Merge pull request #1490 from akohlmey/next_version

Step version number for stable release

cmake/CMakeLists.txt

@@ -87,7 +87,8 @@ 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 ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
+file(GLOB SRC_AUTOGEN_PACKAGES ${LAMMPS_SOURCE_DIR}/packages_*.h)
+list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${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})
@@ -172,21 +173,17 @@ set(LAMMPS_LINK_LIBS)
 set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
-set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
-  SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
-  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
-  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
-  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-ADIOS)
+set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
+  REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
+  USER-MANIFOLD 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-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
-set(OTHER_PACKAGES CORESHELL QEQ)
-foreach(PKG ${DEFAULT_PACKAGES})
-  option(PKG_${PKG} "Build ${PKG} Package" OFF)
-endforeach()
-foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
@@ -203,7 +200,6 @@ 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
@@ -213,7 +209,6 @@ if(PKG_USER-ADIOS)
   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})
@@ -233,7 +228,6 @@ else()
   list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
 endif()
 
-
 set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
@@ -322,7 +316,18 @@ pkg_depends(USER-SCAFACOS MPI)
 
 include(CheckIncludeFileCXX)
 find_package(OpenMP QUIET)
-option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+
+# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
+# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
+# where we assume older GCC semantics. For the time being, we disable OpenMP by default
+# for GCC 9.x and beyond. People may manually turn it on, but need to run the script
+# src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9.
+if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9))
+  option(BUILD_OMP "Build with OpenMP support" OFF)
+else()
+  option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+endif()
+
 if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
   check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
@@ -446,7 +451,6 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-
 if(PKG_VORONOI)
   find_package(VORO)
   if(VORO_FOUND)
@@ -895,6 +899,8 @@ foreach(PKG ${DEFAULT_PACKAGES})
     list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
     include_directories(${${PKG}_SOURCES_DIR})
   endif()
+
+  RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
 # packages that need defines set
@@ -913,6 +919,8 @@ foreach(PKG ${ACCEL_PACKAGES})
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
+
+  RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
 ##############################################
@@ -961,7 +969,6 @@ if(PKG_USER-H5MD)
   include_directories(${HDF5_INCLUDE_DIRS})
 endif()
 
-
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
@@ -1438,10 +1445,12 @@ endif()
 ######################################################
 # Generate style headers based on global list of
 # styles registered during package selection
+# Generate packages headers from all packages
 ######################################################
 set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
+GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
@@ -1450,7 +1459,7 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ######################################
 set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
 set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] =  {\n")
-set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
 list(SORT temp_PKG_LIST)
 foreach(PKG ${temp_PKG_LIST})
     if(PKG_${PKG})
@@ -1529,8 +1538,6 @@ if(BUILD_EXE)
 
 endif()
 
-
-
 ###############################################################################
 # Build documentation
 ###############################################################################
@@ -1683,7 +1690,7 @@ endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()

cmake/Modules/StyleHeaderUtils.cmake

@@ -181,3 +181,88 @@ function(DetectBuildSystemConflict lammps_src_dir)
     endforeach()
   endif()
 endfunction(DetectBuildSystemConflict)
+
+
+function(FindPackagesHeaders path style_class file_pattern headers)
+    file(GLOB files "${path}/${file_pattern}*.h")
+    get_property(plist GLOBAL PROPERTY ${headers})
+
+    foreach(file_name ${files})
+        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+        if(is_style)
+            list(APPEND plist ${file_name})
+        endif()
+    endforeach()
+    set_property(GLOBAL PROPERTY ${headers} "${plist}")
+endfunction(FindPackagesHeaders)
+
+function(RegisterPackages search_path)
+    FindPackagesHeaders(${search_path} ANGLE_CLASS     angle_     PKGANGLE     ) # angle     ) # force
+    FindPackagesHeaders(${search_path} ATOM_CLASS      atom_vec_  PKGATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindPackagesHeaders(${search_path} BODY_CLASS      body_      PKGBODY      ) # body      ) # atom_vec_body
+    FindPackagesHeaders(${search_path} BOND_CLASS      bond_      PKGBOND      ) # bond      ) # force
+    FindPackagesHeaders(${search_path} COMMAND_CLASS   "[^.]"     PKGCOMMAND   ) # command   ) # input
+    FindPackagesHeaders(${search_path} COMPUTE_CLASS   compute_   PKGCOMPUTE   ) # compute   ) # modify
+    FindPackagesHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  PKGDIHEDRAL  ) # dihedral  ) # force
+    FindPackagesHeaders(${search_path} DUMP_CLASS      dump_      PKGDUMP      ) # dump      ) # output    write_dump
+    FindPackagesHeaders(${search_path} FIX_CLASS       fix_       PKGFIX       ) # fix       ) # modify
+    FindPackagesHeaders(${search_path} IMPROPER_CLASS  improper_  PKGIMPROPER  ) # improper  ) # force
+    FindPackagesHeaders(${search_path} INTEGRATE_CLASS "[^.]"     PKGINTEGRATE ) # integrate ) # update
+    FindPackagesHeaders(${search_path} KSPACE_CLASS    "[^.]"     PKGKSPACE    ) # kspace    ) # force
+    FindPackagesHeaders(${search_path} MINIMIZE_CLASS  min_       PKGMINIMIZE  ) # minimize  ) # update
+    FindPackagesHeaders(${search_path} NBIN_CLASS      nbin_      PKGNBIN      ) # nbin      ) # neighbor
+    FindPackagesHeaders(${search_path} NPAIR_CLASS     npair_     PKGNPAIR     ) # npair     ) # neighbor
+    FindPackagesHeaders(${search_path} NSTENCIL_CLASS  nstencil_  PKGNSTENCIL  ) # nstencil  ) # neighbor
+    FindPackagesHeaders(${search_path} NTOPO_CLASS     ntopo_     PKGNTOPO     ) # ntopo     ) # neighbor
+    FindPackagesHeaders(${search_path} PAIR_CLASS      pair_      PKGPAIR      ) # pair      ) # force
+    FindPackagesHeaders(${search_path} READER_CLASS    reader_    PKGREADER    ) # reader    ) # read_dump
+    FindPackagesHeaders(${search_path} REGION_CLASS    region_    PKGREGION    ) # region    ) # domain
+endfunction(RegisterPackages)
+
+function(CreatePackagesHeader path filename)
+  set(temp "")
+  if(ARGC GREATER 2)
+    list(REMOVE_AT ARGV 0 1)
+    foreach(FNAME ${ARGV})
+      set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
+      get_filename_component(DNAME ${FNAME} DIRECTORY)
+      get_filename_component(DNAME ${DNAME} NAME)
+      get_filename_component(FNAME ${FNAME} NAME)
+      set(temp "${temp}#undef PACKAGE\n#define PACKAGE \"${DNAME}\"\n")
+      set(temp "${temp}#include \"${DNAME}/${FNAME}\"\n")
+    endforeach()
+  endif()
+  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(CreatePackagesHeader)
+
+function(GeneratePackagesHeader path property style)
+  get_property(files GLOBAL PROPERTY ${property})
+  CreatePackagesHeader("${path}" "packages_${style}.h" ${files})
+endfunction(GeneratePackagesHeader)
+
+function(GeneratePackagesHeaders output_path)
+    GeneratePackagesHeader(${output_path} PKGANGLE      angle     ) # force
+    GeneratePackagesHeader(${output_path} PKGATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GeneratePackagesHeader(${output_path} PKGBODY       body      ) # atom_vec_body
+    GeneratePackagesHeader(${output_path} PKGBOND       bond      ) # force
+    GeneratePackagesHeader(${output_path} PKGCOMMAND    command   ) # input
+    GeneratePackagesHeader(${output_path} PKGCOMPUTE    compute   ) # modify
+    GeneratePackagesHeader(${output_path} PKGDIHEDRAL   dihedral  ) # force
+    GeneratePackagesHeader(${output_path} PKGDUMP       dump      ) # output    write_dump
+    GeneratePackagesHeader(${output_path} PKGFIX        fix       ) # modify
+    GeneratePackagesHeader(${output_path} PKGIMPROPER   improper  ) # force
+    GeneratePackagesHeader(${output_path} PKGINTEGRATE  integrate ) # update
+    GeneratePackagesHeader(${output_path} PKGKSPACE     kspace    ) # force
+    GeneratePackagesHeader(${output_path} PKGMINIMIZE   minimize  ) # update
+    GeneratePackagesHeader(${output_path} PKGNBIN       nbin      ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNPAIR      npair     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNSTENCIL   nstencil  ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNTOPO      ntopo     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGPAIR       pair      ) # force
+    GeneratePackagesHeader(${output_path} PKGREADER     reader    ) # read_dump
+    GeneratePackagesHeader(${output_path} PKGREGION     region    ) # domain
+endfunction(GeneratePackagesHeaders)
+

doc/Makefile

@@ -211,7 +211,7 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx==1.7.6; \
+		pip install Sphinx; \
 		deactivate;\
 	)
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "15 May 2019" "2019-05-15"
+.TH LAMMPS "5 June 2019" "2019-06-05"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_extras.txt

@@ -30,7 +30,6 @@ This is the list of packages that may require additional steps.
 "KIM"_#kim,
 "KOKKOS"_#kokkos,
 "LATTE"_#latte,
-"MEAM"_#meam,
 "MESSAGE"_#message,
 "MSCG"_#mscg,
 "OPT"_#opt,
@@ -351,49 +350,6 @@ the compiler you use on your system to build LATTE.
 
 :line
 
-MEAM package :h4,link(meam)
-
-NOTE: the use of the MEAM package is discouraged, as it has been
-superseded by the USER-MEAMC package, which is a direct translation of
-the Fortran code in the MEAM library to C++. The code in USER-MEAMC
-should be functionally equivalent to the MEAM package, fully supports
-use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
-not), and has optimizations that make it significantly faster than the
-MEAM package.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_MEAM=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the MEAM library in lib/meam.
-You can build the MEAM library manually if you prefer; follow the
-instructions in lib/meam/README.  You can also do it in one step from
-the lammps/src dir, using a command like these, which simply invoke
-the lib/meam/Install.py script with the specified args:
-
-make lib-meam                  # print help message
-make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
-
-NOTE: You should test building the MEAM library with both the Intel
-and GNU compilers to see if a simulation runs faster with one versus
-the other on your system.
-
-The build should produce two files: lib/meam/libmeam.a and
-lib/meam/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (MEAM library).  Typically the two compilers used for LAMMPS
-and the MEAM library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/meam/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-:line
-
 MESSAGE package :h4,link(message)
 
 This package can optionally include support for messaging via sockets,

doc/src/Build_package.txt

@@ -41,7 +41,6 @@ packages:
 "KIM"_Build_extras.html#kim,
 "KOKKOS"_Build_extras.html#kokkos,
 "LATTE"_Build_extras.html#latte,
-"MEAM"_Build_extras.html#meam,
 "MESSAGE"_Build_extras.html#message,
 "MSCG"_Build_extras.html#mscg,
 "OPT"_Build_extras.html#opt,

doc/src/Commands.txt

@@ -33,6 +33,11 @@ commands in it are used to define a LAMMPS simulation.
    Commands_bond
    Commands_kspace
 
+.. toctree::
+   :maxdepth: 1
+
+   Commands_removed
+
 END_RST -->
 
 <!-- HTML_ONLY -->
@@ -49,5 +54,7 @@ END_RST -->
 "Bond, angle, dihedral, improper commands"_Commands_bond.html
 "KSpace solvers"_Commands_kspace.html  :all(b)
 
