PREC=value         # precision setting
+                          # value = double or mixed (default) or single
+-D OCL_TUNE=value         # hardware choice for GPU_API=opencl
+                          # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+-D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
+                          # value = sm_XX, see below
+                          # default is Cuda-compiler dependent, but typically sm_20
+-D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
+                          # enables CUDA Performance Primitives Optimizations
+                          # value = yes (default) or no
+-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
+                          # value = yes or no (default) :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
@@ -168,39 +171,33 @@ used to build the GPU library.
 
 KIM package :h4,link(kim)
 
-To build with this package, the KIM library must be downloaded and
-built on your system.  It must include the KIM models that you want to
-use with LAMMPS.
+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 "kim_query"_kim_query.html
+command, you also need to have libcurl installed with the matching
+development headers and the curl-config tool.
 
 Note that in LAMMPS lingo, a KIM model driver is a pair style
 (e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
 element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that installing the KIM API
-library with all its models, may take around 30 min to build.  Of
-course you only need to do that once.
+specific EAM potential file.  Also note that downloading and installing
+the KIM API library with all its models, may take a long time (10s of
+minutes to hours) to build.  Of course you only need to do that once.
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
+https://openkim.org/browse/models/by-model-drivers
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # KIM library file (only needed if a custom location)
--D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
-your system (in a location CMake cannot find it), KIM_LIBRARY is the
-filename (plus path) of the KIM library file, not the directory the
-library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
-file is in.
+your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
+environment variable so that libkim-api can be found.
 
 [Traditional make]:
 
@@ -214,8 +211,8 @@ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
 make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
 make lib-kim args="-b -a everything"     # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
 
 :line
 
@@ -576,6 +573,32 @@ the lib/voronoi/Makefile.lammps file.
 
 :line
 
+USER-ADIOS package :h4,link(user-adios)
+
+The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
+version 2.3.1 or newer. Make sure that you have ADIOS built either with or
+without MPI to match if you build LAMMPS with or without MPI.
+ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
+and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
+installation and the instructions below are followed for the respective build systems.
+
+[CMake build]:
+
+-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+-D PKG_USER-ADIOS=yes     :pre
+
+[Traditional make]:
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+make yes-user-adios                       :pre
+
+otherwise, set ADIOS2_DIR environment variable when turning on the package:
+
+ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre
+
+:line
+
 USER-ATC package :h4,link(user-atc)
 
 The USER-ATC package requires the MANYBODY package also be installed.
@@ -874,7 +897,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -883,7 +916,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 
@@ -932,7 +969,9 @@ LINKFLAGS: -fopenmp             # for GNU Compilers
 LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre
 
 For other platforms and compilers, please consult the documentation
-about OpenMP support for your compiler.
+about OpenMP support for your compiler. Please see the note about
+how to address compatibility "issues with the 'default(none)'
+directive"_Build_basics.html#default-none-issues of some compilers.
 
 :line
 

doc/src/Build_package.txt

@@ -48,6 +48,7 @@ packages:
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
 "VORONOI"_Build_extras.html#voronoi,
+"USER-ADIOS"_Build_extras.html#user-adios,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,
 "USER-COLVARS"_Build_extras.html#user-colvars,

doc/src/Commands_all.txt

@@ -48,12 +48,14 @@ An alphabetic list of all general LAMMPS commands.
 "dimension"_dimension.html,
 "displace_atoms"_displace_atoms.html,
 "dump"_dump.html,
+"dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
 "dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
 "fix_modify"_fix_modify.html,
@@ -66,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
+"kim_query"_kim_query.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -76,6 +79,7 @@ An alphabetic list of all general LAMMPS commands.
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
+"min_style spin"_min_spin.html,
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,

doc/src/Commands_fix.txt

@@ -224,7 +224,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran (o)"_fix_wall_gran.html,
+"wall/gran"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Eqs/min_spin_damping.tex

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

doc/src/Eqs/min_spin_timestep.tex

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

doc/src/Errors_messages.txt

@@ -6988,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
-{KIM neighbor iterator exceeded range} :dt
-
-This should not happen.  It likely indicates a bug
-in the KIM implementation of the interatomic potential
-where it is requesting neighbors incorrectly. :dd
-
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -10185,10 +10179,6 @@ valid. :dd
 
 Self-explanatory. :dd
 
-{Unrecognized virial argument in pair_style command} :dt
-
-Only two options are supported: LAMMPSvirial and KIMvirial :dd
-
 {Unsupported mixing rule in kspace_style ewald/disp} :dt
 
 Only geometric mixing is supported. :dd

doc/src/Errors_warnings.txt

@@ -178,12 +178,6 @@ 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. :dd
 
-{Energy tally does not account for 'zero yes'} :dt
-
-The energy removed by using the 'zero yes' flag is not accounted
-for in the energy tally and thus energy conservation cannot be
-monitored in this case. :dd
-
 {Estimated error in splitting of dispersion coeffs is %g} :dt
 
 Error is greater than 0.0001 percent. :dd

doc/src/Howto_pylammps.txt

@@ -57,6 +57,17 @@ library is then loaded by the Python interface. In this example we enable the
 MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
 output support enabled.
 
+Step 1a: For the CMake based build system, the steps are:
+
+mkdir $LAMMPS_DIR/build-shared
+cd  $LAMMPS_DIR/build-shared :pre
+
+# MPI, PNG, Jpeg, FFMPEG are auto-detected
+cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
+make :pre
+
+Step 1b: For the legacy, make based build system, the steps are:
+
 cd $LAMMPS_DIR/src :pre
 
 # add packages if necessary
@@ -68,10 +79,9 @@ make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS
 Step 2: Installing the LAMMPS Python package :h6
 
 PyLammps is part of the lammps Python package. To install it simply install
-that package into your current Python installation.
+that package into your current Python installation with:
 
-cd $LAMMPS_DIR/python
-python install.py :pre
+make install-python :pre
 
 NOTE: Recompiling the shared library requires re-installing the Python package
 
@@ -94,14 +104,21 @@ apt-get install python-virtualenv :pre
 
 Creating a virtualenv with lammps installed :h6
 
-# create virtualenv name 'testing' :pre
+# create virtualenv named 'testing'
+virtualenv $HOME/python/testing :pre
 
 # activate 'testing' environment
-source testing/bin/activate :pre
+source $HOME/python/testing/bin/activate :pre
+
+Now configure and compile the LAMMPS shared library as outlined above.
+When using CMake and the shared library has already been build, you
+need to re-run CMake to update the location of the python executable
+to the location in the virtual environment with:
+
+cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
 
 # install LAMMPS package in virtualenv
-(testing) cd $LAMMPS_DIR/python
-(testing) python install.py :pre
+(testing) make install-python :pre
 
 # install other useful packages
 (testing) pip install matplotlib jupyter mpi4py :pre

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="8 Feb 2019 version">
+<META NAME="docnumber" CONTENT="29 Mar 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-8 Feb 2019 version :c,h2
+29 Mar 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -63,6 +63,7 @@ as contained in the file name.
 "SRD"_#PKG-SRD,
 "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
 
+"USER-ADIOS"_#PKG-USER-ADIOS,
 "USER-ATC"_#PKG-USER-ATC,
 "USER-AWPMD"_#PKG-USER-AWPMD,
 "USER-BOCS"_#PKG-USER-BOCS,
@@ -340,18 +341,19 @@ KIM package :link(PKG-KIM),h4
 A "pair_style kim"_pair_kim.html command which is a wrapper on the
 Knowledge Base for Interatomic Models (KIM) repository of interatomic
 potentials, enabling any of them to be used in LAMMPS simulations.
+Also a "kim_query"_kim_query.html command, which allows to query
+the OpenKIM database for stored properties.
 
 To use this package you must have the KIM library available on your
 system.
 
 Information about the KIM project can be found at its website:
 https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota) and James Sethna (Cornell U).
+Elliott (U Minnesota).
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
 API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style in collaboration with Valeriu Smirichinski (U
-Minnesota).
+developed the pair style.
 
 [Install:]
 
@@ -975,6 +977,31 @@ examples/voronoi :ul
 
 :line
 
+USER-ADIOS package :link(PKG-USER-ADIOS),h4
+
+[Contents:]
+
+ADIOS is a high-performance I/O library. This package implements the 
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library. 
+
+[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-adios on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ADIOS: filenames -> commands
+src/USER-ADIOS/README
+examples/USER/adios
+https://github.com/ornladios/ADIOS2 :ul
+
+:line
+
 USER-ATC package :link(PKG-USER-ATC),h4
 
 [Contents:]
@@ -1700,14 +1727,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
+And a "dynamical_matrix" command to compute the dynamical matrix
+from finite differences.
+
+[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
+and Charlie Sievers (UC Davis) for "dynamical_matrix"
 
-[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
+"dynamical_matrix"_dynamical_matrix.html
 examples/USER/phonon :ul
 
 :line
@@ -2102,5 +2134,3 @@ src/USER-YAFF/README
 "pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
 "pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
 examples/USER/yaff :ul
-
-

doc/src/Packages_user.txt

@@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
+"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no

doc/src/Python_install.txt

@@ -12,16 +12,23 @@ Installing LAMMPS in Python :h3
 For Python to invoke LAMMPS, there are 2 files it needs to know about:
 
 python/lammps.py
-src/liblammps.so :ul
+liblammps.so or liblammps.dylib :ul
 
-Lammps.py is the Python wrapper on the LAMMPS library interface.
-Liblammps.so is the shared LAMMPS library that Python loads, as
-described above.
+The python source code in lammps.py is the Python wrapper on the
+LAMMPS library interface. The liblammps.so or liblammps.dylib file
+is the shared LAMMPS library that Python loads dynamically.
 
-You can insure Python can find these files in one of two ways:
+You can achieve that Python can find these files in one of two ways:
 
-set two environment variables
-run the python/install.py script :ul
+set two environment variables pointing to the location in the source tree
+run "make install-python" or run the python/install.py script explicitly :ul
+
+When calling "make install-python" LAMMPS will try to install the
+python module and the shared library into the python site-packages folders;
+either the system-wide ones, or the local users ones (in case of insufficient
+permissions for the global install). Python will then find the module
+and shared library file automatically. The exact location of these folders
+depends on your python version and your operating system.
 
 If you set the paths to these files as environment variables, you only
 have to do it once.  For the csh or tcsh shells, add something like
@@ -30,42 +37,28 @@ this to your ~/.cshrc file, one line for each of the two files:
 setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
 setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
 
-If you use the python/install.py script, you need to invoke it every
-time you rebuild LAMMPS (as a shared library) or make changes to the
-python/lammps.py file.
+On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.
+For Bourne/Korn shells accordingly into the corresponding files using
+the "export" shell builtin.
 
-You can invoke install.py from the python directory as
+If you use "make install-python" or the python/install.py script, you need
+to invoke it every time you rebuild LAMMPS (as a shared library) or
+make changes to the python/lammps.py file, so that the site-packages
+files are updated with the new version.
 
-% python install.py \[libdir\] \[pydir\] :pre
+If the default settings of "make install-python" are not what you want,
+you can invoke install.py from the python directory manually as
 
-The optional libdir is where to copy the LAMMPS shared library to; the
-default is /usr/local/lib.  The optional pydir is where to copy the
-lammps.py file to; the default is the site-packages directory of the
-version of Python that is running the install script.
+% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre
 
-Note that libdir must be a location that is in your default
-LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib.  And pydir must be a
-location that Python looks in by default for imported modules, like
-its site-packages dir.  If you want to copy these files to
-non-standard locations, such as within your own user space, you will
-need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
-accordingly, as above.
+The -m flag points to the lammps.py python module file to be installed,
+the -l flag points to the LAMMPS shared library file to be installed,
+the -v flag points to the version.h file in the LAMMPS source
+and the optional -d flag to a custom (legacy) installation folder :ul
 
-If the install.py script does not allow you to copy files into system
-directories, prefix the python command with "sudo".  If you do this,
-make sure that the Python that root runs is the same as the Python you
-run.  E.g. you may need to do something like
-
-% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
-
-You can also invoke install.py from the make command in the src
-directory as
-
-% make install-python :pre
-
-In this mode you cannot append optional arguments.  Again, you may
-need to prefix this with "sudo".  In this mode you cannot control
-which Python is invoked by root.
+If you use a legacy installation folder, you will need to set your
+PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment
+variables accordingly, as described above.
 
 Note that if you want Python to be able to load different versions of
 the LAMMPS shared library (see "this section"_Python_shlib.html), you will

doc/src/Python_overview.txt

@@ -13,11 +13,11 @@ Overview of Python and LAMMPS :h3
 LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the its "library interface"_Howto_library.html, so
 that a Python script can create one or more instances of LAMMPS and
-launch one or more simulations.  In Python lingo, this is "extending"
-Python with LAMMPS.
+launch one or more simulations.  In Python lingo, this is called
+"extending" Python with a LAMMPS module.
 
 Second, a lower-level Python interface can be used indirectly through
-provided PyLammps and IPyLammps wrapper classes, written in Python.
+the provided PyLammps and IPyLammps wrapper classes, written in Python.
 These wrappers try to simplify the usage of LAMMPS in Python by
 providing an object-based interface to common LAMMPS functionality.
 They also reduces the amount of code necessary to parameterize LAMMPS
@@ -25,11 +25,12 @@ scripts through Python and make variables and computes directly
 accessible.
 
 Third, LAMMPS can use the Python interpreter, so that a LAMMPS
-input script can invoke Python code directly, and pass information
-back-and-forth between the input script and Python functions you
-write.  This Python code can also callback to LAMMPS to query or change
-its attributes.  In Python lingo, this is "embedding" Python in
-LAMMPS.  When used in this mode, Python can perform operations that
-the simple LAMMPS input script syntax cannot.
+input script or styles can invoke Python code directly, and pass
+information back-and-forth between the input script and Python
+functions you write.  This Python code can also callback to LAMMPS
+to query or change its attributes through the LAMMPS Python module
+mentioned above.  In Python lingo, this is "embedding" Python in
+LAMMPS.  When used in this mode, Python can perform script operations
+that the simple LAMMPS input script syntax can not.
 
 

doc/src/Speed_intel.txt

@@ -34,6 +34,10 @@ rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
+IMPORTANT NOTE: None of the styles in the USER-INTEL package currently
+support computing per-atom stress.  If any compute or fix in your
+input requires it, LAMMPS will abort with an error message.
+
 [Speed-ups to expect:]
 
 The speedups will depend on your simulation, the hardware, which

doc/src/commands_list.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_adios
    dump_cfg_uef
    dump_h5md
    dump_image
@@ -39,6 +40,7 @@ Commands :h1
    dump_molfile
    dump_netcdf
    dump_vtk
+   dynamical_matrix
    echo
    fix
    fix_modify
@@ -51,6 +53,7 @@ Commands :h1
    include
    info
    jump
+   kim_query
    kspace_modify
    kspace_style
    label
@@ -59,6 +62,7 @@ Commands :h1
    mass
    message
    min_modify
+   min_spin
    min_style
    minimize
    molecule

doc/src/compute.txt

@@ -54,9 +54,10 @@ local quantities have the word "local" in their style,
 e.g. {bond/local}.  Styles with neither "atom" or "local" in their
 style produce global quantities.
 
-Note that a single compute produces either global or per-atom or local
-quantities, but never more than one of these (with only a few
-exceptions, as documented by individual compute commands).
+Note that a single compute can produce either global or per-atom or
+local quantities, but not both global and per-atom.  It can produce
+local quantities in tandem with global or per-atom quantities.  The
+compute doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The

doc/src/compute_group_group.txt

@@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by
 this compute.  For example, 3-body and other many-body potentials,
 such as "Tersoff"_pair_tersoff.html and
 "Stillinger-Weber"_pair_sw.html cannot be used.  "EAM"_pair_eam.html
-potentials only include the pair potential portion of the EAM
-interaction when used by this compute, not the embedding term.
+potentials will re-use previously computed embedding term contributions,
+so the computed pairwise forces and energies are based on the whole
+system and not valid if particles have been moved since.
 
-Not all Kspace styles support calculation of group/group interactions.
-The {ewald} and {pppm} styles do.
+Not all "Kspace styles"_kspace_style.html support the calculation of
+group/group interactions. The regular {ewald} and {pppm} styles do.
 
 [Related commands:] none
 

doc/src/compute_ptm_atom.txt

@@ -38,20 +38,20 @@ ico (icosahedral) = 4
 sc (simple cubic) = 5
 dcub (diamond cubic) = 6
 dhex (diamond hexagonal) = 7
-other = 8 :ul
+graphene = 8 :ul
 
-The value of the PTM structure will be 0 for atoms not in the specified
+The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
 compute group.  The choice of structures to search for can be specified using the "structures"
 argument, which is a hyphen-separated list of structure keywords.
 Two convenient pre-set options are provided:
 
 default: fcc-hcp-bcc-ico
-all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
+all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul
 
 The 'default' setting detects the same structures as the Common Neighbor Analysis method.
-The 'all' setting searches for all structure types.  A small performance penalty is
-incurred for the diamond structures, so it is not recommended to use this option if
-it is known that the simulation does not contain diamond structures.
+The 'all' setting searches for all structure types.  A performance penalty is
+incurred for the diamond and graphene structures, so it is not recommended to use this option if
+it is known that the simulation does not contain these structures.
 
 
 PTM identifies structures using two steps.  First, a graph isomorphism test is used
@@ -93,9 +93,9 @@ interatomic distance
 qw
 qx
 qy
-qw :ul
+qz :ul
 
-The type is a number from 0 to 8.  The rmsd is a positive real number.
+The type is a number from -1 to 8.  The rmsd is a positive real number.
 The interatomic distance is computed from the scale factor in the RMSD equation.
 The (qw,qx,qy,qz) parameters represent the orientation of the local structure
 in quaternion form.  The reference coordinates for each template (from which the

doc/src/dump.txt

@@ -13,6 +13,7 @@ dump command :h3
 "dump netcdf"_dump_netcdf.html command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
+"dump adios"_dump_adios.html command :h3
 
 [Syntax:]
 
@@ -27,10 +28,12 @@ args = list of arguments for a particular style :l
   {atom} args = none
   {atom/gz} args = none
   {atom/mpiio} args = none
+  {atom/adios} args = none,  discussed on "dump adios"_dump_adios.html doc page
   {cfg} args = same as {custom} args, see below
   {cfg/gz} args = same as {custom} args, see below
   {cfg/mpiio} args = same as {custom} args, see below
   {custom}, {custom/gz}, {custom/mpiio} args = see below
+  {custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page
   {dcd} args = none
   {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
   {image} args = discussed on "dump image"_dump_image.html doc page
@@ -653,7 +656,7 @@ package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
+"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
 "dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html,
 "undump"_undump.html
 

doc/src/dump_adios.txt

@@ -0,0 +1,73 @@
+"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
+
+dump atoms/adios  command :h3
+dump custom/adios command :h3
+
+[Syntax:]
+
+dump ID group-ID atoms/adios N file.bp :pre
+dump ID group-ID custom/adios N file.bp args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file.bp = name of file/stream to write to :l
+args = same options as in "{dump custom}"_dump.html command :l
+:ule
+
+
+[Examples:]
+
+dump adios1 all atom/adios   100 atoms.bp
+dump 4a     all custom/adios 100 dump_adios.bp id v_p x y z
+dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in the
+"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS,
+to a stream that can be read on-line by another program.
+ADIOS-BP files are binary, portable and self-describing.
+
+:link(adios,https://github.com/ornladios/ADIOS2)
+
+
+[Use from write_dump:]
+
+It is possible to use these dump styles with the
+"write_dump"_write_dump.html command.  In this case, the sub-intervals
+must not be set at all.  The write_dump command can be used to
+create a new file at each individual dump.
+
+dump 4     all atom/adios 100 dump.bp
+write_dump all atom/adios singledump.bp :pre
+
+:line
+
+[Restrictions:]
+
+The number of atoms per snapshot CAN change with the adios style.
+When using the ADIOS tool 'bpls' to list the content of a .bp file,
+bpls will print {__} for the size of the output table indicating that
+its size is changing every step.
+
+The {atom/adios} and {custom/adios} dump styles are part of the USER-ADIOS
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Build package"_Build_package.html doc page for more info.
+
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+
+:line
+

doc/src/dynamical_matrix.txt

@@ -0,0 +1,52 @@
+"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
+
+dynamical_matrix command :h3
+
+[Syntax:]
+
+dynamical_matrix group-ID style gamma args keyword value ... :pre
+
+group-ID = ID of group of atoms to displace :ulb,l
+style = {regular} or {eskm} :l
+gamma = finite different displacement length (distance units) :l
+one or more keyword/arg pairs may be appended :l
+  keyword = {file} or {binary}
+    {file} name = name of output file for the dynamical matrix
+    {binary} arg = {yes} or {no} or {gzip} :pre
+:ule
+
+[Examples:]
+
+dynamical_matrix 1 regular 0.000001
+dynamical_matrix 1 eskm 0.000001
+dynamical_matrix 3 regular 0.00004 file dynmat.dat
+dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
+
+[Description:]
+
+Calculate the dynamical matrix of the selected group.
+
+[Restrictions:]
+
+The command collects the entire dynamical matrix a single MPI rank,
+so the memory requirements can be very significant for large systems.
+
+This command assumes a periodic system.
+
+This command is part of the USER-PHONON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix phonon"_fix_phonon.html
+
+[Default:]
+
+The default settings are file = "dynmat.dyn", binary = no  

doc/src/fix.txt

@@ -83,8 +83,10 @@ not in the specified fix group.  Local quantities are calculated by
 each processor based on the atoms it owns, but there may be zero or
 more per atoms.
 
