diff --git a/.gitignore b/.gitignore
index 50b970249a7ab02f6c9da09b43da28bc37f7a15b..1ce415678ea6a746a494b09cafc97137b103ed0b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
*~
*.o
*.so
+*.lo
*.cu_o
*.ptx
*_ptx.h
@@ -32,6 +33,7 @@ log.cite
.Trashes
ehthumbs.db
Thumbs.db
+.clang-format
#cmake
/build*
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 51997593dbd6b1a896899a33ed4cd8cf300e4d58..3634138747873daa26fae0f30b293101a4d2cf99 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -43,6 +43,29 @@ function(validate_option name values)
endif()
endfunction(validate_option)
+function(get_lammps_version version_header variable)
+ file(READ ${version_header} line)
+ set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+ string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+ string(STRIP ${day} day)
+ string(STRIP ${month} month)
+ string(STRIP ${year} year)
+ list(FIND MONTHS "${month}" month)
+ string(LENGTH ${day} day_length)
+ string(LENGTH ${month} month_length)
+ if(day_length EQUAL 1)
+ set(day "0${day}")
+ endif()
+ if(month_length EQUAL 1)
+ set(month "0${month}")
+ endif()
+ set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
+
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
@@ -113,6 +136,7 @@ if(BUILD_EXE)
if(LAMMPS_MACHINE)
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
endif()
+ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
endif()
option(BUILD_LIB "Build LAMMPS library" OFF)
@@ -121,10 +145,10 @@ if(BUILD_LIB)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
- set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
- mark_as_advanced(LIB_SUFFIX)
- if(LIB_SUFFIX)
- set(LIB_SUFFIX "_${LIB_SUFFIX}")
+ set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
+ mark_as_advanced(LAMMPS_LIB_SUFFIX)
+ if(LAMMPS_LIB_SUFFIX)
+ set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
endif()
endif()
@@ -183,12 +207,55 @@ endif()
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
option(ENABLE_TESTING "Enable testing" OFF)
-if(ENABLE_TESTING)
+if(ENABLE_TESTING AND BUILD_EXE)
enable_testing()
-endif(ENABLE_TESTING)
+ option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+ option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
+ mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+
+ if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
+ include(FetchContent)
+
+ FetchContent_Declare(lammps-testing
+ GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+ GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
+ )
+
+ FetchContent_GetProperties(lammps-testing)
+ if(NOT lammps-testing_POPULATED)
+ message(STATUS "Downloading tests...")
+ FetchContent_Populate(lammps-testing)
+ endif()
+
+ set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+ elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+ message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+ "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+ endif()
+
+ if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
+ message(STATUS "Running test discovery...")
+
+ file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
+ foreach(script_path ${TEST_SCRIPTS})
+ get_filename_component(TEST_NAME ${script_path} EXT)
+ get_filename_component(SCRIPT_NAME ${script_path} NAME)
+ get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+ string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+ string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+ string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+ set(TEST_NAME "test_core_${TEST_NAME}_serial")
+ add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+ set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+ endforeach()
+ list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+ message(STATUS "Found ${NUM_TESTS} tests.")
+ endif()
+endif()
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
- KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
+ KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX 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
@@ -412,8 +479,8 @@ endif()
if(PKG_USER-NETCDF)
find_package(NetCDF REQUIRED)
- include_directories(NETCDF_INCLUDE_DIR)
- list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
+ include_directories(${NETCDF_INCLUDE_DIRS})
+ list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
@@ -481,6 +548,39 @@ if(PKG_KIM)
include_directories(${KIM_INCLUDE_DIRS})
endif()
+if(PKG_MESSAGE)
+ option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
+ ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
+
+ if(BUILD_SHARED_LIBS)
+ add_library(cslib SHARED ${cslib_SOURCES})
+ else()
+ add_library(cslib STATIC ${cslib_SOURCES})
+ endif()
+
+ if(BUILD_MPI)
+ target_compile_definitions(cslib PRIVATE -DMPI_YES)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+ else()
+ target_compile_definitions(cslib PRIVATE -DMPI_NO)
+ set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+ endif()
+
+ if(MESSAGE_ZMQ)
+ target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+ find_package(ZMQ REQUIRED)
+ target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+ target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+ else()
+ target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+ target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+ endif()
+
+ list(APPEND LAMMPS_LINK_LIBS cslib)
+ include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()
+
if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
@@ -678,7 +778,9 @@ if(PKG_USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
- ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp)
+ ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+ ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+ add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
@@ -1011,7 +1113,9 @@ 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")
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
+list(SORT temp_PKG_LIST)
+foreach(PKG ${temp_PKG_LIST})
if(PKG_${PKG})
set(temp "${temp} \"${PKG}\",\n")
endif()
@@ -1036,14 +1140,14 @@ if(BUILD_LIB)
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
- set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
- if(BUILD_SHARED_LIBS)
- set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
- install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
- install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
- configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
- endif()
+ set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
+ set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
+ install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+ configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+ configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif()
@@ -1059,10 +1163,11 @@ if(BUILD_EXE)
endif()
endif()
- set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
+ set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+ install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(ENABLE_TESTING)
- add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
+ add_test(ShowHelp ${LAMMPS_BINARY} -help)
endif()
endif()
@@ -1130,7 +1235,7 @@ endif()
# Install potential files in data directory
###############################################################################
set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
@@ -1172,7 +1277,7 @@ endif()
###############################################################################
# Print package summary
###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
diff --git a/cmake/FindLAMMPS.cmake.in b/cmake/FindLAMMPS.cmake.in
new file mode 100644
index 0000000000000000000000000000000000000000..586df83c2d080197ea0256794febd395ab81cc63
--- /dev/null
+++ b/cmake/FindLAMMPS.cmake.in
@@ -0,0 +1,48 @@
+# - Find liblammps
+# Find the native liblammps headers and libraries.
+#
+# The following variables will set:
+# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
+# LAMMPS_LIBRARIES - List of libraries when using lammps.
+# LAMMPS_API_DEFINES - lammps library api defines
+# LAMMPS_VERSION - lammps library version
+# LAMMPS_FOUND - True if liblammps found.
+#
+# In addition a LAMMPS::LAMMPS imported target is getting created.
+#
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright (2003) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software. This software is distributed under
+# the GNU General Public License.