+"Removed commands and packages"_Commands_removed.html  :all(b)
+
 <!-- END_HTML_ONLY -->
 

doc/src/Commands_removed.txt

@@ -0,0 +1,66 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+Removed commands and packages :h3
+
+This page lists LAMMPS commands and packages that have been removed from
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
+
+Fix ave/spatial and fix ave/spatial/sphere :h4
+
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the "compute chunk/atom"_compute_chunk_atom.html command
+and then averaging is done using "fix ave/chunk"_fix_ave_chunk.html.
+Please refer to the "chunk HOWTO"_Howto_chunk.html section for an overview.
+
+MEAM package :h4
+
+The MEAM package has been removed since it was superseded by the
+"USER-MEAMC package"_Package_details.html#PKG-USER-MEAMC. The code in
+the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+which removes several restrictions (e.g. there can be multiple instances
+in hybrid pair styles) and allows for some optimizations leading
+to better performance.  The new pair style "meam/c"_pair_meamc.html has
+the exact same syntax as the old "meam" pair style and thus pair style
+"meam"_pair_meamc.html is an alias to the new style and backward
+compatibility of old inputs is preserved.
+
+REAX package :h4
+
+The REAX package has been removed since it was superseded by the
+"USER-REAXC package"_Package_details.html#PKG-USER-REAXC.  The USER-REAXC
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via USER-OMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
+
+USER-CUDA package :h4
+
+The USER-CUDA package had been removed, since it had been unmaintained
+for a long time and had known bugs and problems.  Significant parts of
+the design were transferred to the
+"KOKKOS package"_Package_details.html#PKG-KOKKOS, which has similar
+performance characteristics on Nvidia GPUs. Both, the KOKKOS
+and the "GPU package"_Package_details.html#PKG-GPU are maintained
+and allow running LAMMPS with GPU acceleration.
+
+restart2data tool :h4
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands "read_restart"_read_restart.html and
+"write_data"_write_data.html can be used to the same effect.  For added
+convenience this conversion can also be triggered by "command line
+flags"_Run_options.html

doc/src/Errors_messages.txt

@@ -610,6 +610,62 @@ This means there is something invalid about the topology definitions. :dd
 
 The data file header lists bonds but no bond types. :dd
 
+{Bond/react: Cannot use fix bond/react with non-molecular systems} :dt
+
+Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify. :dd
+
+{Bond/react: Rmax cutoff is longer than pairwise cutoff} :dt
+
+This is not allowed because bond creation is done using the pairwise
+neighbor list. :dd
+
+{Bond/react: Molecule template ID for fix bond/react does not exist} :dt
+
+A valid molecule template must have been created with the molecule
+command. :dd
+
+{Bond/react: Reaction templates must contain the same number of atoms} :dt
+
+There should be a one-to-one correspondence between atoms in the
+pre-reacted and post-reacted templates, as specified by the map file. :dd
+
+{Bond/react: Unknown section in map file} :dt
+
+Please ensure reaction map files are properly formatted. :dd
+
+{Bond/react: Atom affected by reaction too close to template edge} :dt
+
+This means an atom which changes type during the reaction is too close
+to an 'edge' atom defined in the superimpose file. This could cause
+incorrect assignment of bonds, angle, etc. Generally, this means you
+must include more atoms in your templates, such that there are at
+least two atoms between each atom involved in the reaction and an edge
+atom. :dd
+
+{Bond/react: Fix bond/react needs ghost atoms from farther away} :dt
+
+This is because a processor needs to superimpose the entire unreacted
+molecule template onto simulation atoms it knows about. The
+comm_modify cutoff command can be used to extend the communication
+range. :dd
+
+{Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted} :dt
+
+Self-explanatory. :dd
+
+{Bond/react special bond generation overflow} :dt
+
+The number of special bonds per-atom created by a reaction exceeds the
+system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
+{Bond/react topology/atom exceed system topology/atom} :dt
+
+The number of bonds, angles etc per-atom created by a reaction exceeds
+the system setting. See the read_data or create_box command for how to
+specify this value. :dd
+
 {Both restart files must use % or neither} :dt
 
 Self-explanatory. :dd
@@ -5828,6 +5884,12 @@ Must have periodic x,y dimensions and non-periodic z dimension to use
 Must have periodic x,y dimensions and non-periodic z dimension to use
 2d slab option with pppm/disp. :dd
 
+{Incorrect conversion in format string} :dt
+
+A format style variable was not using either a %f, a %g, or a %e conversion.
+Or an immediate variable with format suffix was not using either
+a %f, a %g or a %e conversion in the format suffix. :dd
+
 {Incorrect element names in ADP potential file} :dt
 
 The element names in the ADP file do not match those requested. :dd
@@ -7448,6 +7510,11 @@ The Atoms section of a data file must come before a Triangles section. :dd
 The Atoms section of a data file must come before a Velocities
 section. :dd
 
+{Must re-specify non-restarted pair style (xxx) after read_restart} :dt
+
+For pair styles, that do not store their settings in a restart file,
+it must be defined with a new 'pair_style' command after read_restart. :dd
+
 {Must set both respa inner and outer} :dt
 
 Cannot use just the inner or outer option with respa without using the
@@ -9990,25 +10057,25 @@ quote. :dd
 
 Self-explanatory. :dd
 
-{Unexpected end of AngleCoeffs section} :dt
+{Unexpected empty line in AngleCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of BondCoeffs section} :dt
+{Unexpected empty line in BondCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of DihedralCoeffs section} :dt
+{Unexpected empty line in DihedralCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of ImproperCoeffs section} :dt
+{Unexpected empty line in ImproperCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
-{Unexpected end of PairCoeffs section} :dt
+{Unexpected empty line in PairCoeffs section} :dt
 
-Read a blank line. :dd
+Read a blank line where there should be coefficient data. :dd
 
 {Unexpected end of custom file} :dt
 
@@ -10049,19 +10116,19 @@ create_box command. :dd
 A universe or uloop style variable must specify a number of values >= to the
 number of processor partitions. :dd
 
-{Unknown angle style} :dt
+{Unrecognized angle style} :dt
 
 The choice of angle style is unknown. :dd
 
-{Unknown atom style} :dt
+{Unrecognized atom style} :dt
 
 The choice of atom style is unknown. :dd
 
-{Unknown body style} :dt
+{Unrecognized body style} :dt
 
 The choice of body style is unknown. :dd
 
-{Unknown bond style} :dt
+{Unrecognized bond style} :dt
 
 The choice of bond style is unknown. :dd
 
@@ -10077,23 +10144,23 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Unknown command: %s} :dt
+{Unrecognized command: %s} :dt
 
 The command is not known to LAMMPS.  Check the input script. :dd
 
-{Unknown compute style} :dt
+{Unrecognized compute style} :dt
 
 The choice of compute style is unknown. :dd
 
-{Unknown dihedral style} :dt
+{Unrecognized dihedral style} :dt
 
 The choice of dihedral style is unknown. :dd
 
-{Unknown dump reader style} :dt
+{Unrecognized dump reader style} :dt
 
 The choice of dump reader style via the format keyword is unknown. :dd
 
-{Unknown dump style} :dt
+{Unrecognized dump style} :dt
 
 The choice of dump style is unknown. :dd
 
@@ -10101,7 +10168,7 @@ The choice of dump style is unknown. :dd
 
 Self-explanatory. :dd
 
-{Unknown fix style} :dt
+{Unrecognized fix style} :dt
 
 The choice of fix style is unknown. :dd
 
@@ -10109,7 +10176,7 @@ The choice of fix style is unknown. :dd
 
 A section of the data file cannot be read by LAMMPS. :dd
 
-{Unknown improper style} :dt
+{Unrecognized improper style} :dt
 
 The choice of improper style is unknown. :dd
 
@@ -10117,7 +10184,7 @@ The choice of improper style is unknown. :dd
 
 One or more specified keywords are not recognized. :dd
 
-{Unknown kspace style} :dt
+{Unrecognized kspace style} :dt
 
 The choice of kspace style is unknown. :dd
 
@@ -10133,7 +10200,7 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Unknown pair style} :dt
+{Unrecognized pair style} :dt
 
 The choice of pair style is unknown. :dd
 
@@ -10141,7 +10208,7 @@ The choice of pair style is unknown. :dd
 
 The choice of sub-style is unknown. :dd
 
-{Unknown region style} :dt
+{Unrecognized region style} :dt
 
 The choice of region style is unknown. :dd
 

doc/src/Errors_warnings.txt

@@ -82,6 +82,11 @@ bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
 length, multiplying by the number of bonds in the interaction (e.g. 3
 for a dihedral) and adding a small amount of stretch. :dd
 
+{Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type} :dt
+
+You may want to double-check that all atom types are properly assigned
+in the post-reaction template. :dd
+
 {Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
 
 Self-explanatory. :dd

doc/src/Examples.txt

@@ -52,13 +52,14 @@ Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 airebo:   polyethylene with AIREBO potential
+atm:      Axilrod-Teller-Muto potential example
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:     models using the COMB potential
-coreshell: core/shell model using CORESHELL package
 controller: use of fix controller as a thermostat
+coreshell: core/shell model using CORESHELL package
 crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
@@ -70,10 +71,13 @@ friction: frictional contact of spherical asperities between 2d surfaces
 gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
+hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
+message:  demos for LAMMPS client/server coupling with the MESSAGE package
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
@@ -88,6 +92,7 @@ pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   using embedded Python in a LAMMPS input script
 qeq:      use of the QEQ package for charge equilibration
+rdf-adf:  computing radial and angle distribution functions for water
 reax:     RDX and TATB models using the ReaxFF
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
@@ -95,6 +100,7 @@ snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 streitz:  use of Streitz/Mintmire potential with charge equilibration
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
+threebody: regression test input for a variety of manybody potentials
 vashishta: use of the Vashishta potential
 voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)
 
@@ -131,8 +137,10 @@ COUPLE: examples of how to use LAMMPS as a library
 DIFFUSE: compute diffusion coefficients via several methods
 ELASTIC: compute elastic constants at zero temperature
 ELASTIC_T: compute elastic constants at finite temperature
+HEAT: compute thermal conductivity for LJ and water via fix ehex
 KAPPA: compute thermal conductivity via several methods
 MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
+SPIN: examples for features of the SPIN package
 USER: examples for USER packages and USER-contributed commands
 VISCOSITY: compute viscosity via several methods :tb(s=:)
 

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="15 May 2019 version">
+<META NAME="docnumber" CONTENT="5 Jun 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
-15 May 2019 version :c,h2
+5 Jun 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -208,7 +208,7 @@ available on your system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#compress on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -358,7 +358,7 @@ developed the pair style.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#kim on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -404,7 +404,7 @@ lib/kokkos.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#kokkos on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -477,7 +477,7 @@ Cawkwell, Anders Niklasson, and Christian Negre.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#latte on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -654,7 +654,7 @@ University of Chicago.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#mscg on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -686,7 +686,7 @@ and Vincent Natoli (Stone Ridge Technolgy).
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#opt on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -743,7 +743,7 @@ connections at hinge points.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#poems on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -775,7 +775,7 @@ lib/python/README for more details.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#python on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -965,7 +965,7 @@ and LBNL.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#voronoi on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1017,7 +1017,7 @@ atomic information to continuum fields.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-atc on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1044,7 +1044,7 @@ model.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-awpmd on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1184,7 +1184,7 @@ Tribello.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-plumed on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1362,7 +1362,7 @@ H5MD format.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-h5md on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1400,7 +1400,7 @@ NOTE: the USER-INTEL package contains styles that require using the
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-intel on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1620,7 +1620,7 @@ at
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-molfile on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1660,7 +1660,7 @@ tools:
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-netcdf on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1704,7 +1704,7 @@ install/un-install the package and build LAMMPS in the usual manner:
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-omp on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1788,7 +1788,7 @@ without changes to LAMMPS itself.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-qmmm on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1846,7 +1846,7 @@ on your system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-quip on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1964,7 +1964,7 @@ Dynamics, Ernst Mach Institute, Germany).
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-smd on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -2090,7 +2090,7 @@ system.
 [Install:]
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-vtk on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]

doc/src/compute_coord_atom.txt

@@ -15,8 +15,9 @@ compute ID group-ID coord/atom cstyle args ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 coord/atom = style name of this compute command :l
 cstyle = {cutoff} or {orientorder} :l
-  {cutoff} args = cutoff typeN
+  {cutoff} args = cutoff \[group group2-ID\] typeN
     cutoff = distance within which to count coordination neighbors (distance units)
+    group {group2-ID} = select group-ID to restrict which atoms to consider for coordination number (optional)
     typeN = atom type for Nth coordination count (see asterisk form below)
   {orientorder} args = orientorderID threshold
     orientorderID = ID of an orientorder/atom compute
@@ -28,6 +29,7 @@ cstyle = {cutoff} or {orientorder} :l
 compute 1 all coord/atom cutoff 2.0
 compute 1 all coord/atom cutoff 6.0 1 2
 compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 solute coord/atom cutoff 2.0 group solvent
 compute 1 all coord/atom orientorder 2 0.5 :pre
 
 [Description:]
@@ -38,9 +40,14 @@ meaning of the resulting value depend on the {cstyle} keyword used.
 