-Note that a single fix may produces either global or per-atom or local
-quantities (or none at all), but never more than one of these.
+Note that a single fix can produce either global or per-atom or local
+quantities (or none at all), but not both global and per-atom.  It can
+produce local quantities in tandem with global or per-atom quantities.
+The fix doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The

doc/src/fix_adapt.txt

@@ -158,12 +158,6 @@ the pair_*.cpp file associated with the potential.
 
 Some parameters are global settings for the pair style, e.g. the
 viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
-For "pair_kim"_pair_kim.html, all free parameters supported by the
-KIM Model are available (e.g., PARAM_FREE_sigmas provided by the
-LennardJones612_Universal__MO_826355984548_001 Model).  If the free
-parameter corresponds to an array, then the particular array element
-to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to
-adapt the tenth entry of the sigmas array).
 Other parameters apply to atom type pairs within the pair style,
 e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
 

doc/src/fix_ave_histo.txt

@@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
   {mode} arg = {scalar} or {vector}
     scalar = all input values are scalars
     vector = all input values are vectors
+  {kind} arg = {global} or {peratom} or {local}
   {file} arg = filename
     filename = name of file to output histogram(s) to
   {ave} args = {one} or {running} or {window}
@@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities.  Inputs of
 different kinds (e.g. global and per-atom) cannot be mixed.  Atom
 attributes are per-atom vector values.  See the doc page for
 individual "compute" and "fix" commands to see what kinds of
-quantities they generate.
+quantities they generate.  See the optional {kind} keyword below for
+how to force the fix ave/histo command to disambiguate if necessary.
 
 Note that the output of this command is a single histogram for all
 input values combined together, not one histogram per input value.
@@ -231,6 +233,14 @@ keyword is set to {vector}, then all input values must be global or
 per-atom or local vectors, or columns of global or per-atom or local
 arrays.
 
+The {kind} keyword only needs to be set if a compute or fix produces
+more than one kind of output (global, per-atom, local).  If this is
+not the case, then LAMMPS will determine what kind of input is
+provided and whether all the input arguments are consistent.  If a
+compute or fix produces more than one kind of output, the {kind}
+keyword should be used to specify which output will be used.  The
+remaining input arguments must still be consistent.
+
 The {beyond} keyword determines how input values that fall outside the
 {lo} to {hi} bounds are treated.  Values such that {lo} <= value <=
 {hi} are assigned to one bin.  Values on a bin boundary are assigned
@@ -240,7 +250,7 @@ If {beyond} is set to {end} then values < {lo} are counted in the
 first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
-values > {hi} are counted in the last bin (Nbins+1).  Values between
+values > {hi} are counted in the last bin (Nbins+2).  Values between
 {lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
@@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
 
 [Default:] none
 
-The option defaults are mode = scalar, ave = one, start = 0, no file
-output, beyond = ignore, and title 1,2,3 = strings as described above.
+The option defaults are mode = scalar, kind = figured out from input
+arguments, ave = one, start = 0, no file output, beyond = ignore, and
+title 1,2,3 = strings as described above.

doc/src/fix_bond_react.txt

@@ -146,18 +146,18 @@ A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms I,J within the specified react-group-ID of type
 itype and jtype must be separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
-identified: if the bonding atoms in the pre-reacted template are not
-1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
-its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atom I and atom J have each other as their
-nearest bonding partners, these two atoms are identified as the
-bonding atom pair of the reaction site. Once this unique bonding atom
-pair is identified for each reaction, there could two or more
-reactions that involve a given atom on the same timestep. If this is
-the case, only one such reaction is permitted to occur. This reaction
-is chosen randomly from all potential reactions. This capability
-allows e.g. for different reaction pathways to proceed from identical
-reaction sites with user-specified probabilities.
+identified: if the bonding atoms in the pre-reacted template are  1-2
+neighbors, i.e. directly bonded, the farthest bonding atom partner is
+set as its bonding partner; otherwise, the closest potential partner
+is chosen. Then, if both an atom I and atom J have each other as their
+bonding partners, these two atoms are identified as the bonding atom
+pair of the reaction site. Once this unique bonding atom pair is
+identified for each reaction, there could two or more reactions that
+involve a given atom on the same timestep. If this is the case, only
+one such reaction is permitted to occur. This reaction is chosen
+randomly from all potential reactions. This capability allows e.g. for
+different reaction pathways to proceed from identical reaction sites
+with user-specified probabilities.
 
 The pre-reacted molecule template is specified by a molecule command.
 This molecule template file contains a sample reaction site and its
@@ -385,6 +385,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
+When fix bond/react is 'unfixed,' all internally-created groups are
+deleted. Therefore, fix bond/react can only be unfixed after unfixing
+all other fixes that use any group created by fix bond/react.
+
 [Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if

doc/src/fix_hyper_global.txt

@@ -102,7 +102,7 @@ Bi = exp(beta * Vij(max)) :pre
 where beta = 1/kTequil, and {Tequil} is the temperature of the system
 and an argument to this fix.  Note that Bi >= 1 at every step.
 
-NOTE: To run GHD, the input script must also use the "fix
+NOTE: To run a GHD simulation, the input script must also use the "fix
 langevin"_fix_langevin.html command to thermostat the atoms at the
 same {Tequil} as specified by this fix, so that the system is running
 constant-temperature (NVT) dynamics.  LAMMPS does not check that this
@@ -166,9 +166,9 @@ correctly.  There will just be fewer events because the hyper time
 
 NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
-{Vmax} you can use for an LHD model, is to run a sequence of
+{Vmax} you can use for a GHD model, is to run a sequence of
 simulations with smaller and smaller {Vmax} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
 
 The {Tequil} argument is the temperature at which the system is
 simulated; see the comment above about the "fix
@@ -177,7 +177,8 @@ beta term in the exponential factor that determines how much boost is
 achieved as a function of the bias potential.
 
 In general, the lower the value of {Tequil} and the higher the value
-of {Vmax}, the more boost will be achievable by the GHD algorithm.
+of {Vmax}, the more time boost will be achievable by the GHD
+algorithm.
 
 :line
 
@@ -190,41 +191,43 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy of the bias potential to the the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 11, which
+This fix computes a global scalar and global vector of length 12, which
 can be accessed by various "output commands"_Howto_output.html.  The
 scalar is the magnitude of the bias potential (energy units) applied on
 the current timestep.  The vector stores the following quantities:
 
 1 = boost factor on this step (unitless)
-2 = max strain Eij of any bond on this step (unitless)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
 3 = ID of first atom in the max-strain bond
 4 = ID of second atom in the max-strain bond
 5 = average # of bonds/atom on this step :ul
 
-6 = fraction of timesteps with bias = 0.0 during this run
-7 = max drift distance of any atom during this run (distance units)
-8 = max bond length during this run (distance units) :ul
+6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
+7 = fraction of timesteps where the biased bond has negative strain during this run
+8 = max drift distance of any atom during this run (distance units)
+9 = max bond length during this run (distance units) :ul
 
-9 = cumulative hyper time since fix was defined (time units)
-10 = cumulative count of event timesteps since fix was defined
-11 = cumulative count of atoms in events since fix was defined :ul
+10 = cumulative hyper time since fix was defined (time units)
+11 = cumulative count of event timesteps since fix was defined
+12 = cumulative count of atoms in events since fix was defined :ul
 
-The first 5 quantities are for the current timestep.  Quantities 6-8
-are for the current hyper run.  Quantities 9-11 are cumulative across
-multiple runs (since the fix was defined in the input script).
+The first 5 quantities are for the current timestep.  Quantities 6-9
+are for the current hyper run.  They are reset each time a new hyper
+run is performed.  Quantities 19-12 are cumulative across multiple
+runs (since the point in the input script the fix was defined).
 
-For value 7, drift is the distance an atom moves between timesteps
-when the bond list is reset, i.e. between events.  Atoms involved in
-an event will typically move the greatest distance since others are
-typically oscillating around their lattice site.
+For value 8, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
 
-For value 10, events are checked for by the "hyper"_hyper.html command
+For value 11, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 11, each time the "hyper"_hyper.html command checks for an
+For value 12, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
 more than some distance from the previous quench state.  Value 11 is

doc/src/fix_hyper_local.txt

@@ -22,10 +22,9 @@ Dcut = minimum distance between boosted bonds (distance units) :l
 alpha = boostostat relaxation time (time units) :l
 Btarget = desired time boost factor (unitless) :l
 zero or more keyword/value pairs may be appended :l
-keyword = {lost} or {check/bias} or {check/coeff}
-  {lostbond} value = error/warn/ignore
-  {check/bias} values = Nevery error/warn/ignore
-  {check/coeff} values = Nevery error/warn/ignore :pre
+keyword = {check/ghost} or {check/bias} :l
+  {check/ghost} values = none
+  {check/bias} values = Nevery error/warn/ignore :pre
 :ule
 
 [Examples:]
@@ -65,8 +64,8 @@ To understand this description, you should first read the description
 of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
 doc page.  This description of LHD builds on the GHD description.
 
-The definition of bonds, Eij, and Emax are the same for GHD and LHD.
-The formulas for Vij(max) and Fij(max) are also the same except for a
+The definition of bonds and Eij are the same for GHD and LHD.  The
+formulas for Vij(max) and Fij(max) are also the same except for a
 pre-factor Cij, explained below.
 
 The bias energy Vij applied to a bond IJ with maximum strain is
@@ -117,11 +116,11 @@ where Vkl(max) is the bias energy of the maxstrain bond KL within bond
 IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
 of the system and an argument to this fix.
 
-NOTE: To run LHD, the input script must also use the "fix
-langevin"_fix_langevin.html command to thermostat the atoms at the
-same {Tequil} as specified by this fix, so that the system is running
-constant-temperature (NVT) dynamics.  LAMMPS does not check that this
-is done.
+NOTE: To run an LHD simulation, the input script must also use the
+"fix langevin"_fix_langevin.html command to thermostat the atoms at
+the same {Tequil} as specified by this fix, so that the system is
+running constant-temperature (NVT) dynamics.  LAMMPS does not check
+that this is done.
 
 Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
 otherwise it is not.  But regardless, the boost factor Bij can be
@@ -216,20 +215,20 @@ each pair.  E.g. something like 2x the cutoff of the interatomic
 potential.  In practice a {Dcut} value of ~10 Angstroms seems to work
 well for many solid-state systems.
 
-NOTE: You must also insure that ghost atom communication is performed
-for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
-distance one or more atoms move (between quenched states) to be
-considered an "event".  It is an argument to the "compute
-event/displace" command used to detect events.  By default the ghost
-communication distance is set by the pair_style cutoff, which will
-typically be < {Dcut}.  The "comm_modify cutoff"_comm_modify.html
-command can be used to set the ghost cutoff explicitly, e.g.
+NOTE: You should insure that ghost atom communication is performed for
+a distance of at least {Dcut} + {cutevent} = the distance one or more
+atoms move (between quenched states) to be considered an "event".  It
+is an argument to the "compute event/displace" command used to detect
+events.  By default the ghost communication distance is set by the
+pair_style cutoff, which will typically be < {Dcut}.  The "comm_modify
+cutoff"_comm_modify.html command should be used to override the ghost
+cutoff explicitly, e.g.
 
 comm_modify cutoff 12.0 :pre
 
-This fix does not know the {cutevent} parameter, but uses half the
-bond length as an estimate to warn if the ghost cutoff is not long
-enough.
+Note that this fix does not know the {cutevent} parameter, but uses
+half the {cutbond} parameter as an estimate to warn if the ghost
+cutoff is not long enough.
 
 As described above the {alpha} argument is a pre-factor in the
 boostostat update equation for each bond's Cij prefactor.  {Alpha} is
@@ -269,7 +268,30 @@ NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
 {Btarget} you can use for an LHD model, is to run a sequence of
 simulations with smaller and smaller {Btarget} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
+
+:line
+
+Here is additional information on the optional keywords for this fix.
+
+The {check/ghost} keyword turns on extra computation each timestep to
+compute statistics about ghost atoms used to determine which bonds to
+bias.  The output of these stats are the vector values 14 and 15,
+described below.  If this keyword is not enabled, the output
+of the stats will be zero.
+
+The {check/bias} keyword turns on extra computation and communication
+to check if any biased bonds are closer than {Dcut} to each other,
+which should not be the case if LHD is operating correctly.  Thus it
+is a debugging check.  The {Nevery} setting determines how often the
+check is made.  The {error}, {warn}, or {ignore} setting determines
+what is done if the count of too-close bonds is not zero.  Either the
+code will exit, or issue a warning, or silently tally the count.  The
+count can be output as vector value 17, as described below.  If this
+keyword is not enabled, the output of that statistic will be 0.
+
+Note that both of these computations are costly, hence they are only
+enabled by these keywords.
 
 :line
 
@@ -282,95 +304,120 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy of the bias potential to the the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 23,
-which can be accessed by various "output
-commands"_Howto_output.html.  The scalar is the magnitude of
-the bias potential (energy units) applied on the current timestep,
-summed over all biased bonds.  The vector stores the following
-quantities:
+This fix computes a global scalar and global vector of length 21,
+which can be accessed by various "output commands"_Howto_output.html.
+The scalar is the magnitude of the bias potential (energy units)
+applied on the current timestep, summed over all biased bonds.  The
+vector stores the following quantities:
 
 1 = # of biased bonds on this step
-2 = max strain Eij of any bond on this step (unitless)
-3 = average bias potential for all biased bonds on this step (energy units)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
+3 = average bias coeff for all bonds on this step (unitless)
 4 = average # of bonds/atom on this step
 5 = average neighbor bonds/bond on this step within {Dcut} :ul
 
-6 = fraction of steps and bonds with no bias during this run
-7 = max drift distance of any atom during this run (distance units)
-8 = max bond length during this run (distance units)
-9 = average # of biased bonds/step during this run
-10 = average bias potential for all biased bonds during this run (energy units)
-11 = max bias potential for any biased bond during this run (energy units)
-12 = min bias potential for any biased bond during this run (energy units)
-13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
-14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
-15 = count of ghost neighbor atoms not found on reneighbor steps during this run
-16 = count of lost bond partners during this run
-17 = average bias coeff for lost bond partners during this run
-18 = count of bias overlaps found during this run
-19 = count of non-matching bias coefficients found during this run :ul
+6 = max bond length during this run (distance units)
+7 = average # of biased bonds/step during this run
+8 = fraction of biased bonds with no bias during this run
+9 = fraction of biased bonds with negative strain during this run
+10 = average bias coeff for all bonds during this run (unitless)
+11 = min bias coeff for any bond during this run (unitless)
+12 = max bias coeff for any bond during this run (unitless)
 
-20 = cumulative hyper time since fix created (time units)
-21 = cumulative count of event timesteps since fix created
-22 = cumulative count of atoms in events since fix created
-23 = cumulative # of new bonds since fix created :ul
+13 = max drift distance of any bond atom during this run (distance units)
+14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
+15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
+16 = count of ghost atoms that could not be found on reneighbor steps during this run
+17 = count of bias overlaps (< Dcut) found during this run
+
+18 = cumulative hyper time since fix created (time units)
+19 = cumulative count of event timesteps since fix created
+20 = cumulative count of atoms in events since fix created
+21 = cumulative # of new bonds formed since fix created :ul
 
 The first quantities (1-5) are for the current timestep.  Quantities
-6-19 are for the current hyper run.  They are reset each time a new
-hyper run is performed.  Quantities 20-23 are cumulative across
-multiple runs (since the fix was defined in the input script).
+6-17 are for the current hyper run.  They are reset each time a new
+hyper run is performed.  Quantities 18-21 are cumulative across
+multiple runs (since the point in the input script the fix was
+defined).
 
-For value 6, the numerator is a count of all biased bonds on every
+For value 8, the numerator is a count of all biased bonds on each
 timestep whose bias energy = 0.0 due to Eij >= {qfactor}.  The
 denominator is the count of all biased bonds on all timesteps.
 
-For value 7, drift is the distance an atom moves between timesteps
-when the bond list is reset, i.e. between events.  Atoms involved in
-an event will typically move the greatest distance since others are
-typically oscillating around their lattice site.
+For value 9, the numerator is a count of all biased bonds on each
+timestep with negative strain.  The denominator is the count of all
+biased bonds on all timesteps.
 
-For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
-of any bond it is part of, and it is checked for ghost atoms within
-the bond neighbor cutoff.
+Values 13-17 are mostly useful for debugging and diagnostic purposes.
 
-Values 15-19 are mostly useful for debugging and diagnostic purposes.
+For value 13, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
 
-For values 15-17, it is possible that a ghost atom owned by another
-processor will move far enough (e.g. as part of an event-in-progress)
-that it will no longer be within the communication cutoff distance for
-acquiring ghost atoms.  Likewise it may be a ghost atom bond partner
-that cannot be found because it has moved too far.  These values count
-those occurrences.  Because they typically involve atoms that are part
-of events, they do not usually indicate bad dynamics.  Value 16 is the
-average bias coefficient for bonds where a partner atom was lost.
+For values 14-16, neighbor atoms in the full neighbor list with cutoff
+{Dcut} may be ghost atoms outside a processor's sub-box.  Before the
+next event occurs they may move further than {Dcut} away from the
+sub-box boundary.  Value 14 is the furthest (from the sub-box) any
+ghost atom in the neighbor list with maxstrain < {qfactor} was
+accessed during the run.  Value 15 is the same except that the ghost
+atom's maxstrain may be >= {qfactor}, which may mean it is about to
+participate in an event.  Value 16 is a count of how many ghost atoms
+could not be found on reneighbor steps, presumably because they moved
+too far away due to their participation in an event (which will likely
+be detected at the next quench).
 
-For value 18, no two bonds should be biased if they are within a
+Typical values for 14 and 15 should be slightly larger than {Dcut},
+which accounts for ghost atoms initially at a {Dcut} distance moving
+thermally before the next event takes place.
+
+Note that for values 14 and 15 to be computed, the optional keyword
+{check/ghost} must be specified.  Otherwise these values will be zero.
+This is because computing them incurs overhead, so the values are only
+computed if requested.
+
+Value 16 should be zero or small.  As explained above a small count
+likely means some ghost atoms were participating in their own events
+and moved a longer distance.  If the value is large, it likely means
+the communication cutoff for ghosts is too close to {Dcut} leading to
+many not-found ghost atoms before the next event.  This may lead to a
+reduced number of bonds being selected for biasing, since the code
+assumes those atoms are part of highly strained bonds.  As explained
+above, the "comm_modify cutoff"_comm_modify.html command can be used
+to set a longer cutoff.
+
+For value 17, no two bonds should be biased if they are within a
 {Dcut} distance of each other.  This value should be zero, indicating
-that no pair of bonds "overlap", meaning they are closer than {Dcut}
-from each other.
+that no pair of biased bonds are closer than {Dcut} from each other.
 
-For value 19, the same bias coefficient is stored by both atoms in an
-IJ bond.  This value should be zero, indicating that for all bonds,
-each atom in the bond stores the a bias coefficient with the same
-value.
+Note that for values 17 to be computed, the optional keyword
+{check/bias} must be specified and it determines how often this check
+is performed.  This is because performing the check incurs overhead,
+so if only computed as often as requested.
 
-Value 20 is simply the specified {boost} factor times the number of
-timestep times the timestep size.
+The result at the end of the run is the cumulative total from every
+timestep the check was made.  Note that the value is a count of atoms
+in bonds which found other atoms in bonds too close, so it is almost
+always an over-count of the number of too-close bonds.
 
-For value 21, events are checked for by the "hyper"_hyper.html command
+Value 18 is simply the specified {boost} factor times the number of
+timesteps times the timestep size.
+
+For value 19, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 22, each time the "hyper"_hyper.html command checks for an
+For value 20, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
-more than some distance from the previous quench state.  Value 22 is
+more than some distance from the previous quench state.  Value 20 is
 the cumulative count of the number of atoms participating in any of
 the events that were found.
 