+#
+# See the README file in the top-level LAMMPS directory.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
+find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
+
+set(LAMMPS_VERSION @LAMMPS_VERSION@)
+set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
+
+find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+
+set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
+set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
+
+mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
+
+if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
+ add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
+ set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
+endif()
diff --git a/cmake/Modules/FindZMQ.cmake b/cmake/Modules/FindZMQ.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..608ccda777336f9d84dfabd40a9c6bdba1bd12be
--- /dev/null
+++ b/cmake/Modules/FindZMQ.cmake
@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake
index 29ea3725972ce2e1166ef70297c3d6067e90c769..2b00a81c8da6f20efb5a7a9f2aa71c8f335d9deb 100644
--- a/cmake/Modules/StyleHeaderUtils.cmake
+++ b/cmake/Modules/StyleHeaderUtils.cmake
@@ -48,8 +48,13 @@ function(CreateStyleHeader path filename)
set(temp "")
if(ARGC GREATER 2)
list(REMOVE_AT ARGV 0 1)
+ set(header_list)
foreach(FNAME ${ARGV})
get_filename_component(FNAME ${FNAME} NAME)
+ list(APPEND header_list ${FNAME})
+ endforeach()
+ list(SORT header_list)
+ foreach(FNAME ${header_list})
set(temp "${temp}#include \"${FNAME}\"\n")
endforeach()
endif()
diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in
index 400b7593cff4034539df766111dd53d6fbbeaac9..7850972f3b50017407318888b53bd824f0a3b85a 100644
--- a/cmake/pkgconfig/liblammps.pc.in
+++ b/cmake/pkgconfig/liblammps.pc.in
@@ -4,15 +4,15 @@
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
Requires:
-Libs: -L${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
diff --git a/doc/lammps.1 b/doc/lammps.1
new file mode 100644
index 0000000000000000000000000000000000000000..d49650bfaad03678902a67c1937db7264f758004
--- /dev/null
+++ b/doc/lammps.1
@@ -0,0 +1,45 @@
+.TH LAMMPS "2018-08-22"
+.SH NAME
+.B LAMMPS
+\- Molecular Dynamics Simulator.
+
+.SH SYNOPSIS
+.B lmp
+-in in.file
+
+or
+
+mpirun \-np 2
+.B lmp
+-in in.file
+
+.SH DESCRIPTION
+.B LAMMPS
+LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale
+Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft
+materials (biomolecules, polymers) and solid-state materials (metals,
+semiconductors) and coarse-grained or mesoscopic systems. It can be used to
+model atoms or, more generically, as a parallel particle simulator at the
+atomic, meso, or continuum scale.
+
+See http://lammps.sandia.gov/ for documentation.
+
+.SH OPTIONS
+See https://lammps.sandia.gov/doc/Run_options.html for details on
+command-line options.
+
+.SH COPYRIGHT
+© 2003--2018 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL-2'.
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 088ffd8972f3d8b5228ab73c454b03558fd7f9bd..1e3744b7fbb4e7bc72604139ef6bf2cc1c6438d0 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -31,6 +31,7 @@ This is the list of packages that may require additional steps.
"KOKKOS"_#kokkos,
"LATTE"_#latte,
"MEAM"_#meam,
+"MESSAGE"_#message,
"MSCG"_#mscg,
"OPT"_#opt,
"POEMS"_#poems,
@@ -361,6 +362,10 @@ make lib-meam args="-m mpi" # build with default Fortran compiler compatible
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
@@ -373,6 +378,35 @@ file.
:line
+MESSAGE package :h4,link(message)
+
+This package can optionally include support for messaging via sockets,
+using the open-source "ZeroMQ library"_http://zeromq.org, which must
+be installed on your system.
+
+[CMake build]:
+
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the CSlib library in
+lib/message. You can build the CSlib library manually if you prefer;
+follow the instructions in lib/message/README. You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/message/Install.py script with the specified args:
+
+make lib-message # print help message
+make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
+make lib-message args="-s" # build as serial lib with no ZMQ support
+
+The build should produce two files: lib/message/cslib/src/libmessage.a
+and lib/message/Makefile.lammps. The latter is copied from an
+existing Makefile.lammps.* and has settings to link with the ZeroMQ
+library if requested in the build.
+
+:line
+
MSCG package :h4,link(mscg)
To build with this package, you must download and build the MS-CG
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 4f71e9eb18067d4ef3210aada08a8722e38e8687..aaa340f3024f3c309186f223777a2b03e5542186 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -42,6 +42,7 @@ packages:
"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,
"POEMS"_Build_extras.html#poems,
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index aec5a9db8b726453d16a36211fd54eddf7b35754..6f54681342b14d64ba543d4f021fcb1ee7c078b3 100644
--- a/doc/src/Commands_all.txt
+++ b/doc/src/Commands_all.txt
@@ -71,6 +71,7 @@ An alphabetic list of all LAMMPS commands.
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
+"message"_message.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
@@ -103,6 +104,7 @@ An alphabetic list of all LAMMPS commands.
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
+"server"_server.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index eaf272061347931f1fda5dedf9776170ca8eb41a..33890df1febbf789067fb90b0bcc94644ee64cbe 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -33,6 +33,7 @@ OPT.
"agni (o)"_pair_agni.html,
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
+"atm"_pair_atm.html,
"awpmd/cut"_pair_awpmd.html,
"beck (go)"_pair_beck.html,
"body/nparticle"_pair_body_nparticle.html,
diff --git a/doc/src/Eqs/pair_atm.jpg b/doc/src/Eqs/pair_atm.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..d2e6d704e930c2def4801301c928998f7542f54b
Binary files /dev/null and b/doc/src/Eqs/pair_atm.jpg differ
diff --git a/doc/src/Eqs/pair_atm.tex b/doc/src/Eqs/pair_atm.tex
new file mode 100644
index 0000000000000000000000000000000000000000..fce1db99b8b8641ae0b2bf47a6ac1e4bd8b4fd8a
--- /dev/null
+++ b/doc/src/Eqs/pair_atm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
+\end{equation}
+
+\end{document}
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index 438ea561a10f9fa87f0e119aedd26bdbd13e89dd..730b492699d908a1be6918853f81dbfb5d59713f 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -54,6 +54,7 @@ General howto :h3
Howto_replica
Howto_library
Howto_couple
+ Howto_client_server
END_RST -->
@@ -64,7 +65,8 @@ END_RST -->
"Run multiple simulations from one input script"_Howto_multiple.html
"Multi-replica simulations"_Howto_replica.html
"Library interface to LAMMPS"_Howto_library.html
-"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+"Couple LAMMPS to other codes"_Howto_couple.html
+"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt
new file mode 100644
index 0000000000000000000000000000000000000000..714c23f0669eed55eaa15e31f100d117e5e2448c
--- /dev/null
+++ b/doc/src/Howto_client_server.txt
@@ -0,0 +1,131 @@
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Using LAMMPS in client/server mode
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages to a "server" code. The server responds to
+each request with a reply message. This enables the two codes to work
+in tandem to perform a simulation. LAMMPS can act as either a client
+or server code.
+
+Some advantages of client/server coupling are that the two codes run
+as stand-alone executables; they are not linked together. Thus
+neither code needs to have a library interface. This often makes it
+easier to run the two codes on different numbers of processors. If a
+message protocol (format and content) is defined for a particular kind
+of simulation, then in principle any code that implements the
+client-side protocol can be used in tandem with any code that
+implements the server-side protocol, without the two codes needing to
+know anything more specific about each other.