 The {cutoff} cstyle calculates one or more traditional coordination
 numbers for each atom.  A coordination number is defined as the number
-of neighbor atoms with specified atom type(s) that are within the
-specified cutoff distance from the central atom.  Atoms not in the
-specified group are included in the coordination number tally.
+of neighbor atoms with specified atom type(s), and optionally within
+the specified group, that are within the specified cutoff distance from
+the central atom. The compute group selects only the central atoms; all
+neighboring atoms, unless selected by type, type range, or group option,
+are included in the coordination number tally.
+
+The optional {group} keyword allows to specify from which group atoms
+contribute to the coordination number. Default setting is group 'all'. 
 
 The {typeN} keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is
@@ -122,7 +129,9 @@ explained above.
 "compute cluster/atom"_compute_cluster_atom.html
 "compute orientorder/atom"_compute_orientorder_atom.html
 
-[Default:] none
+[Default:]
+
+group = all
 
 :line
 

doc/src/fix_atom_swap.txt

@@ -141,11 +141,16 @@ specify if this should be done.
 
 This fix writes the state of the fix to "binary restart
 files"_restart.html.  This includes information about the random
-number generator seed, the next timestep for MC exchanges, etc.  See
+number generator seed, the next timestep for MC exchanges, the number
+of exchange attempts and successes etc.  See
 the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.
 

doc/src/fix_bond_react.txt

@@ -18,8 +18,8 @@ fix ID group-ID bond/react common_keyword values ...
 
 ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
 bond/react = style name of this fix command :l
-zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
-these apply to all reaction specifications (below) :l
+the common keyword/values may be appended directly after 'bond/react' :l
+this applies to all reaction specifications (below) :l
 common_keyword = {stabilization} :l
   {stabilization} values = {no} or {yes} {group-ID} {xmax}
     {no} = no reaction site stabilization
@@ -136,10 +136,12 @@ words, can be customized for each reaction, or reaction step):
 A check for possible new reaction sites is performed every {Nevery}
 timesteps.
 
-Two conditions must be met for a reaction to occur. First a bonding
-atom pair must be identified. Second, the topology surrounding the
-bonding atom pair must match the topology of the pre-reaction
-template. If both these conditions are met, the reaction site is
+Three physical conditions must be met for a reaction to occur. First,
+a bonding atom pair must be identified within the reaction distance
+cutoffs. Second, the topology surrounding the bonding atom pair must
+match the topology of the pre-reaction template. Finally, any reaction
+constraints listed in the map file (see below) must be satisfied. If
+all of these conditions are met, the reaction site is eligible to be
 modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
@@ -203,14 +205,24 @@ new types must also be defined during the setup of a given simulation.
 A discussion of correctly handling this is also provided on the
 "molecule"_molecule.html command page.
 
+NOTE: When a reaction occurs, it is possible that the resulting
+topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
+the existing system and reaction templates. As when inserting
+molecules, enough space for this increased topology/atom must be
+reserved by using the relevant "extra" keywords to the
+"read_data"_read_data.html or "create_box"_create_box.html commands.
+
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and three optional keywords. The
-mandatory keyword is 'equivalences' and the optional keywords are
-'edgeIDs' and 'deleteIDs' and 'customIDs':
+contains one mandatory keyword and four optional keywords. The
+mandatory keyword is 'equivalences':
+
+N {equivalences} = # of atoms N in the reaction molecule templates :pre
+
+The optional keywords are 'edgeIDs', 'deleteIDs', 'customIDs' and
+'constraints':
 
-N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
 N {deleteIDs} = # of atoms N that are specified for deletion
 N {customIDs} = # of atoms N that are specified for a custom update
@@ -244,8 +256,8 @@ A sample map file is given below:
 
 # this is a map file :pre
 
-2 edgeIDs
-7 equivalences :pre
+7 equivalences
+2 edgeIDs :pre
 
 BondingIDs :pre
 
@@ -297,26 +309,25 @@ can allow for the possibility of one or more reverse reactions.
 
 The optional keywords deal with the probability of a given reaction
 occurring as well as the stable equilibration of each reaction site as
-it occurs.
+it occurs:
 
-The {prob} keyword can affect whether an eligible reaction actually
-occurs. The fraction setting must be a value between 0.0 and 1.0. A
-uniform random number between 0.0 and 1.0 is generated and the
+The {prob} keyword can affect whether or not an eligible reaction
+actually occurs. The fraction setting must be a value between 0.0 and
+1.0. A uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
 fraction. Up to N reactions are permitted to occur, as optionally
 specified by the {max_rxn} keyword.
 
 The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the
-overall system thermostat.
-
-In order to produce the most physical behavior, this 'reaction site
-equilibration time' should be tuned to be as small as possible while
-retaining stability for a given system or reaction step. After a
-limited number of case studies, this number has been set to a default
-of 60 timesteps. Ideally, it should be individually tuned for each fix
-reaction step. Note that in some situations, decreasing rather than
-increasing this parameter will result in an increase in stability.
+overall system thermostat. In order to produce the most physical
+behavior, this 'reaction site equilibration time' should be tuned to
+be as small as possible while retaining stability for a given system
+or reaction step. After a limited number of case studies, this number
+has been set to a default of 60 timesteps. Ideally, it should be
+individually tuned for each fix reaction step. Note that in some
+situations, decreasing rather than increasing this parameter will
+result in an increase in stability.
 
 The {update_edges} keyword can increase the number of atoms whose
 atomic charges are updated, when the pre-reaction template contains
@@ -324,11 +335,11 @@ edge atoms. When the value is set to 'charges,' all atoms' atomic
 charges are updated to those specified by the post-reaction template,
 including atoms near the edge of reaction templates. When the value is
 set to 'custom,' an additional section must be included in the map
-file that specifies whether to update charges, on a per-atom basis.
-The format of this section is detailed above. Listing a pre-reaction
-atom ID with a value of 'charges' will force the update of the atom's
-charge, even if it is near a template edge. Atoms not near a template
-edge are unaffected by this setting.
+file that specifies whether or not to update charges, on a per-atom
+basis. The format of this section is detailed above. Listing a
+pre-reaction atom ID with a value of 'charges' will force the update
+of the atom's charge, even if it is near a template edge. Atoms not
+near a template edge are unaffected by this setting.
 
 A few other considerations:
 

doc/src/fix_deposit.txt

@@ -261,6 +261,10 @@ next timestep for deposition, etc.  See the
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 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
 access by various "output commands"_Howto_output.html.  No parameter

doc/src/fix_gcmc.txt

@@ -373,11 +373,16 @@ adds all inserted atoms of the specified type to the
 
 This fix writes the state of the fix to "binary restart
 files"_restart.html.  This includes information about the random
-number generator seed, the next timestep for MC exchanges, etc.  See
+number generator seed, the next timestep for MC exchanges,  the number
+of MC step attempts and successes etc.  See
 the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+NOTE: For this to work correctly, the timestep must [not] be changed
+after reading the restart with "reset_timestep"_reset_timestep.html.
+The fix will try to detect it and stop with an error.
+
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.
 

doc/src/pair_e3b.txt

@@ -99,7 +99,7 @@ This pair style does not support the "pair_modify"_pair_modify.html
 shift, table, and tail options.
 
 This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
+files"_restart.html.  Thus, you
 need to re-specify the pair_style and pair_coeff commands in an input
 script that reads a restart file.
 

doc/src/pair_quip.txt

@@ -92,10 +92,6 @@ pairs from the neighbor list. This needs to be very carefully tested,
 because it may remove pairs from the neighbor list that are still
 required.
 
-Pair style {quip} cannot be used with pair style {hybrid}, only
-with {hybrid/overlay} and only the {quip} sub-style is applied to
-all atom types.
-
 [Related commands:]
 
 "pair_coeff"_pair_coeff.html

doc/src/variable.txt

@@ -865,7 +865,7 @@ The {is_active()} function allows to query for active settings which
 are grouped by categories. Currently supported categories and
 arguments are:
 
-{package} (argument = {cuda} or {gpu} or {intel} or {kokkos} or {omp})
+{package} (argument = {gpu} or {intel} or {kokkos} or {omp})
 {newton} (argument = {pair} or {bond} or {any})
 {pair} (argument = {single} or {respa} or {manybody} or {tail} or {shift})
 {comm_style} (argument = {brick} or {tiled})
@@ -894,7 +894,7 @@ kspace_style pppm :pre
 
 Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step
 
-timestep $(2.0*(1.0+*is_active(pair,respa))
+timestep $(2.0*(1.0+2.0*is_active(pair,respa))
 if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3" :pre
 
 The {is_defined()} function allows to query categories like {compute},

doc/utils/sphinx-config/false_positives.txt

@@ -2708,6 +2708,7 @@ Thiaville
 Thibaudeau
 Thijsse
 Thirumalai
+threebody
 thrid
 ThunderX
 thylakoid
@@ -2843,6 +2844,7 @@ unoptimized
 unpadded
 unphysical
 unphysically
+unreacted
 unscaled
 unsets
 unsmoothed

examples/HEAT/README

@@ -1,6 +1,6 @@
 This directory contains 4 input scripts for carrying out NEMD
 simulations of thermal gradients for a Lennard-Jones fluid and SPC/E
-water using the HEX/a (fix heat) and eHEX/a (fix ehex) algorithms.
+water using the HEX/a (fix ehex w/ hex option) and eHEX/a (fix ehex) algorithms.
 
 All input scripts are part of the supplementary (open access) material
 supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,

examples/README

@@ -64,37 +64,37 @@ balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
-comb:	  models using the COMB potential
+comb:     models using the COMB potential
 coreshell: adiabatic core/shell model
 controller: use of fix controller as a thermostat
-crack:	  crack propagation in a 2d solid
+crack:    crack propagation in a 2d solid
 deposit:  deposition of atoms and molecules onto a 3d substrate
 dipole:   point dipolar particles, 2d system
 dreiding: methanol via Dreiding FF
 eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
-flow:	  Couette and Poiseuille flow in a 2d channel
+flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
 gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
-indent:	  spherical indenter into a 2d solid
+indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
 latte:    use of LATTE density-functional tight-binding quantum code
-meam:	  MEAM test for SiC and shear (same as shear examples)
-melt:	  rapid melt of 3d LJ system
+meam:     MEAM test for SiC and shear (same as shear examples)
+melt:     rapid melt of 3d LJ system
 message:  client/server coupling of 2 codes
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
-min:	  energy minimization of 2d LJ melt
+min:      energy minimization of 2d LJ melt
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
-msst:	  MSST shock dynamics
+msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
-neb:	  nudged elastic band (NEB) calculation for barrier finding
-nemd:	  non-equilibrium MD of 2d sheared system
+neb:      nudged elastic band (NEB) calculation for barrier finding
+nemd:     non-equilibrium MD of 2d sheared system
 obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
-peri:	  Peridynamic model of cylinder impacted by indenter
+peri:     Peridynamic model of cylinder impacted by indenter
 pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
@@ -107,6 +107,7 @@ srd:      stochastic rotation dynamics (SRD) particles as solvent
 snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 streitz:  Streitz-Mintmire potential for Al2O3
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
+threebody: regression test input for a variety of manybody potentials
 vashishta: models using the Vashishta potential
 voronoi:  Voronoi tesselation via compute voronoi/atom command
 
@@ -117,9 +118,7 @@ cp ../../src/lmp_mpi .           # copy LAMMPS executable to this dir
 lmp_mpi -in in.indent              # run the problem
 
 Running the simulation produces the files {dump.indent} and
-{log.lammps}.  You can visualize the dump file as follows:
-
-../../tools/xmovie/xmovie -scale dump.indent
+{log.lammps}.
 