-Value 23 tallies the number of new bonds created by the bond reset
+Value 21 tallies the number of new bonds created by the bond reset
 operation.  Bonds between a specific I,J pair of atoms may persist for
 the entire hyperdynamics simulation if neither I or J are involved in
 an event.
@@ -378,6 +425,16 @@ an event.
 The scalar and vector values calculated by this fix are all
 "intensive".
 
+This fix also computes a local vector of length the number of bonds
+currently in the system.  The value for each bond is its Cij prefactor
+(bias coefficient).  These values can be can be accessed by various
+"output commands"_Howto_output.html.  A particularly useful one is the
+"fix ave/histo"_fix_ave_histo.html command which can be used to
+histogram the Cij values to see if they are distributed reasonably
+close to 1.0, which indicates a good choice of {Vmax}.
+
+The local values calculated by this fix are unitless.
+
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
@@ -392,7 +449,9 @@ doc page for more info.
 
 "hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
 
-[Default:] None
+[Default:]
+
+The check/ghost and check/bias keywords are not enabled by default.
 
 :line
 

doc/src/fix_langevin.txt

@@ -217,10 +217,6 @@ the particles.  As described below, this energy can then be printed
 out or added to the potential energy of the system to monitor energy
 conservation.
 
-NOTE: this accumulated energy does NOT include kinetic energy removed
-by the {zero} flag. LAMMPS will print a warning when both options are
-active.
-
 The keyword {zero} can be used to eliminate drift due to the
 thermostat. Because the random forces on different atoms are
 independent, they do not sum exactly to zero.  As a result, this fix

doc/src/fix_phonon.txt

@@ -179,7 +179,8 @@ settings"_Build_settings.html doc page for details.
 
 [Related commands:]
 
-"compute msd"_compute_msd.html
+"compute msd"_compute_msd.html,
+"dynamical_matrix"_dynamical_matrix.html
 
 [Default:]
 

doc/src/fix_wall_gran.txt

@@ -7,22 +7,24 @@
 :line
 
 fix wall/gran command :h3
-fix wall/gran/omp command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/gran fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... :pre
+fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 wall/gran = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
-  possible choices: hooke, hooke/history, hertz/history :pre
-Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
-Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
-gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
-gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
-xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
-dampflag = 0 or 1 if tangential damping force is excluded or included :l
+  possible choices: hooke, hooke/history, hertz/history, granular :pre
+fstyle_params = parameters associated with force interaction style :l
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
 args = list of arguments for a particular style :l
   {xplane} or {yplane} or {zplane} args = lo hi
@@ -44,7 +46,10 @@ keyword = {wiggle} or {shear} :l
 
 fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
 fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
-fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 :pre
+fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 
+fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
+fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
+fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
 
 [Description:]
 
@@ -54,31 +59,40 @@ close enough to touch it.
 
 The nature of the wall/particle interactions are determined by the
 {fstyle} setting.  It can be any of the styles defined by the
-"pair_style granular"_pair_gran.html commands.  Currently this is
-{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
-force between the wall and particles touching it is the same as the
-corresponding equation on the "pair_style granular"_pair_gran.html doc
-page, in the limit of one of the two particles going to infinite
-radius and mass (flat wall).  Specifically, delta = radius - r =
-overlap of particle with wall, m_eff = mass of particle, and the
-effective radius of contact = RiRj/Ri+Rj is just the radius of the
-particle.
+"pair_style gran/*"_pair_gran.html or the more general "pair_style
+granular"_pair_granular.html" commands.  Currently the options are
+{hooke}, {hooke/history}, or {hertz/history} for the former, and
+{granular} with all the possible options of the associated
+{pair_coeff} command for the latter.  The equation for the force
+between the wall and particles touching it is the same as the
+corresponding equation on the "pair_style gran/*"_pair_gran.html and
+"pair_style_granular"_pair_granular.html doc pages, in the limit of
+one of the two particles going to infinite radius and mass (flat
+wall).  Specifically, delta = radius - r = overlap of particle with
+wall, m_eff = mass of particle, and the effective radius of contact =
+RiRj/Ri+Rj is set to the radius of the particle.
 
 The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
 have the same meaning and units as those specified with the
-"pair_style granular"_pair_gran.html commands.  This means a NULL can
-be used for either {Kt} or {gamma_t} as described on that page.  If a
+"pair_style gran/*"_pair_gran.html commands.  This means a NULL can be
+used for either {Kt} or {gamma_t} as described on that page.  If a
 NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
 {Kn}.  If a NULL is used for {gamma_t}, then a default value is used
 where {gamma_t} = 1/2 {gamma_n}.
 
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the "pair_style
+granular"_pair_granular.html through its {pair_coeff} command are also
+supported for walls. These are discussed in greater detail on the doc
+page for "pair_style granular"_pair_granular.html.
+
 Note that you can choose a different force styles and/or different
-values for the 6 wall/particle coefficients than for particle/particle
+values for the wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
 material.
 
 NOTE: As discussed on the doc page for "pair_style
-granular"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
+gran/*"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
 different equation for Hertzian interactions.  This means Hertizian
 wall/particle interactions have also changed.  They now include a
 sqrt(radius) term which was not present before.  Also the previous
@@ -108,14 +122,14 @@ Optionally, the wall can be moving, if the {wiggle} or {shear}
 keywords are appended.  Both keywords cannot be used together.
 
 For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
-the oscillations of particles which can be specified by the
-"fix move"_fix_move.html command.  This is useful in packing
-simulations of granular particles.  The arguments to the {wiggle}
-keyword specify a dimension for the motion, as well as it's
-{amplitude} and {period}.  Note that if the dimension is in the plane
-of the wall, this is effectively a shearing motion.  If the dimension
-is perpendicular to the wall, it is more of a shaking motion.  A
-{zcylinder} wall can only be wiggled in the z dimension.
+the oscillations of particles which can be specified by the "fix
+move"_fix_move.html command.  This is useful in packing simulations of
+granular particles.  The arguments to the {wiggle} keyword specify a
+dimension for the motion, as well as it's {amplitude} and {period}.
+Note that if the dimension is in the plane of the wall, this is
+effectively a shearing motion.  If the dimension is perpendicular to
+the wall, it is more of a shaking motion.  A {zcylinder} wall can only
+be wiggled in the z dimension.
 
 Each timestep, the position of a wiggled wall in the appropriate {dim}
 is set according to this equation:
@@ -137,28 +151,6 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
 {vshear} < 0.  In this case, {vshear} is the tangential velocity of
 the wall at whatever {radius} has been defined.
 
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the shear friction state of atoms interacting with the
@@ -188,6 +180,7 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 "fix move"_fix_move.html,
 "fix wall/gran/region"_fix_wall_gran_region.html,
-"pair_style granular"_pair_gran.html
+"pair_style gran/*"_pair_gran.html
+"pair_style granular"_pair_granular.html
 
 [Default:] none

doc/src/fix_wall_gran_region.txt

@@ -10,24 +10,30 @@ fix wall/gran/region command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
+fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 wall/region = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
-  possible choices: hooke, hooke/history, hertz/history :pre
-Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
-Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
-gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
-gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
-xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
-dampflag = 0 or 1 if tangential damping force is excluded or included :l
+  possible choices: hooke, hooke/history, hertz/history, granular :pre
+fstyle_params = parameters associated with force interaction style :l
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
 region-ID = region whose boundary will act as wall :l,ule
 
 [Examples:]
 
-fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone 
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
+fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
 
 [Description:]
 
@@ -42,8 +48,8 @@ Here are snapshots of example models using this command.
 Corresponding input scripts can be found in examples/granregion.
 Click on the images to see a bigger picture.  Movies of these
 simulations are "here on the Movies
-page"_http://lammps.sandia.gov/movies.html#granregion of the
-LAMMPS web site.
+page"_http://lammps.sandia.gov/movies.html#granregion of the LAMMPS
+web site.
 
 :image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
 :image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
@@ -71,12 +77,13 @@ exterior surfaces of regions.
 Regions can either be primitive shapes (block, sphere, cylinder, etc)
 or combinations of primitive shapes specified via the {union} or
 {intersect} region styles.  These latter styles can be used to
-construct particle containers with complex shapes.  Regions can also
-move dynamically via the "region"_region.html command keywords (move)
-and {rotate}, or change their shape by use of variables as inputs to
-the "region"_region.html command.  If such a region is used with this
-fix, then the region surface will move in time in the corresponding
-manner.
+construct particle containers with complex shapes.
+
+Regions can also move dynamically via the "region"_region.html command
+keywords (move) and {rotate}, or change their shape by use of variables
+as inputs to the "region"_region.html command.  If such a region is used
+with this fix, then the region surface will move in time in the
+corresponding manner.
 
 NOTE: As discussed on the "region"_region.html command doc page,
 regions in LAMMPS do not get wrapped across periodic boundaries.  It
@@ -122,12 +129,16 @@ to make the two faces differ by epsilon in their position.
 
 The nature of the wall/particle interactions are determined by the
 {fstyle} setting.  It can be any of the styles defined by the
-"pair_style granular"_pair_gran.html commands.  Currently this is
-{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
-force between the wall and particles touching it is the same as the
-corresponding equation on the "pair_style granular"_pair_gran.html doc
-page, but the effective radius is calculated using the radius of the
-particle and the radius of curvature of the wall at the contact point.
+"pair_style gran/*"_pair_gran.html or the more general "pair_style
+granular"_pair_granular.html" commands.  Currently the options are
+{hooke}, {hooke/history}, or {hertz/history} for the former, and
+{granular} with all the possible options of the associated
+{pair_coeff} command for the latter.  The equation for the force
+between the wall and particles touching it is the same as the
+corresponding equation on the "pair_style gran/*"_pair_gran.html and
+"pair_style_granular"_pair_granular.html doc pages, but the effective
+radius is calculated using the radius of the particle and the radius
+of curvature of the wall at the contact point.
 
 Specifically, delta = radius - r = overlap of particle with wall,
 m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
@@ -140,12 +151,18 @@ particle.
 
 The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
 have the same meaning and units as those specified with the
-"pair_style granular"_pair_gran.html commands.  This means a NULL can
-be used for either {Kt} or {gamma_t} as described on that page.  If a
+"pair_style gran/*"_pair_gran.html commands.  This means a NULL can be
+used for either {Kt} or {gamma_t} as described on that page.  If a
 NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
 {Kn}.  If a NULL is used for {gamma_t}, then a default value is used
 where {gamma_t} = 1/2 {gamma_n}.
 
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the "pair_style
+granular"_pair_granular.html through its {pair_coeff} command are also
+supported for walls. These are discussed in greater detail on the doc
+page for "pair_style granular"_pair_granular.html.
+
 Note that you can choose a different force styles and/or different
 values for the 6 wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
@@ -153,9 +170,9 @@ material.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-Similar to "fix wall/gran"_fix_wall_gran.html command, this fix
-writes the shear friction state of atoms interacting with the wall to
-"binary restart files"_restart.html, so that a simulation can continue
+Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes
+the shear friction state of atoms interacting with the wall to "binary
+restart files"_restart.html, so that a simulation can continue
 correctly if granular potentials with shear "history" effects are
 being used.  This fix also includes info about a moving region in the
 restart file.  See the "read_restart"_read_restart.html command for
@@ -169,14 +186,14 @@ So you must re-define your region and if it is a moving region, define
 its motion attributes in a way that is consistent with the simulation
 that wrote the restart file.  In particular, if you want to change the
 region motion attributes (e.g. its velocity), then you should ensure
-the position/orientation of the region at the initial restart
-timestep is the same as it was on the timestep the restart file was
-written.  If this is not possible, you may need to ignore info in the
-restart file by defining a new fix wall/gran/region command in your
-restart script, e.g. with a different fix ID.  Or if you want to keep
-the shear history info but discard the region motion information, you
-can use the same fix ID for fix wall/gran/region, but assign it a
-region with a different region ID.
+the position/orientation of the region at the initial restart timestep
+is the same as it was on the timestep the restart file was written.
+If this is not possible, you may need to ignore info in the restart
+file by defining a new fix wall/gran/region command in your restart
+script, e.g. with a different fix ID.  Or if you want to keep the
+shear history info but discard the region motion information, you can
+use the same fix ID for fix wall/gran/region, but assign it a region
+with a different region ID.
 
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for

doc/src/kim_query.txt

@@ -0,0 +1,45 @@
+"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
+
+kim_query command :h3
+
+[Syntax:]
+
+kim_query variable query_function web_query_flags :pre
+
+variable = name of a (string style) variable where the result of the query is stored
+query_function = name of the OpenKIM web API query function to be used
+web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
+
+[Examples:]
+
+kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
+  prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
+
+[Description:]
+
+The kim_query command allows to retrieve properties from the OpenKIM
+through a web query. The result is stored in a string style
+"variable"_variable.html, the name of which must be given as the first
+argument of the kim_query command. The second required argument is the
+name of the actual query function (e.g. {get_test_result}). All following
+arguments are parameters handed over to the web query in the format
+{keyword=value}. This list of supported keywords and the type of how
+the value has to be encoded depends on the query function used.
+For more details on this, please refer to the OpenKIM homepage.
+
+[Restrictions:]
+
+This command is part of the KIM package.  It is only enabled if
+LAMMPS was built with that package.  Furthermore, its correct
+functioning depends on compiling LAMMPS with libcurl support.
+See the "Build package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_style kim"_pair_kim.html, "variable"_variable.html

doc/src/lammps.book

@@ -1,5 +1,5 @@
 #HTMLDOC 1.8.28
--t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all  --owner-password ""  --user-password "" --browserwidth 680 --no-strict --no-overflow
+-t pdf14 -f "Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all  --owner-password ""  --user-password "" --browserwidth 680 --no-strict --no-overflow
 Manual.html
 Intro.html
 Intro_overview.html
@@ -150,6 +150,7 @@ dielectric.html
 dimension.html
 displace_atoms.html
 dump.html
+dump_adios.html
 dump_h5md.html
 dump_image.html
 dump_modify.html
@@ -157,6 +158,7 @@ dump_molfile.html
 dump_netcdf.html
 dump_vtk.html
 dump_cfg_uef.html
+dynamical_matrix.html
 echo.html
 group.html
 group2ndx.html
@@ -165,6 +167,7 @@ if.html
 include.html
 info.html
 jump.html
+kim_query.html
 label.html
 lattice.html
 log.html
@@ -172,6 +175,7 @@ mass.html
 message.html
 min_modify.html
 min_style.html
+min_spin.html
 minimize.html
 molecule.html
 neb.html
@@ -576,6 +580,7 @@ pair_extep.html
 pair_gauss.html
 pair_gayberne.html
 pair_gran.html
+pair_granular.html
 pair_gromacs.html
 pair_gw.html
 pair_ilp_graphene_hbn.html

doc/src/min_modify.txt

@@ -13,11 +13,15 @@ min_modify command :h3
 min_modify keyword values ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {dmax} or {line}
+keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
   {dmax} value = max
     max = maximum distance for line search to move (distance units)
   {line} value = {backtrack} or {quadratic} or {forcezero}
-    backtrack,quadratic,forcezero = style of linesearch to use :pre
+    backtrack,quadratic,forcezero = style of linesearch to use 
+  {alpha_damp} value = damping
+    damping = fictitious Gilbert damping for spin minimization (adim)
+  {discrete_factor} value = factor
+    factor = discretization factor for adaptive spin timestep (adim) :pre
 :ule
 
 [Examples:]
@@ -65,6 +69,17 @@ difference of two large values (energy before and energy after) and
 that difference may be smaller than machine epsilon even if atoms
 could move in the gradient direction to reduce forces further.
 
+Keywords {alpha_damp} and {discrete_factor} only make sense when
+a "min_spin"_min_spin.html command is declared. 
+Keyword {alpha_damp} defines an analog of a magnetic Gilbert
+damping. It defines a relaxation rate toward an equilibrium for
+a given magnetic system. 
+Keyword {discrete_factor} defines a discretization factor for the
+adaptive timestep used in the {spin} minimization. 
+See "min_spin"_min_spin.html for more information about those
+quantities. 
+Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
+
 [Restrictions:] none
 
 [Related commands:]

doc/src/min_spin.txt

@@ -0,0 +1,65 @@
+"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+:line
+
+min_style spin command :h3
+
+[Syntax:]
+
+min_style spin :pre
+
+[Examples:]
+
+min_style 	spin :pre 
+
+[Description:]
+
+Apply a minimization algorithm to use when a "minimize"_minimize.html
+command is performed.
+
+Style {spin} defines a damped spin dynamics with an adaptive
+timestep, according to:
+
+:c,image(Eqs/min_spin_damping.jpg)
+
+with lambda a damping coefficient (similar to a Gilbert
+damping).
+Lambda can be defined by setting the {alpha_damp} keyword with the 
+"min_modify"_min_modify.html command. 
+
+The minimization procedure solves this equation using an
+adaptive timestep. The value of this timestep is defined 
+by the largest precession frequency that has to be solved in the 
+system:
+
+:c,image(Eqs/min_spin_timestep.jpg)
+
+with {|omega|_{max}} the norm of the largest precession frequency
+in the system (across all processes, and across all replicas if a
+spin/neb calculation is performed). 
+
+Kappa defines a discretization factor {discrete_factor} for the 
+definition of this timestep. 
+{discrete_factor} can be defined with the "min_modify"_min_modify.html
+command.
+
+NOTE: The {spin} style replaces the force tolerance by a torque
+tolerance. See "minimize"_minimize.html for more explanation. 
+
+[Restrictions:] 
+
+This minimization procedure is only applied to spin degrees of
+freedom for a frozen lattice configuration.
+
+[Related commands:]
+
+"min_style"_min_style.html, "minimize"_minimize.html, 
+"min_modify"_min_modify.html
+
+[Default:]
+
+The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
+10.0.

doc/src/min_style.txt

@@ -11,11 +11,12 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
+style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
 
 [Examples:]
 
 min_style cg
+min_style spin
 min_style fire :pre
 
 [Description:]
@@ -61,6 +62,10 @@ the velocity non-parallel to the current force vector.  The velocity
 of each atom is initialized to 0.0 by this style, at the beginning of
 a minimization.
 