+
+A simple example of client/server coupling is where LAMMPS is the
+client code performing MD timestepping. Each timestep it sends a
+message to a server quantum code containing current coords of all the
+atoms. The quantum code computes energy and forces based on the
+coords. It returns them as a message to LAMMPS, which completes the
+timestep.
+
+Alternate methods for code coupling with LAMMPS are described on
+the "Howto couple"_Howto_couple.html doc page.
+
+LAMMPS support for client/server coupling is in its "MESSAGE
+package"_Packages_details.html#PKG-MESSAGE which implements several
+commands that enable LAMMPS to act as a client or server, as discussed
+below. The MESSAGE package also wraps a client/server library called
+CSlib which enables two codes to exchange messages in different ways,
+either via files, sockets, or MPI. The CSlib is provided with LAMMPS
+in the lib/message dir. The CSlib has its own
+"website"_http://cslib.sandia.gov with documentation and test
+programs.
+
+NOTE: For client/server coupling to work between LAMMPS and another
+code, the other code also has to use the CSlib. This can sometimes be
+done without any modifications to the other code by simply wrapping it
+with a Python script that exchanges CSlib messages with LAMMPS and
+prepares input for or processes output from the other code. The other
+code also has to implement a matching protocol for the format and
+content of messages that LAMMPS exchanges with it.
+
+These are the commands currently in the MESSAGE package for two
+protocols, MD and MC (Monte Carlo). New protocols can easily be
+defined and added to this directory, where LAMMPS acts as either the
+client or server.
+
+"message"_message.html
+"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
+"server md"_server_md.html = LAMMPS is a server for computing MD forces
+"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
+
+The server doc files give details of the message protocols
+for data that is exchanged bewteen the client and server.
+
+These example directories illustrate how to use LAMMPS as either a
+client or server code:
+
+examples/message
+examples/COUPLE/README
+examples/COUPLE/lammps_mc
+examples/COUPLE/lammps_vasp :ul
+
+The examples/message dir couples a client instance of LAMMPS to a
+server instance of LAMMPS.
+
+The lammps_mc dir shows how to couple LAMMPS as a server to a simple
+Monte Carlo client code as the driver.
+
+The lammps_vasp dir shows how to couple LAMMPS as a client code
+running MD timestepping to VASP acting as a server providing quantum
+DFT forces, thru a Python wrapper script on VASP.
+
+Here is how to launch a client and server code together for any of the
+4 modes of message exchange that the "message"_message.html command
+and the CSlib support. Here LAMMPS is used as both the client and
+server code. Another code could be subsitituted for either.
+
+The examples below show launching both codes from the same window (or
+batch script), using the "&" character to launch the first code in the
+background. For all modes except {mpi/one}, you could also launch the
+codes in separate windows on your desktop machine. It does not
+matter whether you launch the client or server first.
+
+In these examples either code can be run on one or more processors.
+If running in a non-MPI mode (file or zmq) you can launch a code on a
+single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch both codes via
+mpirun, even if one or both of them runs on a single processor. This
+is so that MPI can figure out how to connect both MPI processes
+together to exchange MPI messages between them.
+
+For message exchange in {file}, {zmq}, or {mpi/two} modes:
+
+% mpirun -np 1 lmp_mpi -log log.client < in.client &
+% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 4 lmp_mpi -log log.client < in.client &
+% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
+
+% mpirun -np 2 lmp_mpi -log log.client < in.client &
+% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
+
+For message exchange in {mpi/one} mode:
+
+Launch both codes in a single mpirun command:
+
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as their its option, where color is an integer
+label that will be used to distinguish one executable from another in
+the multiple executables that the mpirun command launches. In this
+example the client was colored with a 0, and the server with a 1.
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index d7b4924d8cda690ef5204f6adabab34f2fff0a7d..0214db1ececec361d41e6e16d7efbfe3a90a70c0 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element
nodal points, compute a FE solution, and return interpolated forces on
MD atoms.
-LAMMPS can be coupled to other codes in at least 3 ways. Each has
+LAMMPS can be coupled to other codes in at least 4 ways. Each has
advantages and disadvantages, which you'll have to think about in the
context of your application.
+:line
+
(1) Define a new "fix"_fix.html command that calls the other code. In
this scenario, LAMMPS is the driver code. During its timestepping,
the fix is invoked, and can make library calls to the other code,
@@ -32,6 +34,8 @@ LAMMPS.
:link(poems,http://www.rpi.edu/~anderk5/lab)
+:line
+
(2) Define a new LAMMPS command that calls the other code. This is
conceptually similar to method (1), but in this case LAMMPS and the
other code are on a more equal footing. Note that now the other code
@@ -52,6 +56,8 @@ command writes and reads.
See the "Modify command"_Modify_command.html doc page for info on how
to add a new command to LAMMPS.
+:line
+
(3) Use LAMMPS as a library called by another code. In this case the
other code is the driver and calls LAMMPS as needed. Or a wrapper
code could link and call both LAMMPS and another code as libraries.
@@ -102,3 +108,9 @@ on all the processors. Or it might allocate half the processors to
LAMMPS and half to the other code and run both codes simultaneously
before syncing them up periodically. Or it might instantiate multiple
instances of LAMMPS to perform different calculations.
+
+:line
+
+(4) Couple LAMMPS with another code in a client/server mode. This is
+described on the "Howto client/server"_Howto_client_server.html doc
+page.
diff --git a/doc/src/JPG/pair_atm_dia.jpg b/doc/src/JPG/pair_atm_dia.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..fd8edc5e676ee9973dd4ca1aced98b641c4157c7
Binary files /dev/null and b/doc/src/JPG/pair_atm_dia.jpg differ
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ad3e66a4b27b93645e0f7ed4b2ec628e160597b9..e442aa1808d1cc4a4b1ff917aa702fd38c6543bf 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Aug 2018 version">
+<META NAME="docnumber" CONTENT="31 Aug 2018 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
-22 Aug 2018 version :c,h2
+31 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 381dc2e99589f5702dfd4ebf3f5ec615c2dd307b..a4ed1e3ff4fc3fa3cd0ead029bfdcf28a61b8546 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -549,10 +549,6 @@ This package has "specific installation
instructions"_Build_extras.html#gpu on the "Build
extras"_Build_extras.html doc page.
-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.
-
[Supporting info:]
src/MEAM: filenames -> commands
@@ -563,6 +559,31 @@ examples/meam :ul
:line
+MESSAGE package :link(PKG-MESSAGE),h4
+
+[Contents:]
+
+Commands to use LAMMPS as either a client or server and couple it to
+another application.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#message on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/MESSAGE: filenames -> commands
+lib/message/README
+"message"_message.html
+"fix client/md"_fix_client_md.html
+"server md"_server_md.html
+"server mc"_server_mc.html
+examples/message :ul
+
+:line
+
MISC package :link(PKG-MISC),h4
[Contents:]
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 2feb4e142d32f63c3008ffa3bc582dc2a2257062..583ecf39fe39ab603168d2956c9c4f2c035860c2 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
+"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt
index 9c862d7b8ec136b75fe95e5126a500a3801bc359..27f436ed55e4825886789259778e22f0b51819ce 100644
--- a/doc/src/Run_options.txt
+++ b/doc/src/Run_options.txt
@@ -18,6 +18,7 @@ letter abbreviation can be used:
"-i or -in"_#file
"-k or -kokkos"_#run-kokkos
"-l or -log"_#log
+"-m or -mpicolor"_#mpicolor
"-nc or -nocite"_#nocite
"-pk or -package"_#package
"-p or -partition"_#partition
@@ -175,6 +176,30 @@ Option -plog will override the name of the partition log files file.N.