 If you uncomment the dump image line(s) in the input script a series
 of JPG images will be produced by the run.  These can be viewed

src/.gitignore

@@ -5,6 +5,7 @@
 /lmp_*
 
 /style_*.h
+/packages_*.h
 /lmpinstalledpkgs.h
 /lmpgitversion.h
 

src/KOKKOS/neigh_bond_kokkos.cpp

@@ -200,6 +200,7 @@ void NeighBondKokkos<DeviceType>::build_topology_kk()
 {
   atomKK->sync(execution_space, X_MASK | TAG_MASK);
   int nall = atom->nlocal + atom->nghost;
+  int nmax = atom->nmax;
 
   nlocal = atom->nlocal;
   x = atomKK->k_x.view<DeviceType>();
@@ -215,7 +216,9 @@ void NeighBondKokkos<DeviceType>::build_topology_kk()
 
   int* map_array_host = atom->get_map_array();
   int map_size = atom->get_map_size();
-  k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_size);
+  int map_maxarray = atom->get_map_maxarray();
+  if (map_maxarray > k_map_array.extent(0))
+    k_map_array = DAT::tdual_int_1d("NeighBond:map_array",map_maxarray);
   for (int i=0; i<map_size; i++)
     k_map_array.h_view[i] = map_array_host[i];
   k_map_array.template modify<LMPHostType>();
@@ -223,7 +226,8 @@ void NeighBondKokkos<DeviceType>::build_topology_kk()
   map_array = k_map_array.view<DeviceType>();
 
   int* sametag_host = atomKK->sametag;
-  k_sametag = DAT::tdual_int_1d("NeighBond:sametag",nall);
+  if (nmax > k_sametag.extent(0))
+    k_sametag = DAT::tdual_int_1d("NeighBond:sametag",nmax);
   for (int i=0; i<nall; i++)
     k_sametag.h_view[i] = sametag_host[i];
   k_sametag.template modify<LMPHostType>();

src/KOKKOS/pair_eam_alloy_kokkos.cpp

@@ -569,13 +569,13 @@ void PairEAMAlloyKokkos<DeviceType>::operator()(TagPairEAMAlloyKernelA<NEIGHFLAG
                   d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
       if (NEWTON_PAIR || j < nlocal) {
         const int d_type2rhor_ij = d_type2rhor(itype,jtype);
-        rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
+       a_rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
                     d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
       }
     }
 
   }
-  rho[i] += rhotmp;
+  a_rho[i] += rhotmp;
 }
 
 /* ---------------------------------------------------------------------- */

src/KOKKOS/pair_eam_fs_kokkos.cpp

@@ -569,13 +569,13 @@ void PairEAMFSKokkos<DeviceType>::operator()(TagPairEAMFSKernelA<NEIGHFLAG,NEWTO
                   d_rhor_spline(d_type2rhor_ji,m,5))*p + d_rhor_spline(d_type2rhor_ji,m,6);
       if (NEWTON_PAIR || j < nlocal) {
         const int d_type2rhor_ij = d_type2rhor(itype,jtype);
-        rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
+       a_rho[j] += ((d_rhor_spline(d_type2rhor_ij,m,3)*p + d_rhor_spline(d_type2rhor_ij,m,4))*p +
                     d_rhor_spline(d_type2rhor_ij,m,5))*p + d_rhor_spline(d_type2rhor_ij,m,6);
       }
     }
 
   }
-  rho[i] += rhotmp;
+  a_rho[i] += rhotmp;
 }
 
 /* ---------------------------------------------------------------------- */

src/MC/fix_atom_swap.cpp

@@ -771,10 +771,13 @@ double FixAtomSwap::memory_usage()
 void FixAtomSwap::write_restart(FILE *fp)
 {
   int n = 0;
-  double list[4];
+  double list[6];
   list[n++] = random_equal->state();
   list[n++] = random_unequal->state();
-  list[n++] = next_reneighbor;
+  list[n++] = ubuf(next_reneighbor).d;
+  list[n++] = nswap_attempts;
+  list[n++] = nswap_successes;
+  list[n++] = ubuf(update->ntimestep).d;
 
   if (comm->me == 0) {
     int size = n * sizeof(double);
@@ -798,5 +801,12 @@ void FixAtomSwap::restart(char *buf)
   seed = static_cast<int> (list[n++]);
   random_unequal->reset(seed);
 
-  next_reneighbor = static_cast<int> (list[n++]);
+  next_reneighbor = (bigint) ubuf(list[n++]).i;
+
+  nswap_attempts = static_cast<int>(list[n++]);
+  nswap_successes = static_cast<int>(list[n++]);
+
+  bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
+  if (ntimestep_restart != update->ntimestep)
+    error->all(FLERR,"Must not reset timestep when restarting fix atom/swap");
 }

src/MC/fix_gcmc.cpp

@@ -2531,10 +2531,19 @@ double FixGCMC::memory_usage()
 void FixGCMC::write_restart(FILE *fp)
 {
   int n = 0;
-  double list[4];
+  double list[12];
   list[n++] = random_equal->state();
   list[n++] = random_unequal->state();
-  list[n++] = next_reneighbor;
+  list[n++] = ubuf(next_reneighbor).d;
+  list[n++] = ntranslation_attempts;
+  list[n++] = ntranslation_successes;
+  list[n++] = nrotation_attempts;
+  list[n++] = nrotation_successes;
+  list[n++] = ndeletion_attempts;
+  list[n++] = ndeletion_successes;
+  list[n++] = ninsertion_attempts;
+  list[n++] = ninsertion_successes;
+  list[n++] = ubuf(update->ntimestep).d;
 
   if (comm->me == 0) {
     int size = n * sizeof(double);
@@ -2558,7 +2567,20 @@ void FixGCMC::restart(char *buf)
   seed = static_cast<int> (list[n++]);
   random_unequal->reset(seed);
 
-  next_reneighbor = static_cast<int> (list[n++]);
+  next_reneighbor = (bigint) ubuf(list[n++]).i;
+
+  ntranslation_attempts  = list[n++];
+  ntranslation_successes = list[n++];
+  nrotation_attempts     = list[n++];
+  nrotation_successes    = list[n++];
+  ndeletion_attempts     = list[n++];
+  ndeletion_successes    = list[n++];
+  ninsertion_attempts    = list[n++];
+  ninsertion_successes   = list[n++];
+
+  bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
+  if (ntimestep_restart != update->ntimestep)
+    error->all(FLERR,"Must not reset timestep when restarting fix gcmc");
 }
 
 void FixGCMC::grow_molecule_arrays(int nmolatoms) {

src/MISC/fix_deposit.cpp

@@ -798,11 +798,12 @@ void FixDeposit::options(int narg, char **arg)
 void FixDeposit::write_restart(FILE *fp)
 {
   int n = 0;
-  double list[4];
+  double list[5];
   list[n++] = random->state();
   list[n++] = ninserted;
   list[n++] = nfirst;
-  list[n++] = next_reneighbor;
+  list[n++] = ubuf(next_reneighbor).d;
+  list[n++] = ubuf(update->ntimestep).d;
 
   if (comm->me == 0) {
     int size = n * sizeof(double);
@@ -823,7 +824,11 @@ void FixDeposit::restart(char *buf)
   seed = static_cast<int> (list[n++]);
   ninserted = static_cast<int> (list[n++]);
   nfirst = static_cast<int> (list[n++]);
-  next_reneighbor = static_cast<int> (list[n++]);
+  next_reneighbor = (bigint) ubuf(list[n++]).i;
+
+  bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
+  if (ntimestep_restart != update->ntimestep)
+    error->all(FLERR,"Must not reset timestep when restarting this fix");
 
   random->reset(seed);
 }

src/Make.sh

@@ -55,6 +55,34 @@ style () {
   fi
 }
 
+packages () {
+  list=`grep -sl $1 */$2*.h`
+  if (test -e packages_$3.tmp) then
+    rm -f packages_$3.tmp
+  fi
+  for file in $list; do
+    dir="\"`dirname $file`\""
+    echo "#undef PACKAGE" >> packages_$3.tmp
+    echo "#define PACKAGE $dir" >> packages_$3.tmp
+    qfile="\"$file\""
+    echo "#include $qfile" >> packages_$3.tmp
+  done
+  if (test ! -e packages_$3.tmp) then
+    if (test ! -e packages_$3.h) then
+      touch packages_$3.h
+    elif (test "`cat packages_$3.h`" != "") then
+      rm -f packages_$3.h
+      touch packages_$3.h
+    fi
+  elif (test ! -e packages_$3.h) then
+    mv packages_$3.tmp packages_$3.h
+  elif (test "`diff --brief packages_$3.h packages_$3.tmp`" != "") then
+    mv packages_$3.tmp packages_$3.h
+  else
+    rm -f packages_$3.tmp
+  fi
+}
+
 # create individual style files
 # called by "make machine"
 # col 1 = string to search for
@@ -63,28 +91,30 @@ style () {
 # col 4 = file that includes the style file
 # col 5 = optional 2nd file that includes the style file
 
-if (test $1 = "style") then
+cmd=$1
 
-  style ANGLE_CLASS     angle_      angle      force
-  style ATOM_CLASS      atom_vec_   atom       atom      atom_vec_hybrid
-  style BODY_CLASS      body_       body       atom_vec_body
-  style BOND_CLASS      bond_       bond       force
-  style COMMAND_CLASS   ""          command    input
-  style COMPUTE_CLASS   compute_    compute    modify
-  style DIHEDRAL_CLASS  dihedral_   dihedral   force
-  style DUMP_CLASS      dump_       dump       output    write_dump
-  style FIX_CLASS       fix_        fix        modify
-  style IMPROPER_CLASS  improper_   improper   force
-  style INTEGRATE_CLASS ""          integrate  update
-  style KSPACE_CLASS    ""          kspace     force
-  style MINIMIZE_CLASS  min_        minimize   update
-  style NBIN_CLASS      nbin_       nbin       neighbor
-  style NPAIR_CLASS     npair_      npair      neighbor
-  style NSTENCIL_CLASS  nstencil_   nstencil   neighbor
-  style NTOPO_CLASS     ntopo_      ntopo      neighbor
-  style PAIR_CLASS      pair_       pair       force
-  style READER_CLASS    reader_     reader     read_dump
-  style REGION_CLASS    region_     region     domain
+if (test $cmd = "style") || (test $cmd = "packages") then
+
+  $cmd ANGLE_CLASS     angle_      angle      force
+  $cmd ATOM_CLASS      atom_vec_   atom       atom      atom_vec_hybrid
+  $cmd BODY_CLASS      body_       body       atom_vec_body
+  $cmd BOND_CLASS      bond_       bond       force
+  $cmd COMMAND_CLASS   ""          command    input
+  $cmd COMPUTE_CLASS   compute_    compute    modify
+  $cmd DIHEDRAL_CLASS  dihedral_   dihedral   force
+  $cmd DUMP_CLASS      dump_       dump       output    write_dump
+  $cmd FIX_CLASS       fix_        fix        modify
+  $cmd IMPROPER_CLASS  improper_   improper   force
+  $cmd INTEGRATE_CLASS ""          integrate  update
+  $cmd KSPACE_CLASS    ""          kspace     force
+  $cmd MINIMIZE_CLASS  min_        minimize   update
+  $cmd NBIN_CLASS      nbin_       nbin       neighbor
+  $cmd NPAIR_CLASS     npair_      npair      neighbor
+  $cmd NSTENCIL_CLASS  nstencil_   nstencil   neighbor
+  $cmd NTOPO_CLASS     ntopo_      ntopo      neighbor
+  $cmd PAIR_CLASS      pair_       pair       force
+  $cmd READER_CLASS    reader_     reader     read_dump
+  $cmd REGION_CLASS    region_     region     domain
 
 # edit Makefile.lib, for creating non-shared lib
 # called by "make makelib"

src/Makefile

@@ -205,6 +205,7 @@ gitversion:
 	  -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@
 	@if [ ! -d $(objdir) ]; then mkdir $(objdir); fi
 	@$(SHELL) Make.sh style
+	@$(SHELL) Make.sh packages
 	@$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion
 	@echo 'Compiling LAMMPS for machine $@'
 	@if [ -f MAKE/MACHINES/Makefile.$@ ]; \

src/Purge.list

@@ -22,6 +22,30 @@ style_nbin.h
 style_npair.h
 style_nstencil.h
 style_ntopo.h
+# auto-generated packages files
+packages_angle.h
+packages_atom.h
+packages_body.h
+packages_bond.h
+packages_command.h
+packages_compute.h
+packages_dihedral.h
+packages_dump.h
+packages_fix.h
+packages_improper.h
+packages_integrate.h
+packages_kspace.h
+packages_minimize.h
+packages_pair.h
+packages_reader.h
+packages_region.h
+packages_neigh_bin.h
+packages_neigh_pair.h
+packages_neigh_stencil.h
+packages_nbin.h
+packages_npair.h
+packages_nstencil.h
+packages_ntopo.h
 # other auto-generated files
 lmpinstalledpkgs.h
 lmpgitversion.h

src/STUBS/mpi.c

@@ -148,12 +148,20 @@ int MPI_Finalize()
 
 double MPI_Wtime()
 {
+#if defined(_MSC_VER)
+  double t;
+
+  t = GetTickCount();
+  t /= 1000.0;
+  return t;
+#else
   double time;
   struct timeval tv;
 
   gettimeofday(&tv,NULL);
   time = 1.0 * tv.tv_sec + 1.0e-6 * tv.tv_usec;
   return time;
+#endif
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-MISC/fix_bond_react.cpp