+Style {spin} is a damped spin dynamics with an adaptive 
+timestep.
+See the "min/spin"_min_spin.html doc page for more information.
+
 Either the {quickmin} and {fire} styles are useful in the context of
 nudged elastic band (NEB) calculations via the "neb"_neb.html command.
 

doc/src/minimize.txt

@@ -103,6 +103,13 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
+NOTE: the "minimization style"_min_style.html {spin} replaces
+the force tolerance {ftol} by a torque tolerance.
+The minimization procedure stops if the 2-norm (length) of the 
+global torque vector (defined as the cross product between the 
+spins and their precession vectors omega) is less than {ftol}, 
+or if any of the other criteria are met.
+
 NOTE: You can also use the "fix halt"_fix_halt.html command to specify
 a general criterion for exiting a minimization, that is a calculation
 performed on the state of the current system, as defined by an

doc/src/pair_granular.txt

@@ -0,0 +1,765 @@
+<script type="text/javascript"
+  src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+"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
+
+pair_style granular command :h3
+
+[Syntax:]
+
+pair_style granular cutoff :pre
+
+cutoff = global cutoff (optional).  See discussion below. :l
+
+[Examples:]
+
+pair_style granular
+pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre
+
+pair_style granular
+pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
+
+pair_style granular
+pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
+
+pair_style granular
+pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
+
+pair_style granular
+pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall
+pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre
+
+[Description:]
+
+The {granular} styles support a variety of options for the normal,
+tangential, rolling and twisting forces resulting from contact between
+two granular particles. This expands on the options offered by the
+"pair gran/*"_pair_gran.html pair styles. The total computed forces
+and torques are the sum of various models selected for the normal,
+tangential, rolling and twisting modes of motion.
+
+All model choices and parameters are entered in the
+"pair_coeff"_pair_coeff.html command, as described below.  Unlike
+e.g. "pair gran/hooke"_pair_gran.html, coefficient values are not
+global, but can be set to different values for different combinations
+of particle types, as determined by the "pair_coeff"_pair_coeff.html
+command.  If the contact model choice is the same for two particle
+types, the mixing for the cross-coefficients can be carried out
+automatically. This is shown in the second example, where model
+choices are the same for type 1 - type 1 as for type 2 - type2
+interactions, but coefficients are different. In this case, the
+coefficients for type 2 - type interactions can be determined from
+mixing rules discussed below.  For additional flexibility,
+coefficients as well as model forms can vary between particle types,
+as shown in the third example: type 1- type 1 interactions are based
+on a Hertzian normal contact model and 2-2 interactions are based on a
+DMT cohesive model (see below).  In that example, 1-1 and 2-2
+interactions have different model forms, in which case mixing of
+coefficients cannot be determined, so 1-2 interactions must be
+explicitly defined via the {pair_coeff 1 2} command, otherwise an
+error would result.
+
+:line
+
+The first required keyword for the {pair_coeff} command is the normal
+contact model. Currently supported options for normal contact models
+and their required arguments are:
+
+{hooke} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
+{hertz} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
+{hertz/material} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\)
+{dmt} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\)
+{jkr} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\) :ol
+
+Here, \(k_n\) is spring stiffness (with units that depend on model
+choice, see below); \(\eta_\{n0\}\) is a damping prefactor (or, in its
+place a coefficient of restitution \(e\), depending on the choice of
+damping mode, see below); E is Young's modulus in units of
+{force}/{length}^2, i.e. {pressure}; \(\nu\) is Poisson's ratio and
+\(\gamma\) is a surface energy density, in units of
+{energy}/{length}^2.
+
+For the {hooke} model, the normal, elastic component of force acting
+on particle {i} due to contact with particle {j} is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\}
+\end\{equation\}
+
+Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
+overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} =
+\mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two
+particle centers (note the i-j ordering so that \(F_\{ne\}\) is
+positive for repulsion), and \(\mathbf\{n\} =
+\frac\{\mathbf\{r\}_\{ij\}\}\{\|\mathbf\{r\}_\{ij\}\|\}\).  Therefore,
+for {hooke}, the units of the spring constant \(k_n\) are
+{force}/{distance}, or equivalently {mass}/{time^2}.
+
+For the {hertz} model, the normal component of force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hertz\} = k_N R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
+\end\{equation\}
+
+Here, \(R_\{eff\} = \frac\{R_i R_j\}\{R_i + R_j\}\) is the effective
+radius, denoted for simplicity as {R} from here on.  For {hertz}, the
+units of the spring constant \(k_n\) are {force}/{length}^2, or
+equivalently {pressure}.
+
+For the {hertz/material} model, the force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hertz/material\} = \frac\{4\}\{3\} E_\{eff\} R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
+\end\{equation\}
+
+Here, \(E_\{eff\} = E = \left(\frac\{1-\nu_i^2\}\{E_i\} +
+\frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}\) is the effective Young's
+modulus, with \(\nu_i, \nu_j \) the Poisson ratios of the particles of
+types {i} and {j}. Note that if the elastic modulus and the shear
+modulus of the two particles are the same, the {hertz/material} model
+is equivalent to the {hertz} model with \(k_N = 4/3 E_\{eff\}\)
+
+The {dmt} model corresponds to the
+"(Derjaguin-Muller-Toporov)"_#DMT1975 cohesive model, where the force
+is simply Hertz with an additional attractive cohesion term:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, dmt\} = \left(\frac\{4\}\{3\} E R^\{1/2\}\delta_\{ij\}^\{3/2\} - 4\pi\gamma R\right)\mathbf\{n\}
+\end\{equation\}
+
+The {jkr} model is the "(Johnson-Kendall-Roberts)"_#JKR1971 model,
+where the force is computed as:
+
+\begin\{equation\}
+\label\{eq:force_jkr\}
+\mathbf\{F\}_\{ne, jkr\} = \left(\frac\{4Ea^3\}\{3R\} - 2\pi a^2\sqrt\{\frac\{4\gamma E\}\{\pi a\}\}\right)\mathbf\{n\}
+\end\{equation\}
+
+Here, {a} is the radius of the contact zone, related to the overlap
+\(\delta\) according to:
+
+\begin\{equation\}
+\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}
+\end\{equation\}
+
+LAMMPS internally inverts the equation above to solve for {a} in terms
+of \(\delta\), then solves for the force in the previous
+equation. Additionally, note that the JKR model allows for a tensile
+force beyond contact (i.e. for \(\delta < 0\)), up to a maximum of
+\(3\pi\gamma R\) (also known as the 'pull-off' force).  Note that this
+is a hysteretic effect, where particles that are not contacting
+initially will not experience force until they come into contact
+\(\delta \geq 0\); as they move apart and (\(\delta < 0\)), they
+experience a tensile force up to \(3\pi\gamma R\), at which point they
+lose contact.
+
+:line
+
+In addition, the normal force is augmented by a damping term of the
+following general form:
+
+\begin\{equation\}
+\mathbf\{F\}_\{n,damp\} = -\eta_n \mathbf\{v\}_\{n,rel\}
+\end\{equation\}
+
+Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i)
+\cdot \mathbf\{n\}\) is the component of relative velocity along
+\(\mathbf\{n\}\).
+
+The optional {damping} keyword to the {pair_coeff} command followed by
+a keyword determines the model form of the damping factor \(\eta_n\),
+and the interpretation of the \(\eta_\{n0\}\) or \(e\) coefficients
+specified as part of the normal contact model settings. The {damping}
+keyword and corresponding model form selection may be appended
+anywhere in the {pair coeff} command.  Note that the choice of damping
+model affects both the normal and tangential damping (and depending on
+other settings, potentially also the twisting damping).  The options
+for the damping model currently supported are:
+
+{velocity}
+{viscoelastic}
+{tsuji} :ol
+
+If the {damping} keyword is not specified, the {viscoelastic} model is
+used by default.
+
+For {damping velocity}, the normal damping is simply equal to the
+user-specified damping coefficient in the {normal} model:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\}\
+\end\{equation\}
+
+Here, \(\gamma_n\) is the damping coefficient specified for the normal
+contact model, in units of {mass}/{time},
+
+The {damping viscoelastic} model is based on the viscoelastic
+treatment of "(Brilliantov et al)"_#Brill1996, where the normal
+damping is given by:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\}\ a m_\{eff\}
+\end\{equation\}
+
+Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a}
+is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models
+except {jkr}, for which it is given implicitly according to \(delta =
+a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  In this case, \eta_\{n0\}\ is in
+units of 1/({time}*{distance}).
+
+The {tsuji} model is based on the work of "(Tsuji et
+al)"_#Tsuji1992. Here, the damping coefficient specified as part of
+the normal model is interpreted as a restitution coefficient
+\(e\). The damping constant \(\eta_n\) is given by:
+
+\begin\{equation\}
+\eta_n = \alpha (m_\{eff\}k_n)^\{1/2\}
+\end\{equation\}
+
+For normal contact models based on material parameters, \(k_n =
+4/3Ea\).  The parameter \(\alpha\) is related to the restitution
+coefficient {e} according to:
+
+\begin\{equation\}
+\alpha = 1.2728-4.2783e+11.087e^2-22.348e^3+27.467e^4-18.022e^5+4.8218e^6
+\end\{equation\}
+
+The dimensionless coefficient of restitution \(e\) specified as part
+of the normal contact model parameters should be between 0 and 1, but
+no error check is performed on this.
+
+The total normal force is computed as the sum of the elastic and
+damping components:
+
+\begin\{equation\}
+\mathbf\{F\}_n = \mathbf\{F\}_\{ne\} + \mathbf\{F\}_\{n,damp\}
+\end\{equation\}
+
+ :line
+
+The {pair_coeff} command also requires specification of the tangential
+contact model. The required keyword {tangential} is expected, followed
+by the model choice and associated parameters. Currently supported
+tangential model choices and their expected parameters are as follows:
+
+{linear_nohistory} : \(x_\{\gamma,t\}\), \(\mu_s\)
+{linear_history} : \(k_t\), \(x_\{\gamma,t\}\), \(\mu_s\)
+{mindlin} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\)
+{mindlin_rescale} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\) :ol
+
+Here, \(x_\{\gamma,t\}\) is a dimensionless multiplier for the normal
+damping \(\eta_n\) that determines the magnitude of the tangential
+damping, \(\mu_t\) is the tangential (or sliding) friction
+coefficient, and \(k_t\) is the tangential stiffness coefficient.
+
+For {tangential linear_nohistory}, a simple velocity-dependent Coulomb
+friction criterion is used, which mimics the behavior of the {pair
+gran/hooke} style. The tangential force (\mathbf\{F\}_t\) is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|\mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+The tangential damping force \(\mathbf\{F\}_\mathrm\{t,damp\}\) is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\mathrm\{t,damp\} = -\eta_t \mathbf\{v\}_\{t,rel\}
+\end\{equation\}
+
+The tangential damping prefactor \(\eta_t\) is calculated by scaling
+the normal damping \(\eta_n\) (see above):
+
+\begin\{equation\}
+\eta_t = -x_\{\gamma,t\} \eta_n
+\end\{equation\}
+
+The normal damping prefactor \(\eta_n\) is determined by the choice of
+the {damping} keyword, as discussed above.  Thus, the {damping}
+keyword also affects the tangential damping.  The parameter
+\(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the
+literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
+"Tsuji et al"_#Tsuji1992, "Silbert et al"_#Silbert2001).  The relative
+tangential velocity at the point of contact is given by
+\(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i +
+R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} =
+\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r =
+\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force
+is \(\mathbf\{t\} =
+\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\).
+
+The normal force value \(F_\{n0\}\) used to compute the critical force
+depends on the form of the contact model. For non-cohesive models
+({hertz}, {hertz/material}, {hooke}), it is given by the magnitude of
+the normal force:
+
+\begin\{equation\}
+F_\{n0\} = \|\mathbf\{F\}_n\|
+\end\{equation\}
+
+For cohesive models such as {jkr} and {dmt}, the critical force is
+adjusted so that the critical tangential force approaches \(\mu_t
+F_\{pulloff\}\), see "Marshall"_#Marshall2009, equation 43, and
+"Thornton"_#Thornton1991.  For both models, \(F_\{n0\}\) takes the
+form:
+
+\begin\{equation\}
+F_\{n0\} = \|\mathbf\{F\}_ne + 2 F_\{pulloff\}\|
+\end\{equation\}
+
+Where \(F_\{pulloff\} = 3\pi \gamma R \) for {jkr}, and
+\(F_\{pulloff\} = 4\pi \gamma R \) for {dmt}.
+
+The remaining tangential options all use accumulated tangential
+displacement (i.e. contact history). This is discussed below in the
+context of the {linear_history} option, but the same treatment of the
+accumulated displacement applies to the other options as well.
+
+For {tangential linear_history}, the tangential force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|-k_t\mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+Here, \(\mathbf\{\xi\}\) is the tangential displacement accumulated
+during the entire duration of the contact:
+
+\begin\{equation\}
+\mathbf\{\xi\} = \int_\{t0\}^t \mathbf\{v\}_\{t,rel\}(\tau) \mathrm\{d\}\tau
+\end\{equation\}
+
+This accumulated tangential displacement must be adjusted to account
+for changes in the frame of reference of the contacting pair of
+particles during contact. This occurs due to the overall motion of the
+contacting particles in a rigid-body-like fashion during the duration
+of the contact. There are two modes of motion that are relevant: the
+'tumbling' rotation of the contacting pair, which changes the
+orientation of the plane in which tangential displacement occurs; and
+'spinning' rotation of the contacting pair about the vector connecting
+their centers of mass (\(\mathbf\{n\}\)).  Corrections due to the
+former mode of motion are made by rotating the accumulated
+displacement into the plane that is tangential to the contact vector
+at each step, or equivalently removing any component of the tangential
+displacement that lies along \(\mathbf\{n\}\), and rescaling to
+preserve the magnitude.  This follows the discussion in
+"Luding"_#Luding2008, see equation 17 and relevant discussion in that
+work:
+
+\begin\{equation\}
+\mathbf\{\xi\} = \left(\mathbf\{\xi'\} - (\mathbf\{n\} \cdot \mathbf\{\xi'\})\mathbf\{n\}\right) \frac\{\|\mathbf\{\xi'\}\|\}\{\|\mathbf\{\xi'\}\| - \mathbf\{n\}\cdot\mathbf\{\xi'\}\}
+\label\{eq:rotate_displacements\}
+\end\{equation\}
+
+Here, \(\mathbf\{\xi'\}\) is the accumulated displacement prior to the
+current time step and \(\mathbf\{\xi\}\) is the corrected
+displacement. Corrections to the displacement due to the second mode
+of motion described above (rotations about \(\mathbf\{n\}\)) are not
+currently implemented, but are expected to be minor for most
+simulations.
+
+Furthermore, when the tangential force exceeds the critical force, the
+tangential displacement is re-scaled to match the value for the
+critical force (see "Luding"_#Luding2008, equation 20 and related
+discussion):
+
+\begin\{equation\}
+\mathbf\{\xi\} = -\frac\{1\}\{k_t\}\left(\mu_t F_\{n0\}\mathbf\{t\} + \mathbf\{F\}_\{t,damp\}\right)
+\end\{equation\}
+
+The tangential force is added to the total normal force (elastic plus
+damping) to produce the total force on the particle. The tangential
+force also acts at the contact point (defined as the center of the
+overlap region) to induce a torque on each particle according to:
+
+\begin\{equation\}
+\mathbf\{\tau\}_i = -(R_i - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
+\end\{equation\}
+
+\begin\{equation\}
+\mathbf\{\tau\}_j = -(R_j - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
+\end\{equation\}
+
+For {tangential mindlin}, the "Mindlin"_#Mindlin1949 no-slip solution is used, which differs from the {linear_history}
+option by an additional factor of {a}, the radius of the contact region. The tangential force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+Here, {a} is the radius of the contact region, given by \(a = \delta
+R\) for all normal contact models, except for {jkr}, where it is given
+implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see
+discussion above. To match the Mindlin solution, one should set \(k_t
+= 8G\), where \(G\) is the shear modulus, related to Young's modulus
+\(E\) by \(G = E/(2(1+\nu))\), where \(\nu\) is Poisson's ratio. This
+can also be achieved by specifying {NULL} for \(k_t\), in which case a
+normal contact model that specifies material parameters \(E\) and
+\(\nu\) is required (e.g. {hertz/material}, {dmt} or {jkr}). In this
+case, mixing of the shear modulus for different particle types {i} and
+{j} is done according to:
+
+\begin\{equation\}
+1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j
+\end\{equation\}
+
+The {mindlin_rescale} option uses the same form as {mindlin}, but the
+magnitude of the tangential displacement is re-scaled as the contact
+unloads, i.e. if \(a < a_\{t_\{n-1\}\}\):
+
+\begin\{equation\}
+\mathbf\{\xi\} = \mathbf\{\xi_\{t_\{n-1\}\}\} \frac\{a\}\{a_\{t_\{n-1\}\}\}
+\end\{equation\}
+
+Here, \(t_\{n-1\}\) indicates the value at the previous time
+step. This rescaling accounts for the fact that a decrease in the
+contact area upon unloading leads to the contact being unable to
+support the previous tangential loading, and spurious energy is
+created without the rescaling above ("Walton"_#WaltonPC ). See also
+discussion in "Thornton et al, 2013"_#Thornton2013 , particularly
+equation 18(b) of that work and associated discussion.
+
+:line
+
+The optional {rolling} keyword enables rolling friction, which resists
+pure rolling motion of particles. The options currently supported are:
+
+{none}
+{sds} : \(k_\{roll\}\), \(\gamma_\{roll\}\), \(\mu_\{roll\}\)  :ol
+
+If the {rolling} keyword is not specified, the model defaults to {none}.
+
+For {rolling sds}, rolling friction is computed via a
+spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed
+by "Luding"_#Luding2008. Unlike the formulation in
+"Marshall"_#Marshall2009, this allows for the required adjustment of
+rolling displacement due to changes in the frame of reference of the
+contacting pair.  The rolling pseudo-force is computed analogously to
+the tangential force:
+
+\begin\{equation\}
+\mathbf\{F\}_\{roll,0\} =  k_\{roll\} \mathbf\{\xi\}_\{roll\}  - \gamma_\{roll\} \mathbf\{v\}_\{roll\}
+\end\{equation\}
+
+Here, \(\mathbf\{v\}_\{roll\} = -R(\mathbf\{\Omega\}_i -
+\mathbf\{\Omega\}_j) \times \mathbf\{n\}\) is the relative rolling
+velocity, as given in "Wang et al"_#Wang2015 and
+"Luding"_#Luding2008. This differs from the expressions given by "Kuhn
+and Bagi"_#Kuhn2004 and used in "Marshall"_#Marshall2009; see "Wang et
+al"_#Wang2015 for details. The rolling displacement is given by:
+
+\begin\{equation\}
+\mathbf\{\xi\}_\{roll\} = \int_\{t_0\}^t \mathbf\{v\}_\{roll\} (\tau) \mathrm\{d\} \tau
+\end\{equation\}
+
+A Coulomb friction criterion truncates the rolling pseudo-force if it
+exceeds a critical value:
+
+\begin\{equation\}
+\mathbf\{F\}_\{roll\} =  min(\mu_\{roll\} F_\{n,0\}, \|\mathbf\{F\}_\{roll,0\}\|)\mathbf\{k\}
+\end\{equation\}
+
+Here, \(\mathbf\{k\} =
+\mathbf\{v\}_\{roll\}/\|\mathbf\{v\}_\{roll\}\|\) is the direction of
+the pseudo-force.  As with tangential displacement, the rolling
+displacement is rescaled when the critical force is exceeded, so that
+the spring length corresponds the critical force. Additionally, the
+displacement is adjusted to account for rotations of the frame of
+reference of the two contacting particles in a manner analogous to the
+tangential displacement.
+
+The rolling pseudo-force does not contribute to the total force on
+either particle (hence 'pseudo'), but acts only to induce an equal and
+opposite torque on each particle, according to:
+
+\begin\{equation\}
+\tau_\{roll,i\} =  R_\{eff\} \mathbf\{n\} \times \mathbf\{F\}_\{roll\}
+\end\{equation\}
+
+\begin\{equation\}
+\tau_\{roll,j\} =  -\tau_\{roll,i\}
+\end\{equation\}
+
+:line
+
+The optional {twisting} keyword enables twisting friction, which
+resists rotation of two contacting particles about the vector
+\(\mathbf\{n\}\) that connects their centers. The options currently
+supported are:
+
+{none}
+{sds} : \(k_\{twist\}\), \(\gamma_\{twist\}\), \(\mu_\{twist\}\)
+{marshall} :ol
+
+If the {twisting} keyword is not specified, the model defaults to {none}.
+
+For both {twisting sds} and {twisting marshall}, a history-dependent
+spring-dashpot-slider is used to compute the twisting torque. Because
+twisting displacement is a scalar, there is no need to adjust for
+changes in the frame of reference due to rotations of the particle
+pair. The formulation in "Marshall"_#Marshall2009 therefore provides
+the most straightforward treatment:
+
+\begin\{equation\}
+\tau_\{twist,0\} = -k_\{twist\}\xi_\{twist\} - \gamma_\{twist\}\Omega_\{twist\}
+\end\{equation\}
+
+Here \(\xi_\{twist\} = \int_\{t_0\}^t \Omega_\{twist\} (\tau)
+\mathrm\{d\}\tau\) is the twisting angular displacement, and
+\(\Omega_\{twist\} = (\mathbf\{\Omega\}_i - \mathbf\{\Omega\}_j) \cdot
+\mathbf\{n\}\) is the relative twisting angular velocity. The torque
+is then truncated according to:
+
+\begin\{equation\}
+\tau_\{twist\} = min(\mu_\{twist\} F_\{n,0\}, \tau_\{twist,0\})
+\end\{equation\}
+
+Similar to the sliding and rolling displacement, the angular
+displacement is rescaled so that it corresponds to the critical value
+if the twisting torque exceeds this critical value:
+
+\begin\{equation\}
+\xi_\{twist\} = \frac\{1\}\{k_\{twist\}\} (\mu_\{twist\} F_\{n,0\}sgn(\Omega_\{twist\}) - \gamma_\{twist\}\Omega_\{twist\})
+\end\{equation\}
+
+For {twisting sds}, the coefficients \(k_\{twist\}, \gamma_\{twist\}\)
+and \(\mu_\{twist\}\) are simply the user input parameters that follow
+the {twisting sds} keywords in the {pair_coeff} command.
+
+For {twisting_marshall}, the coefficients are expressed in terms of
+sliding friction coefficients, as discussed in
+"Marshall"_#Marshall2009 (see equations 32 and 33 of that work):
+
+\begin\{equation\}
+k_\{twist\} = 0.5k_ta^2
+\end\{equation\}
+
+\begin\{equation\}
+\eta_\{twist\} = 0.5\eta_ta^2
+\end\{equation\}
+
+\begin\{equation\}
+\mu_\{twist\} = \frac\{2\}\{3\}a\mu_t
+\end\{equation\}
+
+Finally, the twisting torque on each particle is given by:
+
+\begin\{equation\}
+\mathbf\{\tau\}_\{twist,i\} = \tau_\{twist\}\mathbf\{n\}
+\end\{equation\}
+
+\begin\{equation\}
+\mathbf\{\tau\}_\{twist,j\} = -\mathbf\{\tau\}_\{twist,i\}
+\end\{equation\}
+
+:line
+
+LAMMPS automatically sets pairwise cutoff values for {pair_style
+granular} based on particle radii (and in the case of {jkr} pull-off
+distances). In the vast majority of situations, this is adequate.
+However, a cutoff value can optionally be appended to the {pair_style
+granular} command to specify a global cutoff (i.e. a cutoff for all
+atom types). Additionally, the optional {cutoff} keyword can be passed
+to the {pair_coeff} command, followed by a cutoff value.  This will
+set a pairwise cutoff for the atom types in the {pair_coeff} command.
+These options may be useful in some rare cases where the automatic
+cutoff determination is not sufficient, e.g.  if particle diameters
+are being modified via the {fix adapt} command. In that case, the
+global cutoff specified as part of the {pair_style granular} command
+is applied to all atom types, unless it is overridden for a given atom
+type combination by the {cutoff} value specified in the {pair coeff}
+command.  If {cutoff} is only specified in the {pair coeff} command
+and no global cutoff is appended to the {pair_style granular} command,
+then LAMMPS will use that cutoff for the specified atom type
+combination, and automatically set pairwise cutoffs for the remaining
+atom types.
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+The "pair_modify"_pair_modify.html mix, shift, table, and tail options
+are not relevant for granular pair styles.
+
+Mixing of coefficients is carried out using geometric averaging for
+most quantities, e.g. if friction coefficient for type 1-type 1
+interactions is set to \(\mu_1\), and friction coefficient for type
+2-type 2 interactions is set to \(\mu_2\), the friction coefficient
+for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\)
+(unless explicitly specified to a different value by a {pair_coeff 1 2
+...} command. The exception to this is elastic modulus, only
+applicable to {hertz/material}, {dmt} and {jkr} normal contact
+models. In that case, the effective elastic modulus is computed as:
+
+\begin\{equation\}
+E_\{eff,ij\} = \left(\frac\{1-\nu_i^2\}\{E_i\} + \frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}
+\end\{equation\}
+
+If the {i-j} coefficients \(E_\{ij\}\) and \(\nu_\{ij\}\) are
+explicitly specified, the effective modulus is computed as:
+
+\begin\{equation\}
+E_\{eff,ij\} = \left(\frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\} + \frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\}\right)^\{-1\}
+\end\{equation\}
+
+or
+
+\begin\{equation\}
+E_\{eff,ij\} = \frac\{E_\{ij\}\}\{2(1-\nu_\{ij\})\}
+\end\{equation\}
+
+These pair styles write their information to "binary restart
+files"_restart.html, so a pair_style command does not need to be
+specified in an input script that reads a restart file.
+
+These pair styles can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the pairwise interaction force.  However, the single() function also
+calculates 10 extra pairwise quantities.  The first 3 are the
+components of the tangential force between particles I and J, acting
+on particle I.  The 4th is the magnitude of this tangential force.
+The next 3 (5-7) are the components of the rolling torque acting on
+particle I. The next entry (8) is the magnitude of the rolling torque.
+The next entry (9) is the magnitude of the twisting torque acting
+about the vector connecting the two particle centers.
+The last 3 (10-12) are the components of the vector connecting
+the centers of the two particles (x_I - x_J).
+
+These extra quantities can be accessed by the "compute
+pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
+{p12}.
+
+:line
+
+[Restrictions:]
+
+All the granular pair styles are part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+These pair styles require that atoms store torque and angular velocity
+(omega) as defined by the "atom_style"_atom_style.html.  They also
+require a per-particle radius is stored.  The {sphere} atom style does
+all of this.
+
+This pair style requires you to use the "comm_modify vel
+yes"_comm_modify.html command so that velocities are stored by ghost
+atoms.
+
+These pair styles will not restart exactly when using the
+"read_restart"_read_restart.html command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+"read_restart"_read_restart.html command for more details.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair gran/*"_pair_gran.html
+
+[Default:]
+
+For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
+{twisting none}.
+
+[References:]
+
+:link(Brill1996)
+[(Brilliantov et al, 1996)] Brilliantov, N. V., Spahn, F., Hertzsch,
+J. M., & Poschel, T. (1996).  Model for collisions in granular
+gases. Physical review E, 53(5), 5382.
+
+:link(Tsuji1992) 
+[(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
+T. (1992). Lagrangian numerical simulation of plug flow of
+cohesionless particles in a horizontal pipe. Powder technology, 71(3),
+239-250.
+
+:link(JKR1971)
+[(Johnson et al, 1971)] Johnson, K. L., Kendall, K., & Roberts,
+A. D. (1971).  Surface energy and the contact of elastic
+solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
+
+:link(DMT1975)
+[Derjaguin et al, 1975)] Derjaguin, B. V., Muller, V. M., & Toporov,
+Y. P. (1975). Effect of contact deformations on the adhesion of
+particles. Journal of Colloid and interface science, 53(2), 314-326.
+
+:link(Luding2008)
+[(Luding, 2008)] Luding, S. (2008). Cohesive, frictional powders:
+contact models for tension. Granular matter, 10(4), 235.
+
+:link(Marshall2009)
+[(Marshall, 2009)] Marshall, J. S. (2009). Discrete-element modeling
+of particulate aerosol flows.  Journal of Computational Physics,
+228(5), 1541-1561.
+
+:link(Silbert2001)
+[(Silbert, 2001)] Silbert, L. E., Ertas, D., Grest, G. S., Halsey,
+T. C., Levine, D., & Plimpton, S. J. (2001).  Granular flow down an
+inclined plane: Bagnold scaling and rheology. Physical Review E,
+64(5), 051302.
+
+:link(Kuhn2004)
+[(Kuhn and Bagi, 2005)] Kuhn, M. R., & Bagi, K. (2004). Contact
+rolling and deformation in granular media.  International journal of
+solids and structures, 41(21), 5793-5820.
+
+:link(Wang2015)
+[(Wang et al, 2015)] Wang, Y., Alonso-Marroquin, F., & Guo,
+W. W. (2015).  Rolling and sliding in 3-D discrete element
+models. Particuology, 23, 49-55.
+
+:link(Thornton1991)
+[(Thornton, 1991)] Thornton, C. (1991). Interparticle sliding in the
+presence of adhesion.  J. Phys. D: Appl. Phys. 24 1942
+
+:link(Mindlin1949)
+[(Mindlin, 1949)] Mindlin, R. D. (1949). Compliance of elastic bodies
+in contact.  J. Appl. Mech., ASME 16, 259-268.
+
+:link(Thornton2013)
+[(Thornton et al, 2013)] Thornton, C., Cummins, S. J., & Cleary,
+P. W. (2013).  An investigation of the comparative behaviour of
+alternative contact force models during inelastic collisions. Powder
+Technology, 233, 30-46.
+
+:link(WaltonPC)
+[(Otis R. Walton)] Walton, O.R., Personal Communication	