:line
+[-mpicolor] color :link(mpi)
+
+If used, this must be the first command-line argument after the LAMMPS
+executable name. It is only used when LAMMPS is launched by an mpirun
+command which also launches another executable(s) at the same time.
+(The other executable could be LAMMPS as well.) The color is an
+integer value which should be different for each executable (another
+application may set this value in a different way). LAMMPS and the
+other executable(s) perform an MPI_Comm_split() with their own colors
+to shrink the MPI_COMM_WORLD communication to be the subset of
+processors they are actually running on.
+
+Currently, this is only used in LAMMPS to perform client/server
+messaging with another application. LAMMPS can act as either a client
+or server (or both). More details are given on the "Howto
+client/server"_Howto_client_server.html doc page.
+
+Specifically, this refers to the "mpi/one" mode of messaging provided
+by the "message"_message.html command and the CSlib library LAMMPS
+links with from the lib/message directory. See the
+"message"_message.html command for more details.
+
+:line
+
[-nocite] :link(nocite)
Disable writing the log.cite file which is normally written to list
diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt
index 62b973e3a4f65bfead97cae22fffa44879516867..8fae57a718f55599c089712ab73d0ccb36b467ee 100644
--- a/doc/src/commands_list.txt
+++ b/doc/src/commands_list.txt
@@ -56,6 +56,7 @@ Commands :h1
lattice
log
mass
+ message
min_modify
min_style
minimize
@@ -87,6 +88,7 @@ Commands :h1
restart
run
run_style
+ server
set
shell
special_bonds
diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b62d5617d547ff2f2da7b65f484ab0e9022b256
--- /dev/null
+++ b/doc/src/fix_client_md.txt
@@ -0,0 +1,106 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix client/md command :h3
+
+[Syntax:]
+
+fix ID group-ID client/md :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+client/md = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all client/md :pre
+
+[Description:]
+
+This fix style enables LAMMPS to run as a "client" code and
+communicate each timestep with a separate "server" code to perform an
+MD simulation together.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When using this fix, LAMMPS (as the client code) passes the current
+coordinates of all particles to the server code each timestep, which
+computes their interaction, and returns the energy, forces, and virial
+for the interacting particles to LAMMPS, so it can complete the
+timestep.
+
+The server code could be a quantum code, or another classical MD code
+which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
+does not have. In the quantum case, this fix is a mechanism for
+running {ab initio} MD with quantum forces.
+
+The group associated with this fix is ignored.
+
+The protocol and "units"_units.html for message format and content
+that LAMMPS exchanges with the server code is defined on the "server
+md"_server_md.html doc page.
+
+Note that when using LAMMPS as an MD client, your LAMMPS input script
+should not normally contain force field commands, like a
+"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
+"kspace_style"_kspace_style.html commmand. However it is possible for
+a server code to only compute a portion of the full force-field, while
+LAMMPS computes the remaining part. Your LAMMPS script can also
+specify boundary conditions or force constraints in the usual way,
+which will be added to the per-atom forces returned by the server
+code.
+
+See the examples/message dir for example scripts where LAMMPS is both
+the "client" and/or "server" code for this kind of client/server MD
+simulation. The examples/message/README file explains how to launch
+LAMMPS and another code in tandem to perform a coupled simulation.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential energy computed by the server application to
+the system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the server application's contribution to the system's
+virial as part of "thermodynamic output"_thermo_style.html. The
+default is {virial yes}
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Howto_output.html. The scalar is the potential
+energy discussed above. The scalar value calculated by this fix is
+"extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the MESSAGE package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other server code.
+
+[Related commands:]
+
+"message"_message.html, "server"_server.html
+
+[Default:] none
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 47d05570be4670b27907ac2b22783afbaf50cc69..72a07945e7aee608931a25c41c6fb45d55f986a9 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -167,6 +167,7 @@ label.html
lattice.html
log.html
mass.html
+message.html
min_modify.html
min_style.html
minimize.html
@@ -194,6 +195,9 @@ reset_timestep.html
restart.html
run.html
run_style.html
+server.html
+server_mc.html
+server_md.html
set.html
shell.html
special_bonds.html
@@ -241,6 +245,7 @@ fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
+fix_client_md.html
fix_cmap.html
fix_colvars.html
fix_controller.html
@@ -524,6 +529,7 @@ pair_write.html
pair_adp.html
pair_agni.html
pair_airebo.html
+pair_atm.html
pair_awpmd.html
pair_beck.html
pair_body_nparticle.html
diff --git a/doc/src/message.txt b/doc/src/message.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cca1a5b369fd72d8ffe6eb9db99698c9a39c5e43
--- /dev/null
+++ b/doc/src/message.txt
@@ -0,0 +1,162 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Command_all.html)
+
+:line
+
+message command :h3
+
+[Syntax:]
+
+message which protocol mode arg :pre
+
+which = {client} or {server} :ulb,l
+protocol = {md} or {mc} :l
+mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
+ {file} arg = filename
+ filename = file used for message exchanges
+ {zmq} arg = socket-ID
+ socket-ID for client = localhost:5555, see description below
+ socket-ID for server = *:5555, see description below
+ {mpi/one} arg = none
+ {mpi/two} arg = filename
+ filename = file used to establish communication bewteen 2 MPI jobs :pre
+:ule
+
+[Examples:]
+
+message client md file tmp.couple
+message server md file tmp.couple :pre
+
+message client md zmq localhost:5555
+message server md zmq *:5555 :pre
+
+message client md mpi/one
+message server md mpi/one :pre
+
+message client md mpi/two tmp.couple
+message server md mpi/two tmp.couple :pre
+
+[Description:]
+
+Establish a messaging protocol between LAMMPS and another code for the
+purpose of client/server coupling.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+:line
+
+The {which} argument defines LAMMPS to be the client or the server.
+
+:line
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+md = run dynamics with another code
+mc = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client or server. See the
+"server md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+The {mode} argument specifies how messages are exchanged between the
+client and server codes. Both codes must use the same mode and use
+consistent parameters.
+
+For mode {file}, the 2 codes communicate via binary files. They must
+use the same filename, which is actually a file prefix. Several files
+with that prefix will be created and deleted as a simulation runs.
+The filename can include a path. Both codes must be able to access
+the path/file in a common filesystem.