@@ -308,8 +308,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
     onemol->check_attributes(0);
     twomol->check_attributes(0);
     if (onemol->natoms != twomol->natoms)
-      error->all(FLERR,"Post-reacted template must contain the same "
-                       "number of atoms as the pre-reacted template");
+      error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
     get_molxspecials();
     read(i);
     fclose(fp);
@@ -324,7 +323,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
   delete [] files;
 
   if (atom->molecular != 1)
-    error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
+    error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems");
 
   // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
   // if so, we don't need non-bonded neighbor list
@@ -472,17 +471,19 @@ FixBondReact::~FixBondReact()
   delete [] guess_branch;
   delete [] pioneer_count;
 
-  char **newarg;
-  newarg = new char*[2];
-  newarg[0] = master_group;
-  newarg[1] = (char *) "delete";
-  group->assign(2,newarg);
-  if (stabilization_flag == 1) {
-    newarg[0] = exclude_group;
+  if (group) {
+    char **newarg;
+    newarg = new char*[2];
+    newarg[0] = master_group;
+    newarg[1] = (char *) "delete";
     group->assign(2,newarg);
-    delete [] exclude_group;
+    if (stabilization_flag == 1) {
+      newarg[0] = exclude_group;
+      group->assign(2,newarg);
+      delete [] exclude_group;
+    }
+    delete [] newarg;
   }
-  delete [] newarg;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -663,7 +664,7 @@ void FixBondReact::init()
   // check cutoff for iatomtype,jatomtype
   for (int i = 0; i < nreacts; i++) {
     if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
-      error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
+      error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
   }
 
   // need a half neighbor list, built every Nevery steps
@@ -1172,7 +1173,7 @@ void FixBondReact::superimpose_algorithm()
         // let's go ahead and catch the simplest of hangs
         //if (hang_catch > onemol->natoms*4)
         if (hang_catch > atom->nlocal*30) {
-          error->one(FLERR,"Excessive iteration of superimpose algorithm");
+          error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm");
         }
       }
     }
@@ -1285,7 +1286,7 @@ void FixBondReact::make_a_guess()
 
   for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) {
     if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) {
-      error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues.
+      error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away1"); // parallel issues.
     }
     if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) {
       status = GUESSFAIL;
@@ -1396,7 +1397,7 @@ void FixBondReact::check_a_neighbor()
 
             //another check for ghost atoms. perhaps remove the one in make_a_guess
             if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-              error->all(FLERR,"Fix bond/react needs ghost atoms from further away2");
+              error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away2");
             }
 
             for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) {
@@ -1448,7 +1449,7 @@ void FixBondReact::check_a_neighbor()
 
         //another check for ghost atoms. perhaps remove the one in make_a_guess
         if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-          error->all(FLERR,"Fix bond/react needs ghost atoms from further away3");
+          error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away3");
         }
 
         for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) {
@@ -1490,7 +1491,7 @@ void FixBondReact::crosscheck_the_neighbor()
         glove[onemol_xspecial[pion][trace]-1][0] == 0) {
 
       if (avail_guesses == MAXGUESS) {
-        error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info");
+        error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info");
         status = GUESSFAIL;
         return;
       }
@@ -1559,7 +1560,7 @@ void FixBondReact::inner_crosscheck_loop()
 
   //another check for ghost atoms. perhaps remove the one in make_a_guess
   if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) {
-    error->all(FLERR,"Fix bond/react needs ghost atoms from further away4");
+    error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away4");
   }
 
   if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
@@ -1720,7 +1721,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
   // if atoms change types, but aren't landlocked, that's bad
   for (int i = 0; i < twomol->natoms; i++) {
     if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
-      error->one(FLERR,"Atom affected by reaction too close to template edge");
+      error->one(FLERR,"Bond/react: Atom affected by reaction too close to template edge");
   }
 
   // additionally, if a bond changes type, but neither involved atom is landlocked, bad
@@ -1736,7 +1737,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
             onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
             if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
               if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
-                error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
               }
             }
           }
@@ -1746,7 +1747,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
               onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
               if (onemol_batom == equivalences[i][1][myrxn]) {
                 if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
-                  error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                  error->one(FLERR,"Bond/react: Bond type affected by reaction too close to template edge");
                 }
               }
             }
@@ -1762,7 +1763,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
       int ii = reverse_equiv[i][1][myrxn] - 1;
       for (int j = 0; j < twomol_nxspecial[ii][0]; j++) {
         if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) {
-         error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted");
+         error->one(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted");
         }
       }
     }
@@ -1773,7 +1774,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
     for (int i = 0; i < twomol->natoms; i++) {
       if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
         char str[128];
-        sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
+        sprintf(str,"Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
         error->warning(FLERR,str);
         break;
       }
@@ -2261,7 +2262,7 @@ void FixBondReact::update_everything()
           if (landlocked_atoms[j][rxnID] == 1) {
             for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
               if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
-                error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors");
+                error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors");
               }
             }
           }
@@ -2322,6 +2323,8 @@ void FixBondReact::update_everything()
                   nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
                   nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
                 }
+                if (nspecial[atom->map(update_mega_glove[jj+1][i])][2] > atom->maxspecial)
+                  error->one(FLERR,"Bond/react special bond generation overflow");
                 for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
                   special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
                 }
@@ -2383,6 +2386,8 @@ void FixBondReact::update_everything()
                 bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
                 bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
                 num_bond[atom->map(update_mega_glove[jj+1][i])]++;
+                if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom)
+                  error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                 delta_bonds++;
               }
             }
@@ -2457,6 +2462,8 @@ void FixBondReact::update_everything()
                   angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
                   angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
                   num_angle[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_angle++;
                 }
               }
@@ -2538,6 +2545,8 @@ void FixBondReact::update_everything()
                   dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
                   dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
                   num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_dihed++;
                 }
               }
@@ -2619,6 +2628,8 @@ void FixBondReact::update_everything()
                   improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
                   improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
                   num_improper[atom->map(update_mega_glove[jj+1][i])]++;
+                  if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom)
+                    error->one(FLERR,"Bond/react topology/atom exceed system topology/atom");
                   delta_imprp++;
                 }
               }
@@ -2716,7 +2727,7 @@ void FixBondReact::read(int myrxn)
 
   // skip 1st line of file
   eof = fgets(line,MAXLINE,fp);
-  if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file");
+  if (eof == NULL) error->one(FLERR,"Bond/react: Unexpected end of superimpose file");
 
   // read header lines
   // skip blank lines or lines that start with "#"
@@ -2770,7 +2781,7 @@ void FixBondReact::read(int myrxn)
       DeleteAtoms(line, myrxn);
     } else if (strcmp(keyword,"Constraints") == 0) {
       Constraints(line, myrxn);
-    } else error->one(FLERR,"Unknown section in superimpose file");
+    } else error->one(FLERR,"Bond/react: Unknown section in map file");
 
     parse_keyword(1,line,keyword);
 
@@ -2778,13 +2789,13 @@ void FixBondReact::read(int myrxn)
 
   // error check
   if (bondflag == 0 || equivflag == 0)
-    error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n");
+    error->all(FLERR,"Bond/react: Map file missing BondingIDs or Equivalences section\n");
 
   if (update_edges_flag[myrxn] == 2 && customedgesflag == 0)
-    error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n");
+    error->all(FLERR,"Bond/react: Map file must have a Custom Edges section when using 'update_edges custom'\n");
 
   if (update_edges_flag[myrxn] != 2 && customedgesflag == 1)
-    error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n");
+    error->all(FLERR,"Bond/react: Specify 'update_edges custom' to include Custom Edges section in map file\n");
 }
 
 void FixBondReact::EdgeIDs(char *line, int myrxn)
@@ -2830,7 +2841,7 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
     else if (strcmp(edgemode,"charges") == 0)
       custom_edges[tmp-1][myrxn] = 1;
     else
-      error->one(FLERR,"Illegal value in 'Custom Edges' section of map file");
+      error->one(FLERR,"Bond/react: Illegal value in 'Custom Edges' section of map file");
   }
   delete [] edgemode;
 }
@@ -2861,7 +2872,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
       constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
       constraints[myrxn][4] = tmp[3]*tmp[3];
     } else
-      error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file");
+      error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file");
   }
   delete [] constraint_type;
 }
@@ -2871,7 +2882,7 @@ void FixBondReact::open(char *file)
   fp = fopen(file,"r");
   if (fp == NULL) {
     char str[128];
-    snprintf(str,128,"Cannot open superimpose file %s",file);
+    snprintf(str,128,"Bond/react: Cannot open map file %s",file);
     error->one(FLERR,str);
   }
 }
@@ -2884,7 +2895,7 @@ void FixBondReact::readline(char *line)
     else n = strlen(line) + 1;
   }
   MPI_Bcast(&n,1,MPI_INT,0,world);
-  if (n == 0) error->all(FLERR,"Unexpected end of superimpose file");
+  if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file");
   MPI_Bcast(line,n,MPI_CHAR,0,world);
 }
 

src/USER-MISC/fix_bond_react.h

@@ -189,47 +189,65 @@ Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
 
-E: Invalid exclude group name
+E: Bond/react: Cannot use fix bond/react with non-molecular systems
 
-Exclude group name should not previously be defined.
-
-E: Cannot use fix bond/react with non-molecular systems
-
-Only systems with bonds that can be changed can be used.  Atom_style
+Only systems with bonds that can be changed can be used. Atom_style
 template does not qualify.
 
-E: Fix bond/react cutoff is longer than pairwise cutoff
+E: Bond/react: Rmax cutoff is longer than pairwise cutoff
 
-This is not allowed because bond creation is done using the
-pairwise neighbor list.
+This is not allowed because bond creation is done using the pairwise
+neighbor list.
 
-E: Molecule template ID for fix bond/react does not exist
+E: Bond/react: Molecule template ID for fix bond/react does not exist
 
-A valid molecule template must have been created with the molecule command.
+A valid molecule template must have been created with the molecule
+command.
 
-E: Superimpose file errors:
+E: Bond/react: Reaction templates must contain the same number of atoms
 
-Please ensure superimpose file is properly formatted.
+There should be a one-to-one correspondence between atoms in the
+pre-reacted and post-reacted templates, as specified by the map file.
 
-E: Atom affected by reaction too close to template edge
+E: Bond/react: Unknown section in map file
+
+Please ensure reaction map files are properly formatted.
+
+E: Bond/react: Atom affected by reaction too close to template edge
 
 This means an atom which changes type during the reaction is too close
-to an 'edge' atom defined in the superimpose file. This could cause incorrect
-assignment of bonds, angle, etc. Generally, this means you must include
-more atoms in your templates, such that there are at least two atoms
-between each atom involved in the reaction and an edge atom.
+to an 'edge' atom defined in the superimpose file. This could cause
+incorrect assignment of bonds, angle, etc. Generally, this means you
+must include more atoms in your templates, such that there are at
+least two atoms between each atom involved in the reaction and an edge
+atom.
 
-E: Fix bond/react needs ghost atoms from farther away
+E: Bond/react: Fix bond/react needs ghost atoms from farther away
 
 This is because a processor needs to superimpose the entire unreacted
-molecule template onto simulation atoms it can 'see.' The comm_modify cutoff
-command can be used to extend the communication range.
+molecule template onto simulation atoms it knows about. The
+comm_modify cutoff command can be used to extend the communication
+range.
 
-E: Excessive iteration of superimpose algorithm
+E: Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted
 
-You may have discovered a bug! But first, please double check that your
-molecule template atom types, bond types, etc. are consistent with your simulation,
-and that all atoms affected by a reaction are sufficently separated from edge atoms.
-If this issue persists, please contact the developer.
+Self-explanatory.
+
+W: Bond/react: An atom in 'react #%d' changes bond connectivity but not atom type
+
+You may want to double-check that all atom types are properly assigned
+in the post-reaction template.
+
+E: Bond/react special bond generation overflow
+
+The number of special bonds per-atom created by a reaction exceeds the
+system setting. See the read_data or create_box command for how to
+specify this value.
+
+E: Bond/react topology/atom exceed system topology/atom
+
+The number of bonds, angles etc per-atom created by a reaction exceeds
+the system setting. See the read_data or create_box command for how to
+specify this value.
 