doc/src/pair_kim.txt

@@ -10,18 +10,13 @@ pair_style kim command :h3
 
 [Syntax:]
 
-pair_style kim virialmode model printflag :pre
+pair_style kim model :pre
 
-virialmode = KIMvirial or LAMMPSvirial
 model = name of KIM model (potential)
-printflag = 1/0 do or do not print KIM descriptor file, optional :ul
 
 [Examples:]
 
-pair_style kim KIMvirial model_Ar_P_Morse
-pair_coeff * * Ar Ar :pre
-
-pair_style kim KIMvirial model_Ar_P_Morse 1
+pair_style kim ex_model_Ar_P_LJ
 pair_coeff * * Ar Ar :pre
 
 [Description:]
@@ -36,14 +31,10 @@ element or alloy and set of parameters, e.g. EAM for Cu with a
 specific EAM potential file.
 
 See the current list of "KIM model
-drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
+drivers"_https://openkim.org/browse/model-drivers/alphabetical.
 
 See the current list of all "KIM
-models"_https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of "example KIM models"_https://openkim.org/kim-api which
-are included in the KIM library by default, in the "What is in the KIM
-API source package?" section.
+models"_https://openkim.org/browse/models/by-model-drivers
 
 To use this pair style, you must first download and install the KIM
 API library from the "OpenKIM website"_https://openkim.org.  The KIM
@@ -53,23 +44,14 @@ building LAMMPS.
 
 See the examples/kim dir for an input script that uses a KIM model
 (potential) for Lennard-Jones.
-
+ 
 :line
 
-The argument {virialmode} determines how the global virial is
-calculated.  If {KIMvirial} is specified, the KIM model performs the
-global virial calculation (if it knows how).  If {LAMMPSvirial} is
-specified, LAMMPS computes the global virial using its fdotr mechanism.
-
 The argument {model} is the name of the KIM model for a specific
 potential as KIM defines it.  In principle, LAMMPS can invoke any KIM
 model.  You should get an error or warning message from either LAMMPS
 or KIM if there is an incompatibility.
 
-The argument {printflag} is optional.  If it is set to a non-zero
-value then a KIM descriptor file is printed when KIM is invoked.  This
-can be useful for debugging.  The default is to not print this file.
-
 Only a single pair_coeff command is used with the {kim} style which
 specifies the mapping of LAMMPS atom types to KIM elements.  This is
 done by specifying N additional arguments after the * * in the
@@ -86,18 +68,14 @@ pair_coeff * * Si Si Si C :pre
 The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
 defined within KIM.  The final C argument maps LAMMPS atom type 4 to C
-as defined within KIM.  If a mapping value is specified as NULL, the
-mapping is not performed.  This can only be used when a {kim}
-potential is used as part of the {hybrid} pair style.  The NULL values
-are placeholders for atom types that will be used with other
-potentials.
+as defined within KIM.
 
 :line
 
 In addition to the usual LAMMPS error messages, the KIM library itself
 may generate errors, which should be printed to the screen.  In this
 case it is also useful to check the kim.log file for additional error
-information.  This file kim.log should be generated in the same
+information.  The file kim.log should be generated in the same
 directory where LAMMPS is running.
 
 To download, build, and install the KIM library on your system, see
@@ -130,7 +108,7 @@ LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.
 
 This current version of pair_style kim is compatible with the
-kim-api package version 1.6.0 and higher.
+kim-api package version 2.0.0 and higher.
 
 [Related commands:]
 

doc/src/pairs.txt

@@ -42,6 +42,7 @@ Pair Styles :h1
    pair_gauss
    pair_gayberne
    pair_gran
+   pair_granular
    pair_gromacs
    pair_gw
    pair_hbond_dreiding

doc/utils/sphinx-config/conf.py

@@ -211,7 +211,9 @@ latex_elements = {
 #'pointsize': '10pt',
 
 # Additional stuff for the LaTeX preamble.
-#'preamble': '',
+'preamble': r'''
+\setcounter{tocdepth}{2}
+'''
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
@@ -229,7 +231,7 @@ latex_documents = [
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 #latex_use_parts = False
-
+latex_toplevel_sectioning = 'part'
 # If true, show page references after internal links.
 #latex_show_pagerefs = False
 

doc/utils/sphinx-config/false_positives.txt

@@ -156,6 +156,8 @@ ba
 Babadi
 backcolor
 Baczewski
+Bagi
+Bagnold
 Bal
 balancer
 Balankura
@@ -250,7 +252,10 @@ Boresch
 Botero
 Botu
 Bouguet
+Bourne
 boxcolor
+bp
+bpls
 bpclermont
 br
 Branduardi
@@ -344,6 +349,7 @@ Cij
 cis
 civ
 clearstore
+Cleary
 Clebsch
 clemson
 Clermont
@@ -370,6 +376,7 @@ Coeff
 CoefficientN
 coeffs
 Coeffs
+cohesionless
 Coker
 Colberg
 coleman
@@ -447,6 +454,7 @@ cuda
 Cuda
 CUDA
 CuH
+Cummins
 Curk
 customIDs
 cutbond
@@ -490,6 +498,7 @@ darkturquoise
 darkviolet
 Das
 Dasgupta
+dashpot
 dat
 datafile
 datums
@@ -527,6 +536,7 @@ Dequidt
 der
 derekt
 Derjagin
+Derjaguin
 Derlet
 Deserno
 Destree
@@ -625,8 +635,11 @@ dVx
 dW
 dx
 dy
+dylib
+dyn
 dyne
 dynes
+dynmat
 Dyre
 Dzyaloshinskii
 Eaa
@@ -1075,6 +1088,7 @@ Hyoungki
 hyperdynamics
 hyperradius
 hyperspherical
+hysteretic
 Ibanez
 ibar
 ibm
@@ -1134,6 +1148,7 @@ interconvert
 interial
 interlayer
 intermolecular
+Interparticle
 interstitials
 Intr
 intra
@@ -1152,6 +1167,7 @@ IPython
 Isele
 isenthalpic
 ish
+Ishida
 iso
 isodemic
 isoenergetic
@@ -1261,6 +1277,7 @@ kcl
 Kd
 KDevelop
 ke
+kepler
 KE
 Keblinski
 keflag
@@ -1294,6 +1311,7 @@ Kondor
 konglt
 Koning
 Kooser
+Korn
 Koskinen
 Koster
 Kosztin
@@ -1378,12 +1396,14 @@ libAtoms
 libawpmd
 libch
 libcolvars
+libcurl
 libdir
 libdl
 libfftw
 libgcc
 libgpu
 libjpeg
+libkim
 liblammps
 Liblammps
 liblink
@@ -1444,6 +1464,7 @@ logfile
 logfreq
 logicals
 Lomdahl
+Lond
 lookups
 Lookups
 LoopVar
@@ -1459,6 +1480,7 @@ lsfftw
 ltbbmalloc
 lubricateU
 lucy
+Luding
 Lussetti
 Lustig
 lwsock
@@ -1497,6 +1519,7 @@ manybody
 MANYBODY
 Maras
 Marrink
+Marroquin
 Marsaglia
 Marseille
 Martyna
@@ -1508,6 +1531,7 @@ masstotal
 Masuhiro
 Matchett
 Materias
+mathbf
 matlab
 matplotlib
 Mattox
@@ -1596,6 +1620,7 @@ Mie
 Mikami
 Militzer
 Minary
+Mindlin
 mincap
 mingw
 minima
@@ -1666,6 +1691,7 @@ mpiexec
 mpiio
 mpirun
 mplayer
+mps
 Mryglod
 mscg
 MSCG
@@ -1949,8 +1975,10 @@ oneway
 onn
 ons
 OO
+opencl
 openKIM
 OpenMP
+openmp
 openmpi
 opls
 Oppelstrup
@@ -2044,6 +2072,7 @@ peru
 Peskin
 Pettifor
 pfactor
+pgi
 ph
 Phillpot
 phiphi
@@ -2081,6 +2110,7 @@ Pmolrotate
 Pmoltrans
 pN
 png
+Podhorszki
 Poiseuille
 Polak
 polarizabilities
@@ -2278,6 +2308,7 @@ rg
 Rg
 Rhaphson
 rheological
+rheology
 rhodo
 Rhodo
 rhodopsin
@@ -2433,6 +2464,7 @@ shockvel
 si
 SiC
 Siepmann
+Sievers
 Sij
 Sikandar
 Silbert
@@ -2593,6 +2625,7 @@ Tait
 taitwater
 Tajkhorshid
 Tamaskovics
+Tanaka
 tanh
 Tartakovsky
 taskset
@@ -2680,6 +2713,7 @@ tokyo
 tol
 toolchain
 topologies
+Toporov
 Torder
 torsions
 Tosi
@@ -2724,6 +2758,7 @@ Tsrd
 Tstart
 tstat
 Tstop
+Tsuji
 Tsuzuki
 tt
 Tt

examples/SPIN/spinmin/in.spinmin.bfo

@@ -0,0 +1,55 @@
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100

examples/SPIN/spinmin/in.spinmin.iron

@@ -0,0 +1,55 @@
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	bcc 2.8665
+region 		box block 0.0 4.0 0.0 4.0 0.0 4.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 100000 1000

examples/USER/adios/adios2_config.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<adios-config>
+
+    <!-- example engines 
+
+        <engine type="BPFile">
+            <parameter key="substreams" value="10"/>
+        </engine>
+
+        <engine type="HDF5">
+
+
+        The 'substreams' parameter in BPFile controls how many 
+        files on disk are created. This number should be proportional 
+        to the number of servers in the parallel file system, 
+        NOT to the number of processes. 
+        substreams=1 is generally a very inefficient setting for large parallel runs.
+    -->
+
+    <!--====================================================
+           Configuration for the dump atom/adios command
+        ====================================================-->
+
+    <io name="atom">
+        <engine type="BPFile">
+            <parameter key="substreams" value="1"/>
+        </engine>
+    </io>
+
+    <!--====================================================
+           Configuration for the dump custom/adios command
+        ====================================================-->
+
+    <io name="custom">
+        <engine type="BPFile">
+            <parameter key="substreams" value="1"/>
+        </engine>
+    </io>
+
+
+</adios-config>

examples/USER/adios/in.adios_balance

@@ -0,0 +1,57 @@
+# 2d circle of particles inside a box with LJ walls
+
+variable        b index 0
+
+variable	x index 50
+variable	y index 20
+variable	d index 20
+variable	v index 5
+variable	w index 2
+                
+units		lj
+dimension       2
+atom_style	atomic
+boundary        f f p
+
+lattice		hex 0.85
+region		box block 0 $x 0 $y -0.5 0.5
+create_box	1 box
+region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+create_atoms	1 region circle
+mass		1 1.0
+
+velocity	all create 0.5 87287 loop geom
+velocity        all set $v $w 0 sum yes
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 10.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+
+comm_style      tiled
+fix             10 all balance 50 0.9 rcb
+
+compute         1 all property/atom proc
+variable        p atom c_1%10
+dump            2 all custom 50 balance.dump id v_p x y z
+dump            3 all custom/adios 50 balance_custom.bp id v_p x y z
+dump            4 all atom/adios 50 balance_atom.bp 
+
+#dump            3 all image 50 image.*.jpg v_p type &
+#                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable        colors string &
+#                "red green blue yellow white &
+#                purple pink orange lime gray"
+#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style    custom step temp epair press f_10[3] f_10
+thermo          100                
+
+run		200
+write_dump      all atom/adios balance_atom_final.bp 

examples/USER/adios/log.balance

@@ -0,0 +1,114 @@
+LAMMPS (4 Jan 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+  using 1 OpenMP thread(s) per MPI task
+# 2d circle of particles inside a box with LJ walls
+
+variable        b index 0
+
+variable	x index 50
+variable	y index 20
+variable	d index 20
+variable	v index 5
+variable	w index 2
+
+units		lj
+dimension       2
+atom_style	atomic
+boundary        f f p
+
+lattice		hex 0.85
+Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
+region		box block 0 $x 0 $y -0.5 0.5
+region		box block 0 50 0 $y -0.5 0.5
+region		box block 0 50 0 20 -0.5 0.5
+create_box	1 box
+Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
+  2 by 2 by 1 MPI processor grid
+region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
+region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
+region		circle sphere 11 6.7735026918962581988 0.0 10
+create_atoms	1 region circle
+Created 361 atoms
+  Time spent = 0.00171804 secs
+mass		1 1.0
+
+velocity	all create 0.5 87287 loop geom
+velocity        all set $v $w 0 sum yes
+velocity        all set 5 $w 0 sum yes
+velocity        all set 5 2 0 sum yes
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 10.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 1 check yes
+
+fix		1 all nve
+
+fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
+fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
+fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
+fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
+
+comm_style      tiled
+fix             10 all balance 50 0.9 rcb
+
+compute         1 all property/atom proc
+variable        p atom c_1%10
+dump            2 all custom 50 balance.dump id v_p x y z
+dump            3 all custom/adios 50 balance_custom.bp id v_p x y z
+dump            4 all atom/adios 50 balance_atom.bp
+
+#dump            3 all image 50 image.*.jpg v_p type #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
+#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
+#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}
+
+thermo_style    custom step temp epair press f_10[3] f_10
+thermo          100
+
+run		200
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 42 29 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.933 | 4.944 Mbytes
+Step Temp E_pair Press f_10[3] f_10 
+       0    25.701528   -29.143179   -1.2407285    3.2354571    1.0526316 
+     100    26.269576   -29.713313    7.9052334    1.2742382    1.0304709 
+     200    26.368336   -29.809962    1.6412462    1.2520776    1.0083102 
+Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms
+
+Performance: 870660.046 tau/day, 2015.417 timesteps/s
+32.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0078368  | 0.0081607  | 0.0085468  |   0.3 |  8.22
+Neigh   | 0.002804   | 0.0045915  | 0.0092173  |   3.9 |  4.63
+Comm    | 0.044407   | 0.05352    | 0.062051   |   3.0 | 53.93
+Output  | 0.011406   | 0.012025   | 0.01342    |   0.7 | 12.12
+Modify  | 0.006305   | 0.0064294  | 0.0066617  |   0.2 |  6.48
+Other   |            | 0.01451    |            |       | 14.62
+
+Nlocal:    90.25 ave 91 max 90 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:    58.25 ave 64 max 51 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    730.75 ave 801 max 671 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 2923
+Ave neighs/atom = 8.09695
+Neighbor list builds = 60
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/phonon/dynamical_matrix_command/Silicon/README.md