+
+For mode {zmq}, the 2 codes communicate via a socket on the server
+code's machine. Support for socket messaging is provided by the
+open-source "ZeroMQ library"_http://zeromq.org, which must be
+installed on your system. The client specifies an IP address (IPv4
+format) or the DNS name of the machine the server code is running on,
+followed by a 4-digit port ID for the socket, separated by a colon.
+E.g.
+
+localhost:5555 # client and server running on same machine
+192.168.1.1:5555 # server is 192.168.1.1
+deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre
+
+The server specifes "*:5555" where "*" represents all available
+interfaces on the server's machine, and the port ID must match
+what the client specifies.
+
+NOTE: What are allowed port IDs?
+
+NOTE: Additional explanation is needed here about how to use the {zmq}
+mode on a parallel machine, e.g. a cluster with many nodes.
+
+For mode {mpi/one}, the 2 codes communicate via MPI and are launched
+by the same mpirun command, e.g. with this syntax for OpenMPI:
+
+mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
+mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre
+
+Note the use of the "-mpicolor color" command-line argument with
+LAMMPS. See the "command-line args"_Run_options.html doc page for
+further explanation.
+
+For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
+be 2 separate mpirun commands. The specified {filename} argument is a
+file the 2 MPI processes will use to exchange info so that an MPI
+inter-communicator can be established to enable the 2 codes to send
+MPI messages to each other. Both codes must be able to access the
+path/file in a common filesystem.
+
+:line
+
+Normally, the message command should be used at the top of a LAMMPS
+input script. It performs an initial handshake with the other code to
+setup messaging and to verify that both codes are using the same
+message protocol and mode. Assuming both codes are launched at
+(nearly) the same time, the other code should perform the same kind of
+initialization.
+
+If LAMMPS is the client code, it will begin sending messages when a
+LAMMPS client command begins its operation. E.g. for the "fix
+client/md"_fix_client_md.html command, it is when a "run"_run.html
+command is executed.
+
+If LAMMPS is the server code, it will begin receiving messages when
+the "server"_server.html command is invoked.
+
+A fix client command will terminate its messaging with the server when
+LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
+server command will terminate its messaging with the client when the
+client signals it. Then the remainder of the LAMMPS input script will
+be processed.
+
+If both codes do something similar, this means a new round of
+client/server messaging can be initiated after termination by re-using
+a 2nd message command in your LAMMPS input script, followed by a new
+fix client or server command.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"server"_server.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63a450c51a0d63223e7009aec6fd784ad57c3330
--- /dev/null
+++ b/doc/src/pair_atm.txt
@@ -0,0 +1,164 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+pair_style atm command :h3
+
+[Syntax:]
+
+pair_style atm cutoff cutoff_triple :pre
+
+cutoff = cutoff for each pair in 3-body interaction (distance units)
+cutoff_triple = additional cutoff applied to product of 3 pairwise distances (distance units) :ul
+
+[Examples:]
+
+pair_style atm 4.5 2.5
+pair_coeff * * * 0.072 :pre
+
+pair_style hybrid/overlay lj/cut 6.5 atm 4.5 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 1 1 atm 1 0.064
+pair_coeff 1 1 atm 2 0.080
+pair_coeff 1 2 atm 2 0.100
+pair_coeff 2 2 atm 2 0.125 :pre
+
+[Description:]
+
+The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod
+potential for the energy E of a system of atoms as
+
+:c,image(Eqs/pair_atm.jpg)
+
+where nu is the three-body interaction strength. The distances
+between pairs of atoms r12, r23, r31 and the angles gamma1, gamma2,
+gamma3 are as shown in this diagram:
+
+:c,image(JPG/pair_atm_dia.jpg)
+
+Note that for the interaction between a triplet of atoms I,J,K, there
+is no "central" atom. The interaction is symmetric with respect to
+permutation of the three atoms. Thus the nu value is
+the same for all those permutations of the atom types of I,J,K
+and needs to be specified only once, as discussed below.
+
+The {atm} potential is typically used in combination with a two-body
+potential using the "pair_style hybrid/overlay"_pair_hybrid.html
+command as in the example above.
+
+The potential for a triplet of atom is calculated only if all 3
+distances r12, r23, r31 between the 3 atoms satisfy rIJ < cutoff.
+In addition, the product of the 3 distances r12*r23*r31 <
+cutoff_triple^3 is required, which excludes from calculation the
+triplets with small contribution to the interaction.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the restart files read by the
+"read_restart"_read_restart.html commands:
+
+K = atom type of the third atom (1 to Ntypes)
+nu = prefactor (energy/distance^9 units) :ul
+
+K can be specified in one of two ways. An explicit numeric value can
+be used, as in the 2nd example above. J <= K is required. LAMMPS
+sets the coefficients for the other 5 symmetric interactions to the
+same values. E.g. if I = 1, J = 2, K = 3, then these 6 values are set
+to the specified nu: nu123, nu132, nu213, nu231, nu312, nu321. This
+enforces the symmetry discussed above.
+
+A wildcard asterisk can be used for K to set the coefficients for
+multiple triplets of atom types. This takes the form "*" or "*n" or
+"n*" or "m*n". If N = the number of atom types, then an asterisk with
+no numeric values means all types from 1 to N. A leading asterisk
+means all types from 1 to n (inclusive). A trailing asterisk means
+all types from n to N (inclusive). A middle asterisk means all types
+from m to n (inclusive). Note that only type triplets with J <= K are
+considered; if asterisks imply type triplets where K < J, they are
+ignored.
+
+Note that a pair_coeff command can override a previous setting for the
+same I,J,K triplet. For example, these commands set nu for all I,J.K
+triplets, then overwrite nu for just the I,J,K = 2,3,4 triplet:
+
+pair_coeff * * * 0.25
+pair_coeff 2 3 4 0.1 :pre
+
+Note that for a simulation with a single atom type, only a single
+entry is required, e.g.
+
+pair_coeff 1 1 1 0.25 :pre
+
+For a simulation with two atom types, four pair_coeff commands will
+specify all possible nu values:
+
+pair_coeff 1 1 1 nu1
+pair_coeff 1 1 2 nu2
+pair_coeff 1 2 2 nu3
+pair_coeff 2 2 2 nu4 :pre
+
+For a simulation with three atom types, ten pair_coeff commands will
+specify all possible nu values:
+
+pair_coeff 1 1 1 nu1
+pair_coeff 1 1 2 nu2
+pair_coeff 1 1 3 nu3
+pair_coeff 1 2 2 nu4
+pair_coeff 1 2 3 nu5
+pair_coeff 1 3 3 nu6
+pair_coeff 2 2 2 nu7
+pair_coeff 2 2 3 nu8
+pair_coeff 2 3 3 nu9
+pair_coeff 3 3 3 nu10 :pre
+
+By default the nu value for all triplets is set to 0.0. Thus it is
+not required to provide pair_coeff commands that enumerate triplet
+interactions for all K types. If some I,J,K combination is not
+speficied, then there will be no 3-body ATM interactions for that
+combination and all its permutations. However, as with all pair
+styles, it is required to specify a pair_coeff command for all I,J
+combinations, else an error will result.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair styles do not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+However, if the {atm} potential is used in combination with other
+potentials using the "pair_style hybrid/overlay"_pair_hybrid.html
+command then pair_coeff commands need to be re-specified
+in the restart input script.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command. It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the MANYBODY package. It is only enabled
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Axilrod)
+[(Axilrod)]
+Axilrod and Teller, J Chem Phys, 11, 299 (1943);
+Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 1441da2b610e26ec5a6be9fb7028fe3189356b13..9dfead300ea5cda19aec67f9073a1bc44b1da51d 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -103,6 +103,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
+"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 4c3eef2cd11c32ea4801ebb830a6a985cc5a734b..d535798482cf6b748331f7c7bb23e39ed2ec1acb 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -8,6 +8,7 @@ Pair Styles :h1
pair_adp
pair_agni
pair_airebo
+ pair_atm
pair_awpmd
pair_beck
pair_body_nparticle
diff --git a/doc/src/server.txt b/doc/src/server.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86fb68d012963be87b30b169c1bf1554c78cfecb
--- /dev/null
+++ b/doc/src/server.txt
@@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server command :h3
+
+[Syntax:]
+
+server protocol :pre
+
+protocol = {md} or {mc} :ul
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it receives
+messages from a separate "client" code and responds by sending a reply
+message back to the client. The specified {protocol} determines the
+format and content of messages LAMMPS expects to receive and how it
+responds.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The {protocol} argument defines the format and content of messages
+that will be exchanged between the two codes. The current options
+are:
+
+"md"_server_md.html = run dynamics with another code
+"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
+
+For protocol {md}, LAMMPS can be either a client (via the "fix
+client/md"_fix_client_md.html command) or server. See the "server
+md"_server_md.html doc page for details on the protocol.
+
+For protocol {mc}, LAMMPS can be the server. See the "server
+mc"_server_mc.html doc page for details on the protocol.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53ccfc8ecd4b1a1f9322fc21182a8666e6aae832
--- /dev/null
+++ b/doc/src/server_mc.txt
@@ -0,0 +1,116 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server mc command :h3
+
+[Syntax:]
+
+server mc :pre
+
+mc = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server mc :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {mc}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The "server"_server.html doc page gives other options for using LAMMPS
+See an example of how this command is used in
+examples/COUPLE/lammps_mc/in.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives
+instructions from a Monte Carlo (MC) driver to displace random atoms,
+compute the energy before and after displacement, and run dynamics to
+equilibrate the system.
+
+The MC driver performs the random displacements on random atoms,
+accepts or rejects the move in an MC sense, and orchestrates the MD
+runs.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
+these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
+example of how an MC driver code can use these messages.
+
+Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
+
+[Client sends one of these kinds of message]:
+
+cs->send(NATOMS,0) # msgID = 1 with no fields :pre
+
+cs->send(EINIT,0) # msgID = 2 with no fields :pre
+
+cs->send(DISPLACE,2) # msgID = 3 with 2 fields
+cs->pack_int(1,ID) # 1st field = ID of atom to displace
+cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
+
+cs->send(ACCEPT,1) # msgID = 4 with 1 field
+cs->pack_int(1,flag) # 1st field = accept/reject flag :pre
+
+cs->send(RUN,1) # msgID = 5 with 1 field
+cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
+
+[Server replies]:
+
+cs->send(NATOMS,1) # msgID = 1 with 1 field
+cs->pack_int(1,natoms) # 1st field = number of atoms :pre
+
+cs->send(EINIT,2) # msgID = 2 with 2 fields
+cs->pack_double(1,poteng) # 1st field = potential energy of system
+cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
+
+cs->send(DISPLACE,1) # msgID = 3 with 1 field
+cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
+
+cs->send(ACCEPT,0) # msgID = 4 with no fields
+
+cs->send(RUN,0) # msgID = 5 with no fields
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+A script that uses this command must also use the
+"message"_message.html command to setup the messaging protocol with
+the other client code.
+
+[Related commands:]
+
+"message"_message.html
+
+[Default:] none
diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0db7bbe16b9422f55997c3f4c7446929c58ac585
--- /dev/null
+++ b/doc/src/server_md.txt
@@ -0,0 +1,147 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+server md command :h3
+
+[Syntax:]
+
+server md :pre
+
+md = the protocol argument to the "server"_server.html command
+
+[Examples:]
+
+server md :pre
+
+[Description:]
+
+This command starts LAMMPS running in "server" mode, where it will
+expect messages from a separate "client" code that match the {md}
+protocol for format and content explained below. For each message
+LAMMPS receives it will send a message back to the client.
+
+The "Howto client/server"_Howto_client_server.html doc page gives an
+overview of client/server coupling of LAMMPS with another code where
+one code is the "client" and sends request messages to a "server"
+code. The server responds to each request with a reply message. This
+enables the two codes to work in tandem to perform a simulation.
+
+When this command is invoked, LAMMPS will run in server mode in an
+endless loop, waiting for messages from the client code. The client
+signals when it is done sending messages to LAMMPS, at which point the
+loop will exit, and the remainder of the LAMMPS script will be
+processed.
+
+The "server"_server.html doc page gives other options for using LAMMPS
+in server mode. See an example of how this command is used in
+examples/message/in.message.server.
+
+:line
+
+When using this command, LAMMPS (as the server code) receives the
+current coordinates of all particles from the client code each
+timestep, computes their interaction, and returns the energy, forces,
+and pressure for the interacting particles to the client code, so it
+can complete the timestep. This command could also be used with a
+client code that performs energy minimization, using the server to
+compute forces and energy each iteration of its minimizer.
+
+When using the "fix client/md" command, LAMMPS (as the client code)
+does the timestepping and receives needed energy, forces, and pressure
+values from the server code.
+
+The format and content of the exchanged messages are explained here in
+a conceptual sense. Python-style pseudo code for the library calls to
+the CSlib is shown, which performs the actual message exchange between
+the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
+pages for more details on the actual library syntax. The "cs" object
+in this pseudo code is a pointer to an instance of the CSlib.
+
+See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
+files for details on how LAMMPS uses these messages. See the
+examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
+a quantum code (VASP) can use use these messages.
+
+The following pseudo-code uses these values, defined as enums.
+
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre
+
+[Client sends 2 kinds of messages]:
+
+# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+# optional fields: UNITS, CHARGE :pre
+
+cs->send(SETUP,nfields) # msgID with nfields :pre
+
+cs->pack_int(DIM,dim) # dimension (2,3) of simulation
+cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+cs->pack_int(NATOMS,natoms) # total number of atoms
+cs->pack_int(NTYPES,ntypes) # number of atom types
+cs->pack(TYPES,natoms,type) # vector of per-atom types
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
+cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
+
+# required fields: COORDS
+# optional fields: ORIGIN, BOX :pre
+
+cs->send(STEP,nfields) # msgID with nfields :pre
+
+cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
+cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
+cs->pack(BOX,9,box) # 3 edge vectors of simulation box
+
+[Server replies to either kind of message]:
+
+# required fields: FORCES, ENERGY, PRESSURE
+# optional fields: ERROR :pre
+
+cs->send(msgID,nfields) # msgID with nfields
+cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
+cs->pack(ENERGY,1,poteng) # total potential energy of system
+cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
+cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre
+
+:line
+
+The units for various quantities that are sent and received iva
+messages are defined for atomic-scale simulations in the table below.
+The client and server codes (including LAMMPS) can use internal units
+different than these (e.g. "real units"_units.html in LAMMPS), so long
+as they convert to these units for meesaging.
+
+COORDS, ORIGIN, BOX = Angstroms
+CHARGE = multiple of electron charge (1.0 is a proton)
+ENERGY = eV
+FORCES = eV/Angstrom
+PRESSURE = bars :ul
+
+Note that these are "metal units"_units.html in LAMMPS.
+
+If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
+units"_units.html, then the client and server should exchange a UNITS
+message as indicated above, and both the client and server should
+agree on the units for the data they exchange.
+
+:line
+
+[Restrictions:]
+
+This command is part of the MESSAGE package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"message"_message.html, "fix client/md"_fix_client_md.html
+
+[Default:] none
diff --git a/examples/COUPLE/README b/examples/COUPLE/README
index 83e7463531de47c29b81883ff74493682139c3eb..0e611befbd3083d0044260695007aa544b6df4db 100644
--- a/examples/COUPLE/README
+++ b/examples/COUPLE/README
@@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
+6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
In all of the examples included here, LAMMPS must first be built as a
library. Basically, in the src dir you type one of
@@ -33,9 +34,13 @@ These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS
+lammps_mc client/server coupling of Monte Carlo client
+ with LAMMPS server for energy evaluation
lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code
+lammps_vasp client/server coupling of LAMMPS client with
+ VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran
diff --git a/examples/COUPLE/lammps_mc/Makefile b/examples/COUPLE/lammps_mc/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..c75bd08c738b6b383edf5deda81f365fa1cd6f7b
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/Makefile
@@ -0,0 +1,33 @@
+# Makefile for MC
+
+SHELL = /bin/sh
+
+SRC = mc.cpp random_park.cpp
+OBJ = $(SRC:.cpp=.o)
+
+# change this line for your machine to path for CSlib src dir
+
+CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
+
+# compiler/linker settings
+
+CC = g++
+CCFLAGS = -g -O3 -I$(CSLIB)
+LINK = g++
+LINKFLAGS = -g -O -L$(CSLIB)
+
+# targets
+
+mc: $(OBJ)
+# first line if built the CSlib within lib/message with ZMQ support
+# second line if built the CSlib without ZMQ support
+ $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
+# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
+
+clean:
+ @rm -f *.o mc
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) -c $<
diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README
new file mode 100644
index 0000000000000000000000000000000000000000..c201a6351cf01278f1b7cfa708c17fcd56df9c04
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/README
@@ -0,0 +1,128 @@
+Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE)
+and Section_howto.html#howto10 for more details on how
+client/server coupling works in LAMMPS.
+
+In this dir, the mc.cpp/h files are a standalone "client" MC code. It
+should be run on a single processor, though it could become a parallel
+program at some point. LAMMPS is also run as a standalone executable
+as a "server" on as many processors as desired using its "server mc"
+command; see it's doc page for details.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the MC
+program became parallel, data could also be exchanged via MPI.
+
+The MC code makes simple MC moves, by displacing a single random atom
+by a small random amount. It uses LAMMPS to calculate the energy
+change, and to run dynamics between MC moves.
+
+----------------
+
+Build LAMMPS with its MESSAGE package installed:
+
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
+
+% cd lammps/lib/message
+% python Install.py -m -z # build CSlib with MPI and ZMQ support
+% cd lammps/src
+% make yes-message
+% make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+----------------
+
+Build the MC client code
+
+The source files for the MC code are in this dir. It links with the
+CSlib library in lib/message/cslib.
+
+You must first build the CSlib in serial mode, e.g.
+
+% cd lammps/lib/message/cslib/src
+% make lib # build serial and parallel lib with ZMQ support
+% make lib zmq=no # build serial and parallel lib without ZMQ support
+
+Then edit the Makefile in this dir. The CSLIB variable should be the
+path to where the LAMMPS lib/message/cslib/src dir is on your system.
+If you built the CSlib without ZMQ support you will also need to
+comment/uncomment one line. Then you can just type
+
+% make
+
+and you should get an "mc" executable.
+
+----------------
+
+To run in client/server mode:
+
+Both the client (MC) and server (LAMMPS) must use the same messaging
+mode, namely file or zmq. This is an argument to the MC code; it can
+be selected by setting the "mode" variable when you run LAMMPS. The
+default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The MC code is always run in serial.
+
+When you run, the server should print out thermodynamic info
+for every MD run it performs (between MC moves). The client
+will print nothing until the simulation ends, then it will
+print stats about the accepted MC moves.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
+
+% mpirun -np 1 mc in.mc file tmp.couple
+% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
+
+% mpirun -np 1 mc in.mc zmq localhost:5555
+% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
+
+--------------
+
+The input script for the MC program is in.mc. You can edit it to run
+longer simulations.
+
+500 nsteps = total # of steps of MD
+100 ndynamics = # of MD steps between MC moves
+0.1 delta = displacement size of MC move
+1.0 temperature = used in MC Boltzman factor
+12345 seed = random number seed
+
+--------------
+
+The problem size that LAMMPS is computing the MC energy for and
+running dynamics on is set by the x,y,z variables in the LAMMPS
+in.mc.server script. The default size is 500 particles. You can
+adjust the size as follows:
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
diff --git a/examples/COUPLE/lammps_mc/in.mc b/examples/COUPLE/lammps_mc/in.mc
new file mode 100644
index 0000000000000000000000000000000000000000..85052d09f1bdd0957a5fc4d030cdd4ef3741e08e
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc
@@ -0,0 +1,7 @@
+# MC params
+
+500 nsteps
+100 ndynamics
+0.1 delta
+1.0 temperature
+12345 seed
diff --git a/examples/COUPLE/lammps_mc/in.mc.server b/examples/COUPLE/lammps_mc/in.mc.server
new file mode 100644
index 0000000000000000000000000000000000000000..8b10bb0f7be97e3f07c2421c5f2b38bbdef7c0b1
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/in.mc.server
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server mc file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server mc zmq *:5555" &
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..0d67c89cf191e9216f51ec574658430694371b50
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000649929 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+93.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+157.3% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..2ae51d246142f346033d126fdf2ffcfef092d0c6
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc file tmp.couple
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000592947 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
+
+59.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.815e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
+
+106.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.04e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
+
+113.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.755e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
+
+117.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.563e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
+
+93.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.994e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
+
+111.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.576e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:02
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..0565487bc6e8bea16240c4dacc3524a15be446e8
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000741005 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19500 ave 19500 max 19500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
+
+52.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.907e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 19501 ave 19501 max 19501 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
+Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
+
+83.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 1.192e-06 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1939 ave 1939 max 1939 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18757 ave 18757 max 18757 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18757
+Ave neighs/atom = 37.514
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.7565013 -5.757431 0 -4.6249485 0.21982657
+ 150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18699 ave 18699 max 18699 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
+ 250 0.73052476 -5.7206316 0 -4.627036 0.39287516
+ 300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+104.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1903 ave 1903 max 1903 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18715 ave 18715 max 18715 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18715
+Ave neighs/atom = 37.43
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76300831 -5.768304 0 -4.6260806 0.15954325
+ 350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
+Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
+
+209.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 9.537e-07 | | |100.00
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1899 ave 1899 max 1899 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18683 ave 18683 max 18683 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18683
+Ave neighs/atom = 37.366
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.72469448 -5.713463 0 -4.6285954 0.44859547
+ 450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
+ 500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4 b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..e74d03235dacc4574db8178724a45e25fa4bd2d4
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
@@ -0,0 +1,254 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones Monte Carlo server script
+
+variable mode index file
+
+if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
+message server mc zmq *:5555
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000576019 secs
+mass 1 1.0
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 20 check no
+
+velocity all create 1.44 87287 loop geom
+
+fix 1 all nve
+
+thermo 50
+
+server mc
+run 0
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
+
+89.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 4.768e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875 ave 4875 max 4875 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 19500
+Ave neighs/atom = 39
+Neighbor list builds = 0
+Dangerous builds not checked
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
+
+94.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.457e-06 | | |100.00
+
+Nlocal: 125 ave 125 max 125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 1099 ave 1099 max 1099 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 4875.25 ave 4885 max 4866 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 19501
+Ave neighs/atom = 39.002
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7723127 0 -4.6166327 -5.015531
+ 50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
+ 100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
+
+115.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 3.04e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 124 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1085.25 ave 1089 max 1079 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs: 4690.25 ave 4996 max 4401 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+
+Total # of neighbors = 18761
+Ave neighs/atom = 37.522
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
+ 150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
+Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
+
+125.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.384e-06 | | |100.00
+
+Nlocal: 125 ave 126 max 123 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost: 1068.5 ave 1076 max 1063 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs: 4674.75 ave 4938 max 4419 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 18699
+Ave neighs/atom = 37.398
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
+ 250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
+ 300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
+
+112.5% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.444e-06 | | |100.00
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Nghost: 1069 ave 1080 max 1055 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs: 4672 ave 4803 max 4600 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 18688
+Ave neighs/atom = 37.376
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
+ 350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+run 0
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
+Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
+
+139.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0 | 0 | 0 | 0.0 | 0.00
+Output | 0 | 0 | 0 | 0.0 | 0.00
+Modify | 0 | 0 | 0 | 0.0 | 0.00
+Other | | 2.146e-06 | | |100.00
+
+Nlocal: 125 ave 132 max 118 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost: 1057.5 ave 1068 max 1049 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs: 4685.75 ave 5045 max 4229 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 18743
+Ave neighs/atom = 37.486
+Neighbor list builds = 0
+Dangerous builds not checked
+Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
+ 450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
+ 500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
+Total wall time: 0:00:00
diff --git a/examples/COUPLE/lammps_mc/mc.cpp b/examples/COUPLE/lammps_mc/mc.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7c2e2ce0391a4305c8e07ee3940bdbdc58f4abcd
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.cpp
@@ -0,0 +1,263 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+// MC code used with LAMMPS in client/server mode
+// MC is the client, LAMMPS is the server
+
+// Syntax: mc infile mode modearg
+// mode = file, zmq
+// modearg = filename for file, localhost:5555 for zmq
+
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include "mc.h"
+#include "random_park.h"
+
+#include "cslib.h"
+using namespace CSLIB_NS;
+
+void error(const char *);
+CSlib *cs_create(char *, char *);
+
+#define MAXLINE 256
+
+/* ---------------------------------------------------------------------- */
+
+// main program
+
+int main(int narg, char **arg)
+{
+ if (narg != 4) {
+ error("Syntax: mc infile mode modearg");
+ exit(1);
+ }
+
+ // initialize CSlib
+
+ CSlib *cs = cs_create(arg[2],arg[3]);
+
+ // create MC class and perform run
+
+ MC *mc = new MC(arg[1],cs);
+ mc->run();
+
+ // final MC stats
+
+ int naccept = mc->naccept;
+ int nattempt = mc->nattempt;
+
+ printf("------ MC stats ------\n");
+ printf("MC attempts = %d\n",nattempt);
+ printf("MC accepts = %d\n",naccept);
+ printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
+
+ // clean up
+
+ delete cs;
+ delete mc;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void error(const char *str)
+{
+ printf("ERROR: %s\n",str);
+ exit(1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib *cs_create(char *mode, char *arg)
+{
+ CSlib *cs = new CSlib(0,mode,arg,NULL);
+
+ // initial handshake to agree on protocol
+
+ cs->send(0,1);
+ cs->pack_string(1,(char *) "mc");
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ return cs;
+}
+
+// ----------------------------------------------------------------------
+// MC class
+// ----------------------------------------------------------------------
+
+MC::MC(char *mcfile, void *cs_caller)
+//MC::MC(char *mcfile, CSlib *cs_caller)
+{
+ cs_void = cs_caller;
+
+ // setup MC params
+
+ options(mcfile);
+
+ // random # generator
+
+ random = new RanPark(seed);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MC::~MC()
+{
+ free(x);
+ delete random;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::run()
+{
+ int iatom,accept,msgID,nfield;
+ double pe_initial,pe_final,edelta;
+ double dx,dy,dz;
+ double xold[3],xnew[3];
+ int *fieldID,*fieldtype,*fieldlen;
+
+ enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+ CSlib *cs = (CSlib *) cs_void;
+
+ // one-time request for atom count from MD
+ // allocate 1d coord buffer
+
+ cs->send(NATOMS,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ natoms = cs->unpack_int(1);
+
+ x = (double *) malloc(3*natoms*sizeof(double));
+
+ // loop over MC moves
+
+ naccept = nattempt = 0;
+
+ for (int iloop = 0; iloop < nloop; iloop++) {
+
+ // request current energy from MD
+ // recv energy, coords from MD
+
+ cs->send(EINIT,0);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_initial = cs->unpack_double(1);
+ double *x = (double *) cs->unpack(2);
+
+ // perform simple MC event
+ // displace a single atom by random amount
+
+ iatom = (int) natoms*random->uniform();
+ xold[0] = x[3*iatom+0];
+ xold[1] = x[3*iatom+1];
+ xold[2] = x[3*iatom+2];
+
+ dx = 2