 */

src/USER-OMP/pair_rebo_omp.cpp

@@ -41,8 +41,6 @@ void PairREBOOMP::settings(int narg, char ** /* arg */)
 void PairREBOOMP::spline_init() {
   PairAIREBO::spline_init();
 
-  int i,j,k;
-
   PCCf[0][2] = 0.007860700254745;
   PCCf[0][3] = 0.016125364564267;
   PCCf[1][1] = 0.003026697473481;

src/USER-QUIP/pair_quip.cpp

@@ -39,11 +39,16 @@ using namespace LAMMPS_NS;
 
 PairQUIP::PairQUIP(LAMMPS *lmp) : Pair(lmp)
 {
-   single_enable = 0;
-   restartinfo = 0;
-   one_coeff = 1;
-   no_virial_fdotr_compute = 1;
-   manybody_flag = 1;
+  single_enable = 0;
+  restartinfo = 0;
+  one_coeff = 1;
+  no_virial_fdotr_compute = 1;
+  manybody_flag = 1;
+
+  map = NULL;
+  quip_potential = NULL;
+  quip_file = NULL;
+  quip_string = NULL;
 }
 
 PairQUIP::~PairQUIP()
@@ -52,8 +57,10 @@ PairQUIP::~PairQUIP()
     memory->destroy(setflag);
     memory->destroy(cutsq);
     delete [] map;
-    delete [] quip_potential;
   }
+  delete [] quip_potential;
+  delete [] quip_file;
+  delete [] quip_string;
 }
 
 void PairQUIP::compute(int eflag, int vflag)
@@ -100,14 +107,14 @@ void PairQUIP::compute(int eflag, int vflag)
     jnum = numneigh[i];
 
     for (jj = 0; jj < jnum; jj++) {
-       quip_neigh[iquip] = (jlist[jj] & NEIGHMASK) + 1;
-       iquip++;
+      quip_neigh[iquip] = (jlist[jj] & NEIGHMASK) + 1;
+      iquip++;
     }
   }
 
   atomic_numbers = new int[ntotal];
   for (ii = 0; ii < ntotal; ii++)
-     atomic_numbers[ii] = map[type[ii]-1];
+     atomic_numbers[ii] = map[type[ii]];
 
   quip_local_e = new double [ntotal];
   quip_force = new double [ntotal*3];
@@ -211,17 +218,20 @@ void PairQUIP::compute(int eflag, int vflag)
    global settings
 ------------------------------------------------------------------------- */
 
-void PairQUIP::settings(int narg, char **/*arg*/)
+void PairQUIP::settings(int narg, char ** /* arg */)
 {
   if (narg != 0) error->all(FLERR,"Illegal pair_style command");
-  if (strcmp(force->pair_style,"hybrid") == 0)
-    error->all(FLERR,"Pair style quip is only compatible with hybrid/overlay");
 
   // check if linked to the correct QUIP library API version
   // as of 2017-07-19 this is API_VERSION 1
   if (quip_lammps_api_version() != 1)
     error->all(FLERR,"QUIP LAMMPS wrapper API version is not compatible "
         "with this version of LAMMPS");
+
+  // QUIP potentials are parameterized in metal units
+
+  if (strcmp("metal",update->unit_style) != 0)
+    error->all(FLERR,"QUIP potentials require 'metal' units");
 }
 
 /* ----------------------------------------------------------------------
@@ -234,48 +244,58 @@ void PairQUIP::allocate()
 
   setflag = memory->create(setflag,n+1,n+1,"pair:setflag");
   cutsq = memory->create(cutsq,n+1,n+1,"pair:cutsq");
-  map = new int[n];
+  map = new int[n+1];
 }
 
 void PairQUIP::coeff(int narg, char **arg)
 {
-   if (!allocated) allocate();
+  if (!allocated) allocate();
 
-   int n = atom->ntypes;
+  int n = atom->ntypes;
+  if (narg != (4+n)) {
+    char str[1024];
+    sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n);
+    error->all(FLERR,str);
+  }
 
   // ensure I,J args are * *
 
-   for (int i = 1; i <= n; i++){
-      for (int j = 1; j <= n; j++) {
-         setflag[i][j] = 1;
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  n_quip_file = strlen(arg[2]);
+  quip_file = new char[n_quip_file+1];
+  strcpy(quip_file,arg[2]);
+
+  n_quip_string = strlen(arg[3]);
+  quip_string = new char[n_quip_string+1];
+  strcpy(quip_string,arg[3]);
+
+  for (int i = 4; i < narg; i++) {
+    if (strcmp(arg[i],"NULL") == 0)
+      map[i-3] = -1;
+    else
+      map[i-3] = force->inumeric(FLERR,arg[i]);
+  }
+
+  // clear setflag since coeff() called once with I,J = * *
+
+  n = atom->ntypes;
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  // set setflag i,j for type pairs where both are mapped to elements
+
+  int count = 0;
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      if (map[i] >= 0 && map[j] >= 0) {
+        setflag[i][j] = 1;
+        count++;
       }
-   }
 
-   if (narg != (4+n)) {
-      char str[1024];
-      sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n);
-      error->all(FLERR,str);
-   }
-
-   if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
-      error->all(FLERR,"Incorrect args for pair coefficients");
-
-   n_quip_file = strlen(arg[2]);
-   quip_file = new char[n_quip_file+1];
-   strcpy(quip_file,arg[2]);
-
-   n_quip_string = strlen(arg[3]);
-   quip_string = new char[n_quip_string+1];
-   strcpy(quip_string,arg[3]);
-
-   for (int i = 4; i < narg; i++) {
-
-      if (0 == sscanf(arg[i],"%d",&map[i-4])) {
-         char str[1024];
-         sprintf(str,"Incorrect atomic number %s at position %d",arg[i],i);
-         error->all(FLERR,str);
-      }
-   }
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
 
   // Initialise potential
   // First call initialises potential via the fortran code in memory, and returns the necessary size

src/USER-QUIP/pair_quip.h

@@ -26,10 +26,10 @@ extern "C"
 {
   int quip_lammps_api_version();
   void quip_lammps_wrapper(int*, int*, int*, int*,
-      int*, int*, int*,
-      int*, int*, double*,
-      int*, int*, double*,
-      double*, double*, double*, double*, double*);
+                           int*, int*, int*,
+                           int*, int*, double*,
+                           int*, int*, double*,
+                           double*, double*, double*, double*, double*);
   void quip_lammps_potential_initialise(int*, int*, double*, char*, int*, char*, int*);
 }
 

src/USER-REAXC/reaxc_tool_box.cpp

@@ -34,8 +34,16 @@ double t_end;
 
 double Get_Time( )
 {
+#if defined(_MSC_VER)
+  double t;
+
+  t = GetTickCount();
+  t /= 1000.0;
+  return t;
+#else
   gettimeofday(&tim, NULL );
   return( tim.tv_sec + (tim.tv_usec / 1000000.0) );
+#endif
 }
 
 int Tokenize( char* s, char*** tok )

src/atom.cpp

@@ -39,6 +39,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 #ifdef LMP_USER_INTEL
 #include "neigh_request.h"
@@ -509,7 +510,7 @@ AtomVec *Atom::new_avec(const char *style, int trysuffix, int &sflag)
     return avec_creator(lmp);
   }
 
-  error->all(FLERR,"Unknown atom style");
+  error->all(FLERR,utils::check_packages_for_style("atom",style,lmp).c_str());
   return NULL;
 }
 

src/atom.h

@@ -286,6 +286,7 @@ class Atom : protected Pointers {
 
   inline int* get_map_array() {return map_array;};
   inline int get_map_size() {return map_tag_max+1;};
+  inline int get_map_maxarray() {return map_maxarray+1;};
 
   bigint memory_usage();
   int memcheck(const char *);
@@ -361,7 +362,7 @@ E: Atom IDs must be used for molecular systems
 
 Atom IDs are used to identify and find partner atoms in bonds.
 
-E: Unknown atom style
+E: Unrecognized atom style
 
 The choice of atom style is unknown.
 

src/atom_vec_body.cpp

@@ -25,6 +25,7 @@
 #include "fix.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -96,7 +97,7 @@ void AtomVecBody::process_args(int narg, char **arg)
 #undef BodyStyle
 #undef BODY_CLASS
 
-  else error->all(FLERR,"Unknown body style");
+  else error->all(FLERR,utils::check_packages_for_style("body",arg[0],lmp).c_str());
 
   bptr->avec = this;
   icp = bptr->icp;

src/atom_vec_body.h

@@ -130,7 +130,7 @@ E: Invalid atom_style body command
 
 No body style argument was provided.
 
-E: Unknown body style
+E: Unrecognized body style
 
 The choice of body style is unknown.
 

src/compute_coord_atom.cpp

@@ -25,6 +25,7 @@
 #include "force.h"
 #include "pair.h"
 #include "comm.h"
+#include "group.h"
 #include "memory.h"
 #include "error.h"
 
@@ -37,10 +38,12 @@ using namespace LAMMPS_NS;
 ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg),
   typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL),
-  id_orientorder(NULL), normv(NULL)
+  group2(NULL), id_orientorder(NULL), normv(NULL)
 {
   if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");
 
+  jgroup = group->find("all");
+  jgroupbit = group->bitmask[jgroup];
   cstyle = NONE;
 
   if (strcmp(arg[3],"cutoff") == 0) {
@@ -48,18 +51,29 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
     double cutoff = force->numeric(FLERR,arg[4]);
     cutsq = cutoff*cutoff;
 
-    ncol = narg-5 + 1;
+    int iarg = 5;
+    if ((narg > 6) && (strcmp(arg[5],"group") == 0)) {
+      int len = strlen(arg[6])+1;
+      group2 = new char[len];
+      strcpy(group2,arg[6]);
+      iarg += 2;
+      jgroup = group->find(group2);
+      if (jgroup == -1)
+        error->all(FLERR,"Compute coord/atom group2 ID does not exist");
+      jgroupbit = group->bitmask[jgroup];
+    }
+
+    ncol = narg-iarg + 1;
     int ntypes = atom->ntypes;
     typelo = new int[ncol];
     typehi = new int[ncol];
 
-    if (narg == 5) {
+    if (narg == iarg) {
       ncol = 1;
       typelo[0] = 1;
       typehi[0] = ntypes;
     } else {
       ncol = 0;
-      int iarg = 5;
       while (iarg < narg) {
         force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
         if (typelo[ncol] > typehi[ncol])
@@ -106,6 +120,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeCoordAtom::~ComputeCoordAtom()
 {
+  delete [] group2;
   delete [] typelo;
   delete [] typehi;
   memory->destroy(cvec);
@@ -143,12 +158,6 @@ void ComputeCoordAtom::init()
   neighbor->requests[irequest]->half = 0;
   neighbor->requests[irequest]->full = 1;
   neighbor->requests[irequest]->occasional = 1;
-
-  int count = 0;
-  for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;
-  if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute coord/atom");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -229,13 +238,15 @@ void ComputeCoordAtom::compute_peratom()
             j = jlist[jj];
             j &= NEIGHMASK;
 
-            jtype = type[j];
-            delx = xtmp - x[j][0];
-            dely = ytmp - x[j][1];
-            delz = ztmp - x[j][2];
-            rsq = delx*delx + dely*dely + delz*delz;
-            if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
-              n++;
+            if (mask[j] & jgroupbit) {
+              jtype = type[j];
+              delx = xtmp - x[j][0];
+              dely = ytmp - x[j][1];
+              delz = ztmp - x[j][2];
+              rsq = delx*delx + dely*dely + delz*delz;
+              if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
+                n++;
+            }
           }
 
           cvec[i] = n;

src/compute_coord_atom.h

@@ -45,6 +45,9 @@ class ComputeCoordAtom : public Compute {
   double *cvec;
   double **carray;
 
+  char *group2;
+  int jgroup,jgroupbit;
+
   class ComputeOrientOrderAtom *c_orientorder;
   char *id_orientorder;
   double threshold;
@@ -94,8 +97,4 @@ E: Compute coord/atom cutoff is longer than pairwise cutoff
 Cannot compute coordination at distances longer than the pair cutoff,
 since those atoms are not in the neighbor list.
 
-W: More than one compute coord/atom
-
-It is not efficient to use compute coord/atom more than once.
-
 */

src/domain.cpp

@@ -40,6 +40,7 @@
 #include "math_const.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -1715,6 +1716,9 @@ void Domain::add_region(int narg, char **arg)
     return;
   }
 
+  if (strcmp(arg[1],"none") == 0)
+    error->all(FLERR,"Unrecognized region style 'none'");
+
   if (find_region(arg[0]) >= 0) error->all(FLERR,"Reuse of region ID");
 
   // extend Region list if necessary
@@ -1753,12 +1757,10 @@ void Domain::add_region(int narg, char **arg)
     }
   }
 
-  if (strcmp(arg[1],"none") == 0) error->all(FLERR,"Unknown region style");
   if (region_map->find(arg[1]) != region_map->end()) {
     RegionCreator region_creator = (*region_map)[arg[1]];
     regions[nregion] = region_creator(lmp, narg, arg);
-  }
-  else error->all(FLERR,"Unknown region style");
+  } else error->all(FLERR,utils::check_packages_for_style("region",arg[1],lmp).c_str());
 
   // initialize any region variables via init()
   // in case region is used between runs, e.g. to print a variable

src/domain.h

@@ -269,7 +269,7 @@ E: Reuse of region ID
 
 A region ID cannot be used twice.
 
-E: Unknown region style
+E: Unrecognized region style
 
 The choice of region style is unknown.
 

src/force.cpp

@@ -258,9 +258,7 @@ Pair *Force::new_pair(const char *style, int trysuffix, int &sflag)
     return pair_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown pair style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("pair",style,lmp).c_str());
 
   return NULL;
 }
@@ -373,9 +371,7 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
     return bond_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown bond style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("bond",style,lmp).c_str());
 
   return NULL;
 }
@@ -454,9 +450,7 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
     return angle_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown angle style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("angle",style,lmp).c_str());
 
   return NULL;
 }
@@ -536,9 +530,7 @@ Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag)
     return dihedral_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown dihedral style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("dihedral",style,lmp).c_str());
 
   return NULL;
 }
@@ -617,9 +609,7 @@ Improper *Force::new_improper(const char *style, int trysuffix, int &sflag)
     return improper_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown improper style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("improper",style,lmp).c_str());
 
   return NULL;
 }
@@ -702,9 +692,7 @@ KSpace *Force::new_kspace(const char *style, int trysuffix, int &sflag)
     return kspace_creator(lmp);
   }
 
-  char str[128];
-  sprintf(str,"Unknown kspace style %s",style);
-  error->all(FLERR,str);
+  error->all(FLERR,utils::check_packages_for_style("kspace",style,lmp).c_str());
 
   return NULL;
 }

src/force.h

@@ -159,35 +159,36 @@ class Force : protected Pointers {
 
 E: Must re-specify non-restarted pair style (%s) after read_restart
 
-UNDOCUMENTED
+For pair styles, that do not store their settings in a restart file,
+it must be defined with a new 'pair_style' command after read_restart.
 
-E: Unknown pair style %s
+E: Unrecognized pair style %s
 
-UNDOCUMENTED
+The choice of pair style is unknown.
 
-E: Unknown bond style %s
+E: Unrecognized bond style %s
 
-UNDOCUMENTED
+The choice of bond style is unknown.
 
-E: Unknown angle style %s
+E: Unrecognized angle style %s
 
-UNDOCUMENTED
+The choice of angle style is unknown.
 
-E: Unknown dihedral style %s
+E: Unrecognized dihedral style %s
 
-UNDOCUMENTED
+The choice of dihedral style is unknown.
 
-E: Unknown improper style %s
+E: Unrecognized improper style %s
 
-UNDOCUMENTED
+The choice of improper style is unknown.
 
 E: Cannot yet use KSpace solver with grid with comm style tiled
 
 This is current restriction in LAMMPS.
 
-E: Unknown kspace style %s
+E: Unrecognized kspace style %s
 
-UNDOCUMENTED
+The choice of kspace style is unknown.
 
 E: Illegal ... command
 

src/input.cpp

@@ -50,6 +50,7 @@
 #include "accelerator_kokkos.h"
 #include "error.h"
 #include "memory.h"
+#include "utils.h"
 
 #ifdef _OPENMP
 #include <omp.h>
@@ -526,6 +527,11 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
           *fmtflag='\0';
         }
 
+        // quick check for proper format string
+
+        if (!utils::strmatch(fmtstr,"%[0-9 ]*\\.[0-9]+[efgEFG]"))
+          error->all(FLERR,"Incorrect conversion in format string");
+
         snprintf(immediate,256,fmtstr,variable->compute_equal(var));
         value = immediate;
 

src/input.h

@@ -173,6 +173,11 @@ E: Unbalanced quotes in input line
 No matching end double quote was found following a leading double
 quote.
 
+E: Incorrect conversion in format string
+
+An immediate variable with format suffix was not using
+either a %f, a %g, or a %e conversion in the format suffix.
+
 E: Input line quote not followed by white-space
 
 An end quote must be followed by white-space.

src/lammps.cpp

@@ -14,6 +14,8 @@
 #include <mpi.h>
 #include <cstring>
 #include <cctype>
+#include <map>
+#include <string>
 #include "lammps.h"
 #include "style_angle.h"
 #include "style_atom.h"
@@ -54,10 +56,29 @@
 #include "lmpinstalledpkgs.h"
 #include "lmpgitversion.h"
 
-using namespace LAMMPS_NS;
-
 static void print_style(FILE *fp, const char *str, int &pos);
 
+struct LAMMPS_NS::package_styles_lists {
+  std::map<std::string,std::string> angle_styles;
+  std::map<std::string,std::string> atom_styles;
+  std::map<std::string,std::string> body_styles;
+  std::map<std::string,std::string> bond_styles;
+  std::map<std::string,std::string> command_styles;
+  std::map<std::string,std::string> compute_styles;
+  std::map<std::string,std::string> dihedral_styles;
+  std::map<std::string,std::string> dump_styles;
+  std::map<std::string,std::string> fix_styles;
+  std::map<std::string,std::string> improper_styles;
+  std::map<std::string,std::string> integrate_styles;
+  std::map<std::string,std::string> kspace_styles;
+  std::map<std::string,std::string> minimize_styles;
+  std::map<std::string,std::string> pair_styles;
+  std::map<std::string,std::string> reader_styles;
+  std::map<std::string,std::string> region_styles;
+};
+
+using namespace LAMMPS_NS;
+
 /* ----------------------------------------------------------------------
    start up LAMMPS
    allocate fundamental classes (memory, error, universe, input)
@@ -86,6 +107,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
 
   initclock = MPI_Wtime();
 
+  init_pkg_lists();
+  
   // check if -mpi is first arg
   // if so, then 2 apps were launched with one mpirun command
   //   this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
@@ -693,6 +716,8 @@ LAMMPS::~LAMMPS()
   delete universe;
   delete error;
   delete memory;
+
+  delete pkg_lists;
 }
 
 /* ----------------------------------------------------------------------
@@ -867,6 +892,149 @@ void LAMMPS::destroy()
   python = NULL;
 }
 
+/* ----------------------------------------------------------------------
+   initialize lists of styles in packages
+------------------------------------------------------------------------- */
+
+void LAMMPS::init_pkg_lists()
+{
+  pkg_lists = new package_styles_lists;
+#define PACKAGE "UNKNOWN"
+#define ANGLE_CLASS
+#define AngleStyle(key,Class)                   \
+  pkg_lists->angle_styles[#key] = PACKAGE;
+#include "packages_angle.h"
+#undef AngleStyle
+#undef ANGLE_CLASS
+#define ATOM_CLASS
+#define AtomStyle(key,Class)                    \
+  pkg_lists->atom_styles[#key] = PACKAGE;
+#include "packages_atom.h"
+#undef AtomStyle
+#undef ATOM_CLASS
+#define BODY_CLASS
+#define BodyStyle(key,Class)                    \
+  pkg_lists->body_styles[#key] = PACKAGE;
+#include "packages_body.h"
+#undef BodyStyle
+#undef BODY_CLASS
+#define BOND_CLASS
+#define BondStyle(key,Class)                    \
+  pkg_lists->bond_styles[#key] = PACKAGE;
+#include "packages_bond.h"
+#undef BondStyle
+#undef BOND_CLASS
+#define COMMAND_CLASS
+#define CommandStyle(key,Class)                 \
+  pkg_lists->command_styles[#key] = PACKAGE;
+#include "packages_command.h"
+#undef CommandStyle
+#undef COMMAND_CLASS
+#define COMPUTE_CLASS
+#define ComputeStyle(key,Class)                 \
+  pkg_lists->compute_styles[#key] = PACKAGE;
+#include "packages_compute.h"
+#undef ComputeStyle
+#undef COMPUTE_CLASS
+#define DIHEDRAL_CLASS
+#define DihedralStyle(key,Class)                \
+  pkg_lists->dihedral_styles[#key] = PACKAGE;
+#include "packages_dihedral.h"
+#undef DihedralStyle
+#undef DIHEDRAL_CLASS
+#define DUMP_CLASS
+#define DumpStyle(key,Class)                    \
+  pkg_lists->dump_styles[#key] = PACKAGE;
+#include "packages_dump.h"
+#undef DumpStyle
+#undef DUMP_CLASS
+#define FIX_CLASS
+#define FixStyle(key,Class)                     \
+  pkg_lists->fix_styles[#key] = PACKAGE;
+#include "packages_fix.h"
+#undef FixStyle
+#undef FIX_CLASS
+#define IMPROPER_CLASS
+#define ImproperStyle(key,Class)                \
+  pkg_lists->improper_styles[#key] = PACKAGE;
+#include "packages_improper.h"
+#undef ImproperStyle
+#undef IMPROPER_CLASS
+#define INTEGRATE_CLASS
+#define IntegrateStyle(key,Class)               \
+  pkg_lists->integrate_styles[#key] = PACKAGE;
+#include "packages_integrate.h"
+#undef IntegrateStyle
+#undef INTEGRATE_CLASS
+#define KSPACE_CLASS
+#define KSpaceStyle(key,Class)                  \
+  pkg_lists->kspace_styles[#key] = PACKAGE;
+#include "packages_kspace.h"
+#undef KSpaceStyle
+#undef KSPACE_CLASS
+#define MINIMIZE_CLASS
+#define MinimizeStyle(key,Class)                \
+  pkg_lists->minimize_styles[#key] = PACKAGE;
+#include "packages_minimize.h"
+#undef MinimizeStyle
+#undef MINIMIZE_CLASS
+#define PAIR_CLASS
+#define PairStyle(key,Class)                    \
+  pkg_lists->pair_styles[#key] = PACKAGE;
+#include "packages_pair.h"
+#undef PairStyle
+#undef PAIR_CLASS
+#define READER_CLASS
+#define ReaderStyle(key,Class)                  \
+  pkg_lists->reader_styles[#key] = PACKAGE;
+#include "packages_reader.h"
+#undef ReaderStyle
+#undef READER_CLASS
+#define REGION_CLASS
+#define RegionStyle(key,Class)                  \
+  pkg_lists->region_styles[#key] = PACKAGE;
+#include "packages_region.h"
+#undef RegionStyle
+#undef REGION_CLASS
+} 
+
+bool LAMMPS::is_installed_pkg(const char *pkg) 
+{
+  for (int i=0; installed_packages[i] != NULL; ++i)
+    if (strcmp(installed_packages[i],pkg) == 0) return true;
+
+  return false;
+}
+
+#define check_for_match(style,list,name)                                \
+  if (strcmp(list,#style) == 0) {                                       \
+    std::map<std::string,std::string> &styles(pkg_lists-> style ## _styles); \
+    if (styles.find(name) != styles.end()) {                            \
+      return styles[name].c_str();                                      \
+    }                                                                   \
+  }
+
+const char *LAMMPS::match_style(const char *style, const char *name)
+{
+  check_for_match(angle,style,name);
+  check_for_match(atom,style,name);
+  check_for_match(body,style,name);
+  check_for_match(bond,style,name);
+  check_for_match(command,style,name);
+  check_for_match(compute,style,name);
+  check_for_match(dump,style,name);
+  check_for_match(fix,style,name);
+  check_for_match(compute,style,name);
+  check_for_match(improper,style,name);
+  check_for_match(integrate,style,name);
+  check_for_match(kspace,style,name);
+  check_for_match(minimize,style,name);
+  check_for_match(pair,style,name);
+  check_for_match(reader,style,name);
+  check_for_match(region,style,name);
+  return NULL;
+}
+
 /* ----------------------------------------------------------------------
    help message for command line options and styles present in executable
 ------------------------------------------------------------------------- */

src/lammps.h

@@ -63,7 +63,9 @@ class LAMMPS {
 
   class CiteMe *citeme;          // citation info
 
+  const char *match_style(const char *style, const char *name);
   static const char * installed_packages[];
+  static bool is_installed_pkg(const char *pkg);
 
   static const bool has_git_info;
   static const char git_commit[];
@@ -79,6 +81,8 @@ class LAMMPS {
   void print_config(FILE *);    // print compile time settings
 
  private:
+  struct package_styles_lists *pkg_lists;
+  void init_pkg_lists();
   void help();
   LAMMPS() {};                   // prohibit using the default constructor
   LAMMPS(const LAMMPS &) {};     // prohibit using the copy constructor

src/lmpwindows.h

@@ -18,8 +18,8 @@
 #define pclose _pclose
 #define strdup _strdup
 
-// the following functions ared defined to get rid of
-// 'ambiguous call to overloaded function' error in VSS for mismathched type arguments
+// the following functions are defined to get rid of
+// 'ambiguous call to overloaded function' error in VSS for mismatched type arguments
 #if !defined(__MINGW32__)
 inline double pow(int i, int j){
   return pow((double)i,j);

src/modify.cpp

@@ -893,11 +893,8 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
     fix[ifix] = fix_creator(lmp,narg,arg);
   }
 
-  if (fix[ifix] == NULL) {
-    char str[128];
-    snprintf(str,128,"Unknown fix style %s",arg[2]);
-    error->all(FLERR,str);
-  }
+  if (fix[ifix] == NULL)
+    error->all(FLERR,utils::check_packages_for_style("fix",arg[2],lmp).c_str());
 
   // check if Fix is in restart_global list
   // if yes, pass state info to the Fix so it can reset itself
@@ -1195,11 +1192,8 @@ void Modify::add_compute(int narg, char **arg, int trysuffix)
     compute[ncompute] = compute_creator(lmp,narg,arg);
   }
 
-  if (compute[ncompute] == NULL) {
-    char str[128];
-    snprintf(str,128,"Unknown compute style %s",arg[2]);
-    error->all(FLERR,str);
-  }
+  if (compute[ncompute] == NULL)
+    error->all(FLERR,utils::check_packages_for_style("compute",arg[2],lmp).c_str());
 
   ncompute++;
 }

src/modify.h

@@ -224,9 +224,9 @@ The ID and style of a fix match for a fix you are changing with a fix
 command, but the new group you are specifying does not match the old
 group.
 
-E: Unknown fix style %s
+E: Unrecognized fix style %s
 
-UNDOCUMENTED
+The choice of fix style is unknown.
 
 E: Could not find fix_modify ID
 
@@ -240,9 +240,9 @@ E: Reuse of compute ID
 
 A compute ID cannot be used twice.
 
-E: Unknown compute style %s
+E: Unrecognized compute style %s
 
-UNDOCUMENTED
+The choice of compute style is unknown.
 
 E: Could not find compute_modify ID
 

src/output.cpp

@@ -32,6 +32,7 @@
 #include "write_restart.h"
 #include "memory.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -585,8 +586,7 @@ void Output::add_dump(int narg, char **arg)
   if (dump_map->find(arg[2]) != dump_map->end()) {
     DumpCreator dump_creator = (*dump_map)[arg[2]];
     dump[ndump] = dump_creator(lmp, narg, arg);
-  }
-  else error->all(FLERR,"Unknown dump style");
+  } else error->all(FLERR,utils::check_packages_for_style("dump",arg[2],lmp).c_str());
 
   every_dump[ndump] = force->inumeric(FLERR,arg[3]);
   if (every_dump[ndump] <= 0) error->all(FLERR,"Illegal dump command");

src/output.h

@@ -152,7 +152,7 @@ E: Invalid dump frequency
 
 Dump frequency must be 1 or greater.
 
-E: Unknown dump style
+E: Unrecognized dump style
 
 The choice of dump style is unknown.
 

src/read_data.cpp

@@ -1768,7 +1768,8 @@ void ReadData::paircoeffs()
     next = strchr(buf,'\n');
     *next = '\0';
     parse_coeffs(buf,NULL,1,2,toffset);
-    if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
+    if (narg == 0)
+      error->all(FLERR,"Unexpected empty line in PairCoeffs section");
     force->pair->coeff(narg,arg);
     buf = next + 1;
   }
@@ -1794,7 +1795,8 @@ void ReadData::pairIJcoeffs()
       next = strchr(buf,'\n');
       *next = '\0';
       parse_coeffs(buf,NULL,0,2,toffset);
-      if (narg == 0) error->all(FLERR,"Unexpected end of PairCoeffs section");
+      if (narg == 0)
+        error->all(FLERR,"Unexpected empty line in PairCoeffs section");
       force->pair->coeff(narg,arg);
       buf = next + 1;
     }
@@ -1818,7 +1820,8 @@ void ReadData::bondcoeffs()
     next = strchr(buf,'\n');
     *next = '\0';
     parse_coeffs(buf,NULL,0,1,boffset);
-    if (narg == 0) error->all(FLERR,"Unexpected end of BondCoeffs section");
+    if (narg == 0)
+      error->all(FLERR,"Unexpected empty line in BondCoeffs section");
     force->bond->coeff(narg,arg);
     buf = next + 1;
   }
@@ -1844,7 +1847,7 @@ void ReadData::anglecoeffs(int which)
     if (which == 0) parse_coeffs(buf,NULL,0,1,aoffset);
     else if (which == 1) parse_coeffs(buf,"bb",0,1,aoffset);
     else if (which == 2) parse_coeffs(buf,"ba",0,1,aoffset);
-    if (narg == 0) error->all(FLERR,"Unexpected end of AngleCoeffs section");
+    if (narg == 0) error->all(FLERR,"Unexpected empty line in AngleCoeffs section");
     force->angle->coeff(narg,arg);
     buf = next + 1;
   }
@@ -1873,7 +1876,8 @@ void ReadData::dihedralcoeffs(int which)
     else if (which == 3) parse_coeffs(buf,"at",0,1,doffset);
     else if (which == 4) parse_coeffs(buf,"aat",0,1,doffset);
     else if (which == 5) parse_coeffs(buf,"bb13",0,1,doffset);
-    if (narg == 0) error->all(FLERR,"Unexpected end of DihedralCoeffs section");
+    if (narg == 0)
+      error->all(FLERR,"Unexpected empty line in DihedralCoeffs section");
     force->dihedral->coeff(narg,arg);
     buf = next + 1;
   }
@@ -1898,7 +1902,7 @@ void ReadData::impropercoeffs(int which)
     *next = '\0';
     if (which == 0) parse_coeffs(buf,NULL,0,1,ioffset);
     else if (which == 1) parse_coeffs(buf,"aa",0,1,ioffset);
-    if (narg == 0) error->all(FLERR,"Unexpected end of ImproperCoeffs section");
+    if (narg == 0) error->all(FLERR,"Unexpected empty line in ImproperCoeffs section");
     force->improper->coeff(narg,arg);
     buf = next + 1;
   }
@@ -2092,6 +2096,10 @@ void ReadData::parse_coeffs(char *line, const char *addstr,
     word = strtok(NULL," \t\n\r\f");
   }
 
+  // to avoid segfaults on empty lines
+
+  if (narg == 0) return;
+  
   if (noffset) {
     int value = force->inumeric(FLERR,arg[0]);
     sprintf(argoffset1,"%d",value+offset);

src/read_data.h

@@ -533,25 +533,25 @@ E: Too many lines in one body in data file - boost MAXBODY
 MAXBODY is a setting at the top of the src/read_data.cpp file.
 Set it larger and re-compile the code.
 
-E: Unexpected end of PairCoeffs section
+E: Unexpected empty line in PairCoeffs section
 
-Read a blank line.
+Read a blank line where there should be coefficient data.
 
-E: Unexpected end of BondCoeffs section
+E: Unexpected empty line in BondCoeffs section
 
-Read a blank line.
+Read a blank line where there should be coefficient data.
 
-E: Unexpected end of AngleCoeffs section
+E: Unexpected empty line in AngleCoeffs section
 
-Read a blank line.
+Read a blank line where there should be coefficient data.
 
-E: Unexpected end of DihedralCoeffs section
+E: Unexpected empty line in DihedralCoeffs section
 
-Read a blank line.
+Read a blank line where there should be coefficient data.
 
-E: Unexpected end of ImproperCoeffs section
+E: Unexpected empty line in ImproperCoeffs section
 
-Read a blank line.
+Read a blank line where there should be coefficient data.
 
 E: Cannot open gzipped file
 

src/read_dump.cpp

@@ -40,6 +40,7 @@
 #include "variable.h"
 #include "error.h"
 #include "memory.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -266,7 +267,7 @@ void ReadDump::setup_reader(int narg, char **arg)
 
   // unrecognized style
 
-  else error->all(FLERR,"Unknown dump reader style");
+  else error->all(FLERR,utils::check_packages_for_style("reader",readerstyle,lmp).c_str());
 
   // pass any arguments to readers
 

src/read_dump.h

@@ -134,7 +134,7 @@ E: Dump file does not contain requested snapshot
 
 Self-explanatory.
 
-E: Unknown dump reader style
+E: Unrecognized dump reader style
 
 The choice of dump reader style via the format keyword is unknown.
 

src/utils.cpp

@@ -11,8 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+#include <mpi.h>
 #include <cstring>
 #include "utils.h"
+#include "lammps.h"
 #include "error.h"
 
 /*! \file utils.cpp */
@@ -123,6 +125,24 @@ void utils::sfgets(const char *srcname, int srcline, char *s, int size,
 
 /* ------------------------------------------------------------------ */
 
+std::string utils::check_packages_for_style(std::string style,
+                                            std::string name, LAMMPS *lmp)
+{
+  std::string errmsg = "Unrecognized " + style + " style '" + name + "'";
+  const char *pkg = lmp->match_style(style.c_str(),name.c_str());
+
+  if (pkg) {
+    errmsg += " is part of the " + std::string(pkg) + " package";
+    if (lmp->is_installed_pkg(pkg))
+      errmsg += ", but seems to be missing because of a dependency";
+    else
+      errmsg += " which is not enabled in this LAMMPS binary.";
+  }
+  return errmsg;
+}
+
+/* ------------------------------------------------------------------ */
+
 extern "C" {
   /* Typedef'd pointer to get abstract datatype. */
   typedef struct regex_t *re_t;

src/utils.h

@@ -23,6 +23,7 @@ namespace LAMMPS_NS {
 
   // forward declarations
   class Error;
+  class LAMMPS;
 
   namespace utils {
 
@@ -66,6 +67,15 @@ namespace LAMMPS_NS {
      */
     void sfgets(const char *srcname, int srcline, char *s, int size,
                 FILE *fp, const char *filename, Error *error);
+
+    /** \brief Report if a requested style is in a package or may have a typo
+     *
+     *  \param style type of style that is to be checked for
+     *  \param name  name of style that was not found
+     *  \param lmp   pointer to top-level LAMMPS class instance
+     *  \return string usable for error messages
+     */
+    std::string check_packages_for_style(std::string style, std::string name, LAMMPS *lmp);
   }
 }
 

src/variable.cpp

@@ -38,6 +38,7 @@
 #include "memory.h"
 #include "info.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -383,6 +384,8 @@ void Variable::set(int narg, char **arg)
     num[nvar] = 3;
     which[nvar] = 0;
     pad[nvar] = 0;
+    if (!utils::strmatch(arg[3],"%[0-9 ]*\\.[0-9]+[efgEFG]"))
+      error->all(FLERR,"Incorrect conversion in format string");
     data[nvar] = new char*[num[nvar]];
     copy(2,&arg[2],data[nvar]);
     data[nvar][2] = new char[VALUELENGTH];

src/variable.h

@@ -210,6 +210,10 @@ E: Invalid variable style with next command
 Variable styles {equal} and {world} cannot be used in a next
 command.
 
+E: Incorrect conversion in format string
+
+A format style variable was not using either a %f, a %g, or a %e conversion.
+
 E: Next command must list all universe and uloop variables
 
 This is to insure they stay in sync.

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "15 May 2019"
+#define LAMMPS_VERSION "5 Jun 2019"

src/write_dump.cpp

@@ -26,6 +26,7 @@
 #include "input.h"
 #include "update.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -64,7 +65,7 @@ void WriteDump::command(int narg, char **arg)
 #include "style_dump.h"
 #undef DUMP_CLASS
 
-  else error->all(FLERR,"Unknown dump style");
+  else error->all(FLERR,utils::check_packages_for_style("dump",arg[1],lmp).c_str());
 
   if (modindex < narg) dump->modify_params(narg-modindex-1,&arg[modindex+1]);
 

src/write_dump.h

@@ -43,7 +43,7 @@ Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
 
-E: Unknown dump style
+E: Unrecognized dump style
 
 The choice of dump style is unknown.