@@ -0,0 +1,21 @@
+# LAMMPS LATTICE DYNAMICS COMMANDS
+
+## DYNAMICAL MATRIX CALCULATOR
+
+This directory contains the ingredients to calculate a dynamical matrix.  
+
+Example:
+```
+NP=4 #number of processors
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
+```
+
+To test out a different silicon example:
+```
+LMP_FILE=amorphous_silicon.lmp
+cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
+NP=4 #number of processors
+mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
+```
+
+## Requires: MANYBODY and MOLECULE packages

examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff

@@ -0,0 +1,66 @@
+# Tersoff parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units:
+#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
+#   other quantities are unitless
+
+# Aidan Thompson (athomps at sandia.gov) takes full blame for this
+# file.  It specifies various potentials published by J. Tersoff for
+# silicon, carbon and germanium. Since Tersoff published several
+# different silicon potentials, I refer to them using atom types
+# Si(B), Si(C) and Si(D). The last two are almost almost identical but
+# refer to two different publications. These names should be used in
+# the LAMMPS command when the file is invoked. For example:
+# pair_coeff * * SiCGe.tersoff Si(B).  The Si(D), C and Ge potentials
+# can be used pure silicon, pure carbon, pure germanium, binary SiC,
+# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
+# generate an error if this file is used with any combination
+# involving C and Ge, since there are no entries for the GeC
+# interactions (Tersoff did not publish parameters for this
+# cross-interaction.)
+
+# format of a single entry (one or more lines):
+#   element 1, element 2, element 3, 
+#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
+
+# The original Tersoff potential for Silicon, Si(B)
+# J. Tersoff, PRB, 37, 6991 (1988) 
+
+Si(B)  Si(B)   Si(B)  3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
+             0.33675  1.3258  95.373  3.0  0.2  3.2394  3264.7
+
+# The later Tersoff potential for Silicon, Si(C)
+# J. Tersoff, PRB, 38, 9902 (1988) 
+
+Si(C)  Si(C)   Si(C)  3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
+             1.0999e-6  1.7322  471.18  2.85  0.15  2.4799  1830.8
+
+# The later Tersoff potential for Carbon, Silicon, and Germanium
+# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
+# The Si and C parameters are very close to those in SiC.tersoff
+
+C      C       C         3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7  2.2119  346.74    1.95    0.15   3.4879  1393.6
+Si(D)  Si(D)   Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.7322  471.18    2.85    0.15   2.4799  1830.8
+Ge     Ge      Ge        3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7  1.7047  419.23    2.95    0.15   2.4451  1769.0
+
+C      Si(D)   Si(D)     3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7  1.97205 395.1451  2.3573  0.1527 2.9839  1597.3111
+C      Si(D)   C         3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0        0.0     0.0       1.95    0.15   0.0     0.0
+C      C       Si(D)     3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0        0.0     0.0       2.3573  0.1527 0.0     0.0
+
+Si(D)  C       C         3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.97205 395.1451  2.3573  0.1527 2.9839  1597.3111
+Si(D)  Si(D)   C         3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.3573  0.1527 0.0     0.0
+Si(D)  C       Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.85    0.15   0.0     0.0
+ 
+Si(D)  Ge      Ge        3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6  1.71845 444.7177  2.8996  0.1500 2.4625  1799.6347
+Si(D)  Si(D)   Ge        3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.8996  0.1500 0.0     0.0
+Si(D)  Ge      Si(D)     3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0        0.0     0.0       2.85    0.15   0.0     0.0
+ 
+Ge     Si(D)   Si(D)     3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7  1.71845 444.7177  2.8996  0.1500 2.4625  1799.6347
+Ge     Si(D)   Ge        3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0        0.0     0.0       2.95    0.15   0.0     0.0
+Ge     Ge      Si(D)     3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0        0.0     0.0       2.8996  0.1500 0.0     0.0
+
+# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) 
+#   element 1, element 2, element 3, 
+#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
+C(O)    C(O)   C(O)     3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7  2.2119  430.0    1.95    0.15   3.4879  1393.6
+

examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp

@@ -0,0 +1,19 @@
+#############################
+#Atoms types - mass - charge#
+#############################
+#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
+
+variable Si equal 1
+
+#############
+#Atom Masses#
+#############
+
+mass ${Si}     28.08550 
+
+###########################
+#Pair Potentials - Tersoff#
+###########################
+
+pair_style      tersoff
+pair_coeff      * *  Si.opt.tersoff Si(D)

examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon

@@ -0,0 +1,89 @@
+###############################mm
+# Atom style - charge/vdw/bonded#
+#################################
+atom_style full
+
+##############################################
+#Units Metal : eV       - ps - angstrom - bar#
+#      Real  : kcal/mol - fs - angstrom - atm#
+##############################################
+units   	metal
+
+############
+#Run number#
+############
+variable run_no   equal   0             # is it a restart? 
+variable res_no   equal   ${run_no}-1   # restart file number 
+
+#######################################
+#Random Seeds and Domain Decomposition#
+#######################################
+variable iseed0 equal 2357  
+variable iseed1 equal 26488 
+variable iseed2 equal 10669 
+processors      * * *
+
+###########
+#Data File#
+###########
+variable inpfile   string   silicon_input_file.lmp
+variable resfile   string   final_restart.${res_no}
+variable ff_file   string   ff-silicon.lmp
+
+##########
+#Run Type#
+##########
+variable minimise equal    0   #Energy Minimization
+
+###############################
+#Molecular Dynamics Parameters#
+###############################
+neighbor 1 bin
+
+################################
+#Energy Minimization Parameters#
+################################
+variable mtraj    equal        1       # trajectory output frequency - all system
+variable etol     equal     1e-5       # % change in energy
+variable ftol     equal     1e-5       # max force threshold (force units)
+variable maxiter  equal    10000       # max # of iterations
+
+########################
+#3D Periodic Simulation#
+########################
+boundary 	p p p
+
+#############################
+#Reading the input structure#
+#############################
+if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
+
+#############
+#Force Field#
+#############
+include ${ff_file}
+
+######################
+#Thermodynamic Output#
+######################
+variable str_basic string 'step time pe temp press'
+
+#####################
+#Energy Minimization#
+#####################
+if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
+  print "Doing CG minimisation"
+  dump mdcd all dcd ${mtraj} min.dcd
+  dump_modify mdcd unwrap yes
+  min_style cg
+  min_modify line quadratic
+  minimize ${etol} ${ftol} ${maxiter} ${maxiter}
+  reset_timestep 0
+  undump mdcd
+label end_minimise
+
+##################
+#Dynamical Matrix#
+##################
+dynamical_matrix all eskm 0.000001 file dynmat.dat binary no
+

examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp

@@ -0,0 +1,534 @@
+LAMMPS description
+
+     512      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      21.848000     xlo xhi
+  0.0000000      21.848000     ylo yhi
+  0.0000000      21.848000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      6.2030000      5.5980000     12.9980000
+      2      2      1      0.0000000     21.3100000      5.6310000     21.1380000
+      3      3      1      0.0000000     19.5320000      6.1170000      3.6940000
+      4      4      1      0.0000000      4.3700000     14.0260000      0.0900000
+      5      5      1      0.0000000     10.1930000      7.4590000      2.3530000
+      6      6      1      0.0000000     17.5070000     14.1860000      3.6790000
+      7      7      1      0.0000000     11.2050000     15.9160000     15.0480000
+      8      8      1      0.0000000      8.6050000     19.8970000     21.0040000
+      9      9      1      0.0000000     15.0360000     17.5650000      1.3640000
+     10     10      1      0.0000000     12.0450000      3.3600000      7.2720000
+     11     11      1      0.0000000      7.1330000     17.4130000     18.0480000
+     12     12      1      0.0000000      8.7340000      6.3830000      3.8480000
+     13     13      1      0.0000000     13.0940000      3.2490000      3.5840000
+     14     14      1      0.0000000     11.3200000      7.2770000     20.4120000
+     15     15      1      0.0000000     19.7770000      8.9110000      0.3000000
+     16     16      1      0.0000000     11.9710000     20.8500000      1.5140000
+     17     17      1      0.0000000     10.4480000     10.3650000     15.4040000
+     18     18      1      0.0000000      9.2060000      9.4670000     10.2240000
+     19     19      1      0.0000000      8.4360000     13.6240000     17.6570000
+     20     20      1      0.0000000     18.2020000     21.1230000      0.1380000
+     21     21      1      0.0000000      3.2970000     19.5740000     14.7410000
+     22     22      1      0.0000000     12.5330000     17.3580000      7.5960000
+     23     23      1      0.0000000      1.4040000     18.1060000      3.1510000
+     24     24      1      0.0000000     17.7440000     13.1530000     16.7940000
+     25     25      1      0.0000000     12.1070000     12.6630000     18.0340000
+     26     26      1      0.0000000      8.7270000     17.1140000     10.4200000
+     27     27      1      0.0000000     13.2330000     16.0380000     13.9210000
+     28     28      1      0.0000000     15.2360000     14.8650000      7.0150000
+     29     29      1      0.0000000      5.5190000     20.8660000     19.9260000
+     30     30      1      0.0000000     16.5810000      9.7460000     15.1710000
+     31     31      1      0.0000000      2.0500000     13.8550000     21.8010000
+     32     32      1      0.0000000     21.2670000     20.8970000     13.6740000
+     33     33      1      0.0000000      9.6900000      6.7650000      0.1950000
+     34     34      1      0.0000000     11.2570000     13.2440000      2.8190000
+     35     35      1      0.0000000     10.7810000     12.7310000     12.1920000
+     36     36      1      0.0000000     16.2630000      7.4100000      1.5360000
+     37     37      1      0.0000000     19.6100000     18.1440000     19.6830000
+     38     38      1      0.0000000      8.1790000      0.1200000     10.1620000
+     39     39      1      0.0000000     17.0520000     20.4210000     15.0450000
+     40     40      1      0.0000000     12.3690000     12.6710000      4.8320000
+     41     41      1      0.0000000      7.8300000     16.6790000     14.2470000
+     42     42      1      0.0000000      1.6790000      9.9500000      1.2660000
+     43     43      1      0.0000000     16.6160000     14.6580000     13.2790000
+     44     44      1      0.0000000     13.7430000     11.9730000     21.5360000
+     45     45      1      0.0000000      5.2590000     15.1850000      9.5720000
+     46     46      1      0.0000000     20.5980000     14.7930000     20.4140000
+     47     47      1      0.0000000      1.5640000     16.8080000     13.0450000
+     48     48      1      0.0000000     21.3670000     11.4610000     20.6420000
+     49     49      1      0.0000000     14.5890000      5.9510000      7.1950000
+     50     50      1      0.0000000      1.0870000     13.5410000     11.3300000
+     51     51      1      0.0000000      6.2040000      4.8970000     16.9420000
+     52     52      1      0.0000000      0.4800000      4.1450000      0.8710000
+     53     53      1      0.0000000      2.0120000      5.7530000      1.8950000
+     54     54      1      0.0000000      9.8460000     19.1320000      7.3060000
+     55     55      1      0.0000000     18.3760000     21.3430000      4.0940000
+     56     56      1      0.0000000      5.2900000      6.5400000      5.3620000
+     57     57      1      0.0000000      1.4110000      6.5750000      4.0580000
+     58     58      1      0.0000000     16.1600000     15.1390000     11.0380000
+     59     59      1      0.0000000     21.0670000     18.3830000      8.6900000
+     60     60      1      0.0000000     18.0250000     17.7750000      1.4340000
+     61     61      1      0.0000000     19.0570000     16.2190000      6.6410000
+     62     62      1      0.0000000      5.1170000     16.5510000     11.5540000
+     63     63      1      0.0000000     14.4810000      7.8720000     12.6320000
+     64     64      1      0.0000000     11.7990000     10.9690000     13.5430000
+     65     65      1      0.0000000     11.2980000     18.5410000      1.5740000
+     66     66      1      0.0000000     16.1280000     19.0390000     19.6440000
+     67     67      1      0.0000000      6.0950000      7.0580000      9.6530000
+     68     68      1      0.0000000      5.3890000     20.2540000     10.7060000
+     69     69      1      0.0000000     17.9160000     18.9070000     21.1540000
+     70     70      1      0.0000000     13.0780000      2.1790000     17.4030000
+     71     71      1      0.0000000      8.0450000     14.3440000     14.0640000
+     72     72      1      0.0000000     14.4380000      6.8780000     14.6950000
+     73     73      1      0.0000000      0.4570000     21.6180000      8.3670000
+     74     74      1      0.0000000      6.4350000     16.9720000     21.7330000
+     75     75      1      0.0000000      8.0530000      4.0310000     20.1860000
+     76     76      1      0.0000000      6.8130000     19.7870000     12.5790000
+     77     77      1      0.0000000     19.0490000     10.8480000      6.0760000
+     78     78      1      0.0000000      2.2540000      7.7370000      0.5320000
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+     80     80      1      0.0000000      2.3620000      2.5500000      7.5690000
+     81     81      1      0.0000000     16.4560000     18.5670000      3.1120000
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+     83     83      1      0.0000000     20.5540000      8.9280000      5.9480000
+     84     84      1      0.0000000     13.5930000      8.4890000     16.2370000
+     85     85      1      0.0000000      9.5270000     18.0720000      3.0190000
+     86     86      1      0.0000000     11.3690000     15.3870000      7.1310000
+     87     87      1      0.0000000      8.3670000     13.3960000     11.8610000
+     88     88      1      0.0000000     14.6370000     11.4110000     11.4870000
+     89     89      1      0.0000000      8.4720000     16.0650000      2.4300000
+     90     90      1      0.0000000      8.2360000      5.2200000     18.1710000
+     91     91      1      0.0000000     11.0620000      2.8760000      0.4170000
+     92     92      1      0.0000000     14.0830000      1.3550000     14.0190000
+     93     93      1      0.0000000     20.5600000      4.1900000     19.4660000
+     94     94      1      0.0000000      4.6340000     13.0980000     10.3670000
+     95     95      1      0.0000000     19.9860000     15.5670000     11.7860000
+     96     96      1      0.0000000     21.5070000      4.1860000     14.8350000
+     97     97      1      0.0000000      3.3000000     11.2060000      2.5350000
+     98     98      1      0.0000000     19.2680000     21.0240000     10.9110000
+     99     99      1      0.0000000     12.2370000     19.4650000     19.9000000
+    100    100      1      0.0000000      8.3790000      9.6670000     14.5440000
+    101    101      1      0.0000000      5.4520000     19.1660000      5.6940000
+    102    102      1      0.0000000     15.8720000     15.4140000      0.3070000
+    103    103      1      0.0000000      6.9830000     19.1480000      0.5830000
+    104    104      1      0.0000000      7.9760000     18.3420000      8.5250000
+    105    105      1      0.0000000     13.9710000      6.7570000      1.1860000
+    106    106      1      0.0000000     18.7050000      7.2110000      9.2350000
+    107    107      1      0.0000000      3.2430000     13.6330000     12.1990000
+    108    108      1      0.0000000      1.9830000     10.8340000      5.4640000
+    109    109      1      0.0000000     16.5770000      5.0400000     11.4490000
+    110    110      1      0.0000000      9.5130000      6.2390000     14.3030000
+    111    111      1      0.0000000     14.1990000      4.0910000     16.7750000
+    112    112      1      0.0000000      8.0160000      3.5600000      2.0280000
+    113    113      1      0.0000000      7.9650000     12.1700000      7.8050000
+    114    114      1      0.0000000      0.3770000      0.0320000     15.5780000
+    115    115      1      0.0000000     19.0860000     17.5690000     12.6230000
+    116    116      1      0.0000000     17.2970000     16.8030000     13.9660000
+    117    117      1      0.0000000      6.7180000     10.5880000     19.5790000
+    118    118      1      0.0000000     21.3930000     21.2940000      6.2410000
+    119    119      1      0.0000000     16.0260000     18.7640000     13.6100000
+    120    120      1      0.0000000      3.1880000      2.1990000     18.5690000
+    121    121      1      0.0000000     20.7860000     13.7840000      4.4870000
+    122    122      1      0.0000000     18.3540000     11.7960000     11.0710000
+    123    123      1      0.0000000     19.3210000      0.4960000      5.9630000
+    124    124      1      0.0000000      3.7260000     13.4120000     18.4840000
+    125    125      1      0.0000000      4.4280000      4.9270000     18.4730000
+    126    126      1      0.0000000      2.7040000     21.7660000     15.2940000
+    127    127      1      0.0000000      9.3640000     14.3230000      3.7130000
+    128    128      1      0.0000000     20.5800000      3.3360000      7.9310000
+    129    129      1      0.0000000      2.4060000      4.1320000     17.3120000
+    130    130      1      0.0000000      0.9210000      2.6080000     11.0930000
+    131    131      1      0.0000000     13.7900000      9.5610000      8.2490000
+    132    132      1      0.0000000      5.5210000      8.6760000      2.5590000
+    133    133      1      0.0000000     11.1320000     11.1160000      6.1310000
+    134    134      1      0.0000000      1.6180000      6.5650000     10.7690000
+    135    135      1      0.0000000     21.0480000     17.3880000      3.1250000
+    136    136      1      0.0000000      2.5950000     13.3430000      3.3870000
+    137    137      1      0.0000000      1.8600000      4.7830000     14.1190000
+    138    138      1      0.0000000      1.2420000     12.9340000      9.0760000
+    139    139      1      0.0000000      2.2650000      8.2300000      7.4350000
+    140    140      1      0.0000000     10.9360000     17.8140000     10.9520000
+    141    141      1      0.0000000     10.3160000     13.8030000     14.5060000
+    142    142      1      0.0000000     11.0500000      2.5760000     12.8090000
+    143    143      1      0.0000000     18.3430000     15.3950000     10.0190000
+    144    144      1      0.0000000      8.2990000      0.3320000      5.4980000
+    145    145      1      0.0000000     17.9730000      3.4330000     17.4260000
+    146    146      1      0.0000000      0.8080000      7.5530000     20.4740000
+    147    147      1      0.0000000     20.6320000     14.4730000      6.7080000
+    148    148      1      0.0000000     19.3400000      2.8450000      5.9340000
+    149    149      1      0.0000000      5.2100000      0.9290000      6.2580000
+    150    150      1      0.0000000      8.6370000      4.0920000      9.2870000
+    151    151      1      0.0000000     16.5730000      2.0050000      1.7720000
+    152    152      1      0.0000000     14.6570000     14.1440000     14.4910000
+    153    153      1      0.0000000     11.1610000      6.0610000     15.8870000
+    154    154      1      0.0000000      3.8100000      4.2040000      2.1350000
+    155    155      1      0.0000000     18.6920000     11.8180000     18.5170000
+    156    156      1      0.0000000     20.4240000     10.6340000     10.7960000
+    157    157      1      0.0000000      8.9050000      9.9220000     20.2310000
+    158    158      1      0.0000000      7.7940000     19.5410000      2.7410000
+    159    159      1      0.0000000      2.7600000     18.2100000      9.0140000
+    160    160      1      0.0000000     11.7480000      5.0280000      4.3170000
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+    449    449      1      0.0000000     11.8150000     12.7440000     20.4040000
+    450    450      1      0.0000000     14.1450000     16.3300000     20.6400000
+    451    451      1      0.0000000     13.9790000     11.9100000     13.7820000
+    452    452      1      0.0000000      5.7860000      9.0870000      8.2180000
+    453    453      1      0.0000000      5.7610000     18.5920000      3.4730000
+    454    454      1      0.0000000     17.1860000     12.2100000     20.2580000
+    455    455      1      0.0000000     19.9590000     17.8190000      5.1360000
+    456    456      1      0.0000000     17.0590000     15.4900000      5.5810000
+    457    457      1      0.0000000      3.6710000      3.1920000      4.2290000
+    458    458      1      0.0000000      9.3110000      4.4320000      0.2320000
+    459    459      1      0.0000000      7.2900000     10.5480000      9.3640000
+    460    460      1      0.0000000      3.1990000     11.3340000     19.5640000
+    461    461      1      0.0000000     18.7960000     19.0310000     15.8960000
+    462    462      1      0.0000000     16.4530000     21.1730000     18.6370000
+    463    463      1      0.0000000     19.0360000      1.4790000     16.6070000
+    464    464      1      0.0000000     15.1190000      6.7220000      5.0610000
+    465    465      1      0.0000000     14.6980000      6.3460000     10.8900000
+    466    466      1      0.0000000      9.5270000     15.6660000      5.6890000
+    467    467      1      0.0000000      9.8670000      0.7250000     18.4290000
+    468    468      1      0.0000000      3.5070000     11.8220000     15.5670000
+    469    469      1      0.0000000      5.2170000      0.8530000      1.6550000
+    470    470      1      0.0000000     14.2830000     11.9310000     17.5860000
+    471    471      1      0.0000000     21.4650000     11.2840000      8.7140000
+    472    472      1      0.0000000      0.2700000     13.5140000     17.1240000
+    473    473      1      0.0000000      8.7330000     20.7300000     17.4130000
+    474    474      1      0.0000000      7.4140000     12.9760000      3.8660000
+    475    475      1      0.0000000      8.5520000      8.7210000     12.3480000
+    476    476      1      0.0000000      7.4770000      9.7280000      1.7090000
+    477    477      1      0.0000000     16.9200000     14.6800000     20.0740000
+    478    478      1      0.0000000      6.5920000     20.9910000      6.6400000
+    479    479      1      0.0000000     18.3870000      7.4290000     18.2380000
+    480    480      1      0.0000000     21.2320000     15.1360000      2.5810000
+    481    481      1      0.0000000     16.7390000      8.6780000     21.4380000
+    482    482      1      0.0000000     18.2260000      6.2380000      5.6140000
+    483    483      1      0.0000000     12.7550000      3.5820000     20.8720000
+    484    484      1      0.0000000     14.8870000      9.0010000     20.0300000
+    485    485      1      0.0000000      6.1970000     16.3000000      3.0880000
+    486    486      1      0.0000000      6.9450000     13.1810000     15.8140000
+    487    487      1      0.0000000     20.1770000     18.7700000      1.5020000
+    488    488      1      0.0000000     19.8750000     14.4220000      0.7710000
+    489    489      1      0.0000000     13.0770000      5.0280000     14.9330000
+    490    490      1      0.0000000     10.9540000      0.5380000      0.0170000
+    491    491      1      0.0000000      0.3310000      3.0520000     18.1720000
+    492    492      1      0.0000000      8.8200000     14.8310000     10.0110000
+    493    493      1      0.0000000      6.9570000     20.3870000      8.9230000
+    494    494      1      0.0000000     21.4900000      6.8560000     12.0490000
+    495    495      1      0.0000000      8.1550000     13.1990000     21.7210000
+    496    496      1      0.0000000      2.1970000      4.5290000     11.8290000
+    497    497      1      0.0000000     14.2880000      5.5560000     18.5960000
+    498    498      1      0.0000000     15.0910000     15.4110000     18.5470000
+    499    499      1      0.0000000     18.9760000     15.1930000     16.8970000
+    500    500      1      0.0000000     19.4100000      5.3490000     17.7540000
+    501    501      1      0.0000000      0.5430000      8.3990000     13.7700000
+    502    502      1      0.0000000     18.0770000     19.1690000      4.8770000
+    503    503      1      0.0000000      3.3760000     17.8650000     19.2940000
+    504    504      1      0.0000000     16.3760000      0.5870000      3.6340000
+    505    505      1      0.0000000     10.4990000     18.5190000     21.1770000
+    506    506      1      0.0000000     15.7320000     12.7570000      3.0200000
+    507    507      1      0.0000000     16.9190000      8.1780000      5.2430000
+    508    508      1      0.0000000      6.9450000      7.4210000      6.8040000
+    509    509      1      0.0000000     11.6120000     21.2610000     15.3620000
+    510    510      1      0.0000000     18.0500000      0.6840000     14.5470000
+    511    511      1      0.0000000     20.4340000      4.0240000      4.2040000
+    512    512      1      0.0000000     18.0190000     10.7210000      0.2160000
+

examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_216.lmp

@@ -0,0 +1,238 @@
+LAMMPS description
+
+     216      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      16.293000     xlo xhi
+  0.0000000      16.293000     ylo yhi
+  0.0000000      16.293000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      0.0000000      0.0000000      0.0000000
+      2      2      1      0.0000000      0.0000000      2.7160000      2.7160000
+      3      3      1      0.0000000      2.7160000      2.7160000      0.0000000
+      4      4      1      0.0000000      2.7160000      0.0000000      2.7160000
+      5      5      1      0.0000000      4.0730000      1.3580000      4.0730000
+      6      6      1      0.0000000      1.3580000      1.3580000      1.3580000
+      7      7      1      0.0000000      1.3580000      4.0730000      4.0730000
+      8      8      1      0.0000000      4.0730000      4.0730000      1.3580000
+      9      9      1      0.0000000      0.0000000      0.0000000      5.4310000
+     10     10      1      0.0000000      0.0000000      2.7160000      8.1460000
+     11     11      1      0.0000000      2.7160000      2.7160000      5.4310000
+     12     12      1      0.0000000      2.7160000      0.0000000      8.1460000
+     13     13      1      0.0000000      4.0730000      1.3580000      9.5040000
+     14     14      1      0.0000000      1.3580000      1.3580000      6.7890000
+     15     15      1      0.0000000      1.3580000      4.0730000      9.5040000
+     16     16      1      0.0000000      4.0730000      4.0730000      6.7890000
+     17     17      1      0.0000000      0.0000000      0.0000000     10.8620000
+     18     18      1      0.0000000      0.0000000      2.7160000     13.5780000
+     19     19      1      0.0000000      2.7160000      2.7160000     10.8620000
+     20     20      1      0.0000000      2.7160000      0.0000000     13.5780000
+     21     21      1      0.0000000      4.0730000      1.3580000     14.9350000
+     22     22      1      0.0000000      1.3580000      1.3580000     12.2200000
+     23     23      1      0.0000000      1.3580000      4.0730000     14.9350000
+     24     24      1      0.0000000      4.0730000      4.0730000     12.2200000
+     25     25      1      0.0000000      0.0000000      5.4310000      0.0000000
+     26     26      1      0.0000000      0.0000000      8.1460000      2.7160000
+     27     27      1      0.0000000      2.7160000      8.1460000      0.0000000
+     28     28      1      0.0000000      2.7160000      5.4310000      2.7160000
+     29     29      1      0.0000000      4.0730000      6.7890000      4.0730000
+     30     30      1      0.0000000      1.3580000      6.7890000      1.3580000
+     31     31      1      0.0000000      1.3580000      9.5040000      4.0730000
+     32     32      1      0.0000000      4.0730000      9.5040000      1.3580000
+     33     33      1      0.0000000      0.0000000      5.4310000      5.4310000
+     34     34      1      0.0000000      0.0000000      8.1460000      8.1460000
+     35     35      1      0.0000000      2.7160000      8.1460000      5.4310000
+     36     36      1      0.0000000      2.7160000      5.4310000      8.1460000
+     37     37      1      0.0000000      4.0730000      6.7890000      9.5040000
+     38     38      1      0.0000000      1.3580000      6.7890000      6.7890000
+     39     39      1      0.0000000      1.3580000      9.5040000      9.5040000
+     40     40      1      0.0000000      4.0730000      9.5040000      6.7890000
+     41     41      1      0.0000000      0.0000000      5.4310000     10.8620000
+     42     42      1      0.0000000      0.0000000      8.1460000     13.5780000
+     43     43      1      0.0000000      2.7160000      8.1460000     10.8620000
+     44     44      1      0.0000000      2.7160000      5.4310000     13.5780000
+     45     45      1      0.0000000      4.0730000      6.7890000     14.9350000
+     46     46      1      0.0000000      1.3580000      6.7890000     12.2200000
+     47     47      1      0.0000000      1.3580000      9.5040000     14.9350000
+     48     48      1      0.0000000      4.0730000      9.5040000     12.2200000
+     49     49      1      0.0000000      0.0000000     10.8620000      0.0000000
+     50     50      1      0.0000000      0.0000000     13.5780000      2.7160000
+     51     51      1      0.0000000      2.7160000     13.5780000      0.0000000
+     52     52      1      0.0000000      2.7160000     10.8620000      2.7160000
+     53     53      1      0.0000000      4.0730000     12.2200000      4.0730000
+     54     54      1      0.0000000      1.3580000     12.2200000      1.3580000
+     55     55      1      0.0000000      1.3580000     14.9350000      4.0730000
+     56     56      1      0.0000000      4.0730000     14.9350000      1.3580000
+     57     57      1      0.0000000      0.0000000     10.8620000      5.4310000
+     58     58      1      0.0000000      0.0000000     13.5780000      8.1460000
+     59     59      1      0.0000000      2.7160000     13.5780000      5.4310000
+     60     60      1      0.0000000      2.7160000     10.8620000      8.1460000
+     61     61      1      0.0000000      4.0730000     12.2200000      9.5040000
+     62     62      1      0.0000000      1.3580000     12.2200000      6.7890000
+     63     63      1      0.0000000      1.3580000     14.9350000      9.5040000
+     64     64      1      0.0000000      4.0730000     14.9350000      6.7890000
+     65     65      1      0.0000000      0.0000000     10.8620000     10.8620000
+     66     66      1      0.0000000      0.0000000     13.5780000     13.5780000
+     67     67      1      0.0000000      2.7160000     13.5780000     10.8620000
+     68     68      1      0.0000000      2.7160000     10.8620000     13.5780000
+     69     69      1      0.0000000      4.0730000     12.2200000     14.9350000
+     70     70      1      0.0000000      1.3580000     12.2200000     12.2200000
+     71     71      1      0.0000000      1.3580000     14.9350000     14.9350000
+     72     72      1      0.0000000      4.0730000     14.9350000     12.2200000
+     73     73      1      0.0000000      5.4310000      0.0000000      0.0000000
+     74     74      1      0.0000000      5.4310000      2.7160000      2.7160000
+     75     75      1      0.0000000      8.1460000      2.7160000      0.0000000
+     76     76      1      0.0000000      8.1460000      0.0000000      2.7160000
+     77     77      1      0.0000000      9.5040000      1.3580000      4.0730000
+     78     78      1      0.0000000      6.7890000      1.3580000      1.3580000
+     79     79      1      0.0000000      6.7890000      4.0730000      4.0730000
+     80     80      1      0.0000000      9.5040000      4.0730000      1.3580000
+     81     81      1      0.0000000      5.4310000      0.0000000      5.4310000
+     82     82      1      0.0000000      5.4310000      2.7160000      8.1460000
+     83     83      1      0.0000000      8.1460000      2.7160000      5.4310000
+     84     84      1      0.0000000      8.1460000      0.0000000      8.1460000
+     85     85      1      0.0000000      9.5040000      1.3580000      9.5040000
+     86     86      1      0.0000000      6.7890000      1.3580000      6.7890000
+     87     87      1      0.0000000      6.7890000      4.0730000      9.5040000
+     88     88      1      0.0000000      9.5040000      4.0730000      6.7890000
+     89     89      1      0.0000000      5.4310000      0.0000000     10.8620000
+     90     90      1      0.0000000      5.4310000      2.7160000     13.5780000
+     91     91      1      0.0000000      8.1460000      2.7160000     10.8620000
+     92     92      1      0.0000000      8.1460000      0.0000000     13.5780000
+     93     93      1      0.0000000      9.5040000      1.3580000     14.9350000
+     94     94      1      0.0000000      6.7890000      1.3580000     12.2200000
+     95     95      1      0.0000000      6.7890000      4.0730000     14.9350000
+     96     96      1      0.0000000      9.5040000      4.0730000     12.2200000
+     97     97      1      0.0000000      5.4310000      5.4310000      0.0000000
+     98     98      1      0.0000000      5.4310000      8.1460000      2.7160000
+     99     99      1      0.0000000      8.1460000      8.1460000      0.0000000
+    100    100      1      0.0000000      8.1460000      5.4310000      2.7160000
+    101    101      1      0.0000000      9.5040000      6.7890000      4.0730000
+    102    102      1      0.0000000      6.7890000      6.7890000      1.3580000
+    103    103      1      0.0000000      6.7890000      9.5040000      4.0730000
+    104    104      1      0.0000000      9.5040000      9.5040000      1.3580000
+    105    105      1      0.0000000      5.4310000      5.4310000      5.4310000
+    106    106      1      0.0000000      5.4310000      8.1460000      8.1460000
+    107    107      1      0.0000000      8.1460000      8.1460000      5.4310000
+    108    108      1      0.0000000      8.1460000      5.4310000      8.1460000
+    109    109      1      0.0000000      9.5040000      6.7890000      9.5040000
+    110    110      1      0.0000000      6.7890000      6.7890000      6.7890000
+    111    111      1      0.0000000      6.7890000      9.5040000      9.5040000
+    112    112      1      0.0000000      9.5040000      9.5040000      6.7890000
+    113    113      1      0.0000000      5.4310000      5.4310000     10.8620000
+    114    114      1      0.0000000      5.4310000      8.1460000     13.5780000
+    115    115      1      0.0000000      8.1460000      8.1460000     10.8620000
+    116    116      1      0.0000000      8.1460000      5.4310000     13.5780000
+    117    117      1      0.0000000      9.5040000      6.7890000     14.9350000
+    118    118      1      0.0000000      6.7890000      6.7890000     12.2200000
+    119    119      1      0.0000000      6.7890000      9.5040000     14.9350000
+    120    120      1      0.0000000      9.5040000      9.5040000     12.2200000
+    121    121      1      0.0000000      5.4310000     10.8620000      0.0000000
+    122    122      1      0.0000000      5.4310000     13.5780000      2.7160000
+    123    123      1      0.0000000      8.1460000     13.5780000      0.0000000
+    124    124      1      0.0000000      8.1460000     10.8620000      2.7160000
+    125    125      1      0.0000000      9.5040000     12.2200000      4.0730000
+    126    126      1      0.0000000      6.7890000     12.2200000      1.3580000
+    127    127      1      0.0000000      6.7890000     14.9350000      4.0730000
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+    131    131      1      0.0000000      8.1460000     13.5780000      5.4310000
+    132    132      1      0.0000000      8.1460000     10.8620000      8.1460000
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+    137    137      1      0.0000000      5.4310000     10.8620000     10.8620000
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+    139    139      1      0.0000000      8.1460000     13.5780000     10.8620000
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+    141    141      1      0.0000000      9.5040000     12.2200000     14.9350000
+    142    142      1      0.0000000      6.7890000     12.2200000     12.2200000
+    143    143      1      0.0000000      6.7890000     14.9350000     14.9350000
+    144    144      1      0.0000000      9.5040000     14.9350000     12.2200000
+    145    145      1      0.0000000     10.8620000      0.0000000      0.0000000
+    146    146      1      0.0000000     10.8620000      2.7160000      2.7160000
+    147    147      1      0.0000000     13.5780000      2.7160000      0.0000000
+    148    148      1      0.0000000     13.5780000      0.0000000      2.7160000
+    149    149      1      0.0000000     14.9350000      1.3580000      4.0730000
+    150    150      1      0.0000000     12.2200000      1.3580000      1.3580000
+    151    151      1      0.0000000     12.2200000      4.0730000      4.0730000
+    152    152      1      0.0000000     14.9350000      4.0730000      1.3580000
+    153    153      1      0.0000000     10.8620000      0.0000000      5.4310000
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+    156    156      1      0.0000000     13.5780000      0.0000000      8.1460000
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+    158    158      1      0.0000000     12.2200000      1.3580000      6.7890000
+    159    159      1      0.0000000     12.2200000      4.0730000      9.5040000
+    160    160      1      0.0000000     14.9350000      4.0730000      6.7890000
+    161    161      1      0.0000000     10.8620000      0.0000000     10.8620000
+    162    162      1      0.0000000     10.8620000      2.7160000     13.5780000
+    163    163      1      0.0000000     13.5780000      2.7160000     10.8620000
+    164    164      1      0.0000000     13.5780000      0.0000000     13.5780000
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+    214    214      1      0.0000000     12.2200000     12.2200000     12.2200000
+    215    215      1      0.0000000     12.2200000     14.9350000     14.9350000
+    216    216      1      0.0000000     14.9350000     14.9350000     12.2200000
+

examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_512.lmp

@@ -0,0 +1,534 @@
+LAMMPS description
+
+     512      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      21.724000     xlo xhi
+  0.0000000      21.724000     ylo yhi
+  0.0000000      21.724000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      0.0000000      0.0000000      0.0000000
+      2      2      1      0.0000000      0.0000000      2.7150000      2.7150000
+      3      3      1      0.0000000      2.7150000      2.7150000      0.0000000
+      4      4      1      0.0000000      2.7150000      0.0000000      2.7150000
+      5      5      1      0.0000000      4.0730000      1.3580000      4.0730000
+      6      6      1      0.0000000      1.3580000      1.3580000      1.3580000
+      7      7      1      0.0000000      1.3580000      4.0730000      4.0730000
+      8      8      1      0.0000000      4.0730000      4.0730000      1.3580000
+      9      9      1      0.0000000      0.0000000      0.0000000      5.4310000
+     10     10      1      0.0000000      0.0000000      2.7150000      8.1460000
+     11     11      1      0.0000000      2.7150000      2.7150000      5.4310000
+     12     12      1      0.0000000      2.7150000      0.0000000      8.1460000
+     13     13      1      0.0000000      4.0730000      1.3580000      9.5040000
+     14     14      1      0.0000000      1.3580000      1.3580000      6.7890000
+     15     15      1      0.0000000      1.3580000      4.0730000      9.5040000
+     16     16      1      0.0000000      4.0730000      4.0730000      6.7890000
+     17     17      1      0.0000000      0.0000000      0.0000000     10.8620000
+     18     18      1      0.0000000      0.0000000      2.7150000     13.5770000
+     19     19      1      0.0000000      2.7150000      2.7150000     10.8620000
+     20     20      1      0.0000000      2.7150000      0.0000000     13.5770000
+     21     21      1      0.0000000      4.0730000      1.3580000     14.9350000
+     22     22      1      0.0000000      1.3580000      1.3580000     12.2200000
+     23     23      1      0.0000000      1.3580000      4.0730000     14.9350000
+     24     24      1      0.0000000      4.0730000      4.0730000     12.2200000
+     25     25      1      0.0000000      0.0000000      0.0000000     16.2930000
+     26     26      1      0.0000000      0.0000000      2.7150000     19.0080000
+     27     27      1      0.0000000      2.7150000      2.7150000     16.2930000
+     28     28      1      0.0000000      2.7150000      0.0000000     19.0080000
+     29     29      1      0.0000000      4.0730000      1.3580000     20.3660000
+     30     30      1      0.0000000      1.3580000      1.3580000     17.6510000
+     31     31      1      0.0000000      1.3580000      4.0730000     20.3660000
+     32     32      1      0.0000000      4.0730000      4.0730000     17.6510000
+     33     33      1      0.0000000      0.0000000      5.4310000      0.0000000
+     34     34      1      0.0000000      0.0000000      8.1460000      2.7150000
+     35     35      1      0.0000000      2.7150000      8.1460000      0.0000000
+     36     36      1      0.0000000      2.7150000      5.4310000      2.7150000
+     37     37      1      0.0000000      4.0730000      6.7890000      4.0730000
+     38     38      1      0.0000000      1.3580000      6.7890000      1.3580000
+     39     39      1      0.0000000      1.3580000      9.5040000      4.0730000
+     40     40      1      0.0000000      4.0730000      9.5040000      1.3580000
+     41     41      1      0.0000000      0.0000000      5.4310000      5.4310000
+     42     42      1      0.0000000      0.0000000      8.1460000      8.1460000
+     43     43      1      0.0000000      2.7150000      8.1460000      5.4310000
+     44     44      1      0.0000000      2.7150000      5.4310000      8.1460000
+     45     45      1      0.0000000      4.0730000      6.7890000      9.5040000
+     46     46      1      0.0000000      1.3580000      6.7890000      6.7890000
+     47     47      1      0.0000000      1.3580000      9.5040000      9.5040000
+     48     48      1      0.0000000      4.0730000      9.5040000      6.7890000
+     49     49      1      0.0000000      0.0000000      5.4310000     10.8620000
+     50     50      1      0.0000000      0.0000000      8.1460000     13.5770000
+     51     51      1      0.0000000      2.7150000      8.1460000     10.8620000
+     52     52      1      0.0000000      2.7150000      5.4310000     13.5770000
+     53     53      1      0.0000000      4.0730000      6.7890000     14.9350000
+     54     54      1      0.0000000      1.3580000      6.7890000     12.2200000
+     55     55      1      0.0000000      1.3580000      9.5040000     14.9350000
+     56     56      1      0.0000000      4.0730000      9.5040000     12.2200000
+     57     57      1      0.0000000      0.0000000      5.4310000     16.2930000
+     58     58      1      0.0000000      0.0000000      8.1460000     19.0080000
+     59     59      1      0.0000000      2.7150000      8.1460000     16.2930000
+     60     60      1      0.0000000      2.7150000      5.4310000     19.0080000
+     61     61      1      0.0000000      4.0730000      6.7890000     20.3660000
+     62     62      1      0.0000000      1.3580000      6.7890000     17.6510000
+     63     63      1      0.0000000      1.3580000      9.5040000     20.3660000
+     64     64      1      0.0000000      4.0730000      9.5040000     17.6510000
+     65     65      1      0.0000000      0.0000000     10.8620000      0.0000000
+     66     66      1      0.0000000      0.0000000     13.5770000      2.7150000
+     67     67      1      0.0000000      2.7150000     13.5770000      0.0000000
+     68     68      1      0.0000000      2.7150000     10.8620000      2.7150000
+     69     69      1      0.0000000      4.0730000     12.2200000      4.0730000
+     70     70      1      0.0000000      1.3580000     12.2200000      1.3580000
+     71     71      1      0.0000000      1.3580000     14.9350000      4.0730000
+     72     72      1      0.0000000      4.0730000     14.9350000      1.3580000
+     73     73      1      0.0000000      0.0000000     10.8620000      5.4310000
+     74     74      1      0.0000000      0.0000000     13.5770000      8.1460000
+     75     75      1      0.0000000      2.7150000     13.5770000      5.4310000
+     76     76      1      0.0000000      2.7150000     10.8620000      8.1460000
+     77     77      1      0.0000000      4.0730000     12.2200000      9.5040000
+     78     78      1      0.0000000      1.3580000     12.2200000      6.7890000
+     79     79      1      0.0000000      1.3580000     14.9350000      9.5040000
+     80     80      1      0.0000000      4.0730000     14.9350000      6.7890000
+     81     81      1      0.0000000      0.0000000     10.8620000     10.8620000
+     82     82      1      0.0000000      0.0000000     13.5770000     13.5770000
+     83     83      1      0.0000000      2.7150000     13.5770000     10.8620000
+     84     84      1      0.0000000      2.7150000     10.8620000     13.5770000
+     85     85      1      0.0000000      4.0730000     12.2200000     14.9350000
+     86     86      1      0.0000000      1.3580000     12.2200000     12.2200000
+     87     87      1      0.0000000      1.3580000     14.9350000     14.9350000
+     88     88      1      0.0000000      4.0730000     14.9350000     12.2200000
+     89     89      1      0.0000000      0.0000000     10.8620000     16.2930000
+     90     90      1      0.0000000      0.0000000     13.5770000     19.0080000
+     91     91      1      0.0000000      2.7150000     13.5770000     16.2930000
+     92     92      1      0.0000000      2.7150000     10.8620000     19.0080000
+     93     93      1      0.0000000      4.0730000     12.2200000     20.3660000
+     94     94      1      0.0000000      1.3580000     12.2200000     17.6510000
+     95     95      1      0.0000000      1.3580000     14.9350000     20.3660000
+     96     96      1      0.0000000      4.0730000     14.9350000     17.6510000
+     97     97      1      0.0000000      0.0000000     16.2930000      0.0000000
+     98     98      1      0.0000000      0.0000000     19.0080000      2.7150000
+     99     99      1      0.0000000      2.7150000     19.0080000      0.0000000
+    100    100      1      0.0000000      2.7150000     16.2930000      2.7150000
+    101    101      1      0.0000000      4.0730000     17.6510000      4.0730000
+    102    102      1      0.0000000      1.3580000     17.6510000      1.3580000
+    103    103      1      0.0000000      1.3580000     20.3660000      4.0730000
+    104    104      1      0.0000000      4.0730000     20.3660000      1.3580000
+    105    105      1      0.0000000      0.0000000     16.2930000      5.4310000
+    106    106      1      0.0000000      0.0000000     19.0080000      8.1460000
+    107    107      1      0.0000000      2.7150000     19.0080000      5.4310000
+    108    108      1      0.0000000      2.7150000     16.2930000      8.1460000
+    109    109      1      0.0000000      4.0730000     17.6510000      9.5040000
+    110    110      1      0.0000000      1.3580000     17.6510000      6.7890000
+    111    111      1      0.0000000      1.3580000     20.3660000      9.5040000
+    112    112      1      0.0000000      4.0730000     20.3660000      6.7890000
+    113    113      1      0.0000000      0.0000000     16.2930000     10.8620000
+    114    114      1      0.0000000      0.0000000     19.0080000     13.5770000
+    115    115      1      0.0000000      2.7150000     19.0080000     10.8620000
+    116    116      1      0.0000000      2.7150000     16.2930000     13.5770000
+    117    117      1      0.0000000      4.0730000     17.6510000     14.9350000
+    118    118      1      0.0000000      1.3580000     17.6510000     12.2200000
+    119    119      1      0.0000000      1.3580000     20.3660000     14.9350000
+    120    120      1      0.0000000      4.0730000     20.3660000     12.2200000
+    121    121      1      0.0000000      0.0000000     16.2930000     16.2930000
+    122    122      1      0.0000000      0.0000000     19.0080000     19.0080000
+    123    123      1      0.0000000      2.7150000     19.0080000     16.2930000
+    124    124      1      0.0000000      2.7150000     16.2930000     19.0080000
+    125    125      1      0.0000000      4.0730000     17.6510000     20.3660000
+    126    126      1      0.0000000      1.3580000     17.6510000     17.6510000
+    127    127      1      0.0000000      1.3580000     20.3660000     20.3660000
+    128    128      1      0.0000000      4.0730000     20.3660000     17.6510000
+    129    129      1      0.0000000      5.4310000      0.0000000      0.0000000
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+    132    132      1      0.0000000      8.1460000      0.0000000      2.7150000
+    133    133      1      0.0000000      9.5040000      1.3580000      4.0730000
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+    137    137      1      0.0000000      5.4310000      0.0000000      5.4310000
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+    139    139      1      0.0000000      8.1460000      2.7150000      5.4310000
+    140    140      1      0.0000000      8.1460000      0.0000000      8.1460000
+    141    141      1      0.0000000      9.5040000      1.3580000      9.5040000
+    142    142      1      0.0000000      6.7890000      1.3580000      6.7890000
+    143    143      1      0.0000000      6.7890000      4.0730000      9.5040000
+    144    144      1      0.0000000      9.5040000      4.0730000      6.7890000
+    145    145      1      0.0000000      5.4310000      0.0000000     10.8620000
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+    147    147      1      0.0000000      8.1460000      2.7150000     10.8620000
+    148    148      1      0.0000000      8.1460000      0.0000000     13.5770000
+    149    149      1      0.0000000      9.5040000      1.3580000     14.9350000
+    150    150      1      0.0000000      6.7890000      1.3580000     12.2200000
+    151    151      1      0.0000000      6.7890000      4.0730000     14.9350000
+    152    152      1      0.0000000      9.5040000      4.0730000     12.2200000
+    153    153      1      0.0000000      5.4310000      0.0000000     16.2930000
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+    159    159      1      0.0000000      6.7890000      4.0730000     20.3660000
+    160    160      1      0.0000000      9.5040000      4.0730000     17.6510000
+    161    161      1      0.0000000      5.4310000      5.4310000      0.0000000
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+    163    163      1      0.0000000      8.1460000      8.1460000      0.0000000
+    164    164      1      0.0000000      8.1460000      5.4310000      2.7150000
+    165    165      1      0.0000000      9.5040000      6.7890000      4.0730000
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+

examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/silicon_8.lmp

@@ -0,0 +1,29 @@
+LAMMPS description
+
+       8      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      5.4310000     xlo xhi
+  0.0000000      5.4310000     ylo yhi
+  0.0000000      5.4310000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      0.0000000      0.0000000      0.0000000
+      2      2      1      0.0000000      1.3577500      1.3577500      1.3572000
+      3      3      1      0.0000000      2.7155000      2.7155000      0.0000000
+      4      4      1      0.0000000      4.0732500      4.0732500      1.3572000
+      5      5      1      0.0000000      2.7155000      0.0000000      2.7144000
+      6      6      1      0.0000000      4.0732500      1.3577500      4.0732500
+      7      7      1      0.0000000      0.0000000      2.7155000      2.7155000
+      8      8      1      0.0000000      1.3577500      4.0732500      4.0732500

examples/USER/phonon/dynamical_matrix_command/Silicon/results/dynmat.dat

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+83.46934214 -0.23660998 -0.00000076
+-1276.15172724 861.66402917 861.66024325
+-193.17585988 -0.00634042 -0.00000031
+-1276.15172694 861.66402940 -861.66024325
+0.11071645 -193.14095243 0.00000046
+-863.24917949 -1277.48270718 862.95613831
+3.05075524 5409.83472478 -0.00000046
+-863.24918117 -1277.48270825 -862.95613923
+0.34066922 -193.17613823 0.00000046
+861.54715094 -1276.01088228 -861.62537295
+-0.09801303 83.46959035 0.00000015
+861.54713538 -1276.01088145 861.62537387
+-0.00000046 -0.00000023 83.84059068
+862.97973867 862.89766010 -1277.71823633
+-0.00000214 -0.00000053 5410.11037574
+-862.97973943 -862.89766079 -1277.71823633
+0.00000015 0.00000008 -193.17558374
+861.52691291 -861.60900269 -1276.08157198
+-0.00000015 -0.00000015 -193.17573814
+-861.52691368 861.60900261 -1276.08157243
+-1277.48271786 -863.13225450 862.89768520
+-193.14089232 0.11950085 -0.11994115
+-1277.34161255 -863.24919673 -862.97975957
+5409.83568051 3.04882517 -2.82007644
+-1277.52243110 863.24943259 863.11330990
+83.46945732 -0.16730494 0.06100319
+-1274.64156796 859.96385342 -860.17328103
+-193.17597041 0.16713331 0.02106477
+-863.24919482 -1277.34161057 862.97975774
+0.11950077 -193.14089270 0.11994160
+-863.13225473 -1277.48271839 -862.89768673
+3.04882502 5409.83568081 2.82007903
+863.24943084 -1277.52242966 -863.11330868
+0.16713324 -193.17597064 -0.02106522
+859.96385510 -1274.64156926 860.17328255
+-0.16730411 83.46945641 -0.06100350
+862.95611161 862.92132537 -1277.71824365
+0.11994725 -0.11994740 83.84083859
+-862.92132606 -862.95611207 -1277.71824548
+-2.82003936 2.82004013 5410.11000806
+862.88110509 -862.88110547 -1277.34764015
+0.06108893 0.02099703 -193.17561792
+-860.25587388 860.25587441 -1274.81548916
+-0.02099726 -0.06108878 -193.17561777
+-193.17613465 -0.23660693 0.00000015
+-1277.52241409 863.24943328 -862.88111478
+83.46934549 0.34066334 -0.00000015
+-1277.52241425 863.24943335 862.88111508
+5404.58897235 -9.71806749 0.00000015
+-1273.31333522 -858.38273960 -858.96245956
+-193.21062369 -0.11938368 0.00000000
+-1273.31333598 -858.38273967 858.96245926
+0.34066342 83.46934572 0.00000015
+863.24943335 -1277.52241402 862.88111478
+-0.23660723 -193.17613480 -0.00000046
+863.24943320 -1277.52241425 -862.88111432
+-9.71806582 5404.58897135 -0.00000183
+-858.38273891 -1273.31333552 -858.96245926
+-0.11938338 -193.21062369 0.00000000
+-858.38273937 -1273.31333598 858.96245987
+-0.00000031 -0.00000008 -193.17559595
+-863.11328229 863.11328297 -1277.34763999
+0.00000000 -0.00000015 -193.17559595
+863.11328305 -863.11328282 -1277.34763984
+0.00000122 -0.00000259 5404.30470550
+-858.80486827 -858.80486866 -1273.17865241
+-0.00000031 0.00000000 83.09905870
+858.80486827 858.80486812 -1273.17865272
+-1276.01089136 861.66402482 -861.60900483
+-193.17596134 -0.16730494 0.02099535
+-1276.15175745 861.54714988 861.52691337
+83.46947097 0.16714109 0.06108436
+-1273.31334651 -858.38273311 -858.80488185
+5404.58493608 -3.04507687 -2.81778617
+-1276.19187193 -861.66399965 861.74280750
+-193.21058304 -0.11920641 -0.12012575
+861.54714972 -1276.15175730 861.52691337
+0.16714140 83.46947120 0.06108451
+861.66402345 -1276.01089022 -861.60900330
+-0.16730487 -193.17596164 0.02099489
+-858.38273281 -1273.31334681 -858.80488063
+-3.04507603 5404.58493554 -2.81778617
+-861.66400079 -1276.19187270 861.74280887
+-0.11920511 -193.21058281 -0.12012498
+-861.62536929 861.66025668 -1276.08157121
+-0.02106026 0.06099877 -193.17561197
+861.66025752 -861.62537051 -1276.08157274
+0.06099923 -0.02106049 -193.17561227
+-858.96244980 -858.96244965 -1273.17866523
+-2.81780608 -2.81780615 5404.30474272
+861.58531232 861.58531248 -1275.71087663
+0.12013467 0.12013460 83.09915619
+83.46958166 -0.00634218 -0.00000023
+-1274.64157002 859.96383191 860.25587098
+-193.17585332 -0.09802844 0.00000023
+-1274.64157155 859.96383290 -860.25587243
+-193.21062064 -0.11939070 -0.00000008
+-1276.19189573 -861.66398638 861.58531118
+5404.58377546 3.62403097 0.00000015
+-1276.19189558 -861.66398615 -861.58531103
+-0.09802859 -193.17585355 -0.00000015
+859.96383206 -1274.64156979 -860.25587113
+-0.00634187 83.46958204 -0.00000008
+859.96383282 -1274.64157132 860.25587212
+-0.11939055 -193.21062041 0.00000000
+-861.66398576 -1276.19189528 861.58531087
+3.62402982 5404.58377698 -0.00000076
+-861.66398927 -1276.19189772 -861.58531331
+0.00000000 0.00000000 -193.17573654
+860.17327676 -860.17327637 -1274.81551212
+0.00000031 0.00000023 -193.17573676
+-860.17327615 860.17327645 -1274.81551258
+0.00000000 0.00000015 83.09907327
+861.74281299 861.74281299 -1275.71086763
+-0.00000046 -0.00000015 5404.30514861
+-861.74281406 -861.74281421 -1275.71086938
+-1276.01088968 861.66402284 861.60900330
+83.46947136 0.16714109 -0.06108436
+-1276.15175722 861.54714957 -861.52691391
+-193.17596141 -0.16730510 -0.02099527
+-1273.31334666 -858.38273281 858.80488124
+-193.21058304 -0.11920641 0.12012636
+-1276.19187285 -861.66400087 -861.74280773
+5404.58493638 -3.04507565 2.81778602
+861.54715133 -1276.15175913 -861.52691490
+-0.16730502 -193.17596118 -0.02099497
+861.66402314 -1276.01088976 861.60900383
+0.16714125 83.46947151 -0.06108497
+-858.38273296 -1273.31334681 858.80488139
+-0.11920686 -193.21058311 0.12012605
+-861.66400079 -1276.19187255 -861.74280811
+-3.04506703 5404.58493432 2.81779319
+861.62536952 -861.66025637 -1276.08157175
+-0.06099938 0.02106080 -193.17561235
+-861.66025645 861.62536929 -1276.08157213
+0.02106049 -0.06099862 -193.17561189
+858.96245049 858.96245041 -1273.17866553
+-0.12013444 -0.12013475 83.09915550
+-861.58531232 -861.58531217 -1275.71087655
+2.81780737 2.81780753 5404.30474547

examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon

@@ -0,0 +1,58 @@
+LAMMPS (16 Jul 2018)
+Reading data file ...
+  orthogonal box = (0 0 0) to (5.431 5.431 5.431)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  8 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4
+  ghost atom cutoff = 4
+  binsize = 2, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Calculating Dynamical Matrix...
+Dynamical Matrix calculation took 0.001183 seconds
+Finished Calculating Dynamical Matrix
+Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms
+
+0.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00016781 | 0.00041345 | 0.00051464 |   0.0 |  0.00
+Bond    | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00056143 | 0.00066602 | 0.00090865 |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.224e+06  |            |       |100.00
+
+Nlocal:    2 ave 3 max 1 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    56 ave 57 max 55 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  32 ave 48 max 16 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp

@@ -0,0 +1,29 @@
+LAMMPS description
+
+       8      atoms    
+       0      bonds    
+       0      angles   
+       0      dihedrals
+       0      impropers
+
+       1      atom types    
+       0      bond types    
+       0      angle types   
+       0      dihedral types
+       0      improper types
+
+
+  0.0000000      5.4310000     xlo xhi
+  0.0000000      5.4310000     ylo yhi
+  0.0000000      5.4310000     zlo zhi
+
+ Atoms
+
+      1      1      1      0.0000000      0.0000000      0.0000000      0.0000000
+      2      2      1      0.0000000      1.3577500      1.3577500      1.3572000
+      3      3      1      0.0000000      2.7155000      2.7155000      0.0000000
+      4      4      1      0.0000000      4.0732500      4.0732500      1.3572000
+      5      5      1      0.0000000      2.7155000      0.0000000      2.7144000
+      6      6      1      0.0000000      4.0732500      1.3577500      4.0732500
+      7      7      1      0.0000000      0.0000000      2.7155000      2.7155000
+      8      8      1      0.0000000      1.3577500      4.0732500      4.0732500

examples/USER/ptm/ptm_example.in

@@ -0,0 +1,47 @@
+# LAMMPS Input File for Grain Boundaries
+# Mark Tschopp, Dec2009
+# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS
+# This file will generate a single Sigma5(310) STGB and run PTM
+
+# ---------- Initialize Simulation ---------------------
+clear
+units metal
+dimension 3
+boundary p p p
+atom_style atomic
+
+# ---------- Create Sigma5(310) Structure ---------
+lattice fcc 4.05
+region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box
+create_box 2 whole
+region upper block INF INF 0.000000 64.0361225 INF INF units box
+lattice fcc 4.05 orient x  0  3  1 orient y  0 -1  3 orient z  1  0  0
+create_atoms 1 region upper
+region lower block INF INF -64.0361225 0.000000 INF INF units box
+lattice fcc 4.05 orient x  0  3 -1 orient y  0  1  3 orient z  1  0  0
+create_atoms 2 region lower
+group upper type 1
+group lower type 2
+
+mass 1 1.0
+mass 2 1.0
+
+# ---------- Define Interatomic Potential ---------------------
+pair_style	lj/cut 2.5
+pair_coeff	* * 1 1
+pair_coeff	1 1 1 1.1 2.8
+
+# ---------- Displace atoms and delete overlapping atoms ---------------------
+displace_atoms upper move 0 0 0 units lattice
+delete_atoms overlap 0.35 lower upper
+
+# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) -------------------
+compute ptm all ptm/atom default 0.1
+
+# ---------- Dump data into Data file -------------
+reset_timestep 0
+dump 		1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7]
+dump_modify     1 element Al Al
+run 1
+
+print "All done"

examples/USER/qtb/methane_qbmsst/methane_qtb.mod

@@ -38,8 +38,9 @@ mass			2  1.007970
 
 ## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
 #Pair Potentials
-pair_style		reax 10.0 1 1 1.0e-6
-pair_coeff		* * ffield.reax 1 2
+pair_style		reax/c NULL
+pair_coeff		* * ffield.reax C H
+fix                     0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
 
 #Neighbor Style
 neighbor		2.5 bin

examples/USER/qtb/methane_qtb/methane_qtb.in

@@ -44,8 +44,9 @@ mass			2  1.007970
 
 ## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
 #Pair Potentials
-pair_style		reax 10.0 1 1 1.0e-6
-pair_coeff		* * ffield.reax 1 2
+pair_style		reax/c NULL
+pair_coeff		* * ffield.reax C H
+fix                     0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
 
 #Neighbor Style
 neighbor		2.5 bin

examples/hyper/in.hyper.global

@@ -12,6 +12,8 @@ variable        cutevent index 1.1
 variable        steps index 100000
 variable        nevent index 1000
 variable        zoom index 1.8
+variable        seed index 826626413
+variable        tol index 1.0e-15
 
 units           metal
 atom_style	atomic
@@ -45,7 +47,7 @@ neighbor	0.5 bin
 neigh_modify    every 1 delay 5 check yes
 
 fix		1 mobile nve
-fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 858872873 zero yes
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
 
 timestep	0.005
 
@@ -92,4 +94,4 @@ dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
 
 # run
 
-hyper           ${steps} ${nevent} HG event min 1.0e-6 1.0e-6 100 100 dump 1
+hyper           ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1

examples/hyper/in.hyper.local

@@ -107,6 +107,12 @@ dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
 dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
 
+# test of histogramming and dump output of bias coeffs
+
+#fix            histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL &
+#               mode vector kind local file tmp.histo
+#dump           2 all local 1000 tmp.local f_HL
+
 # run
 
 hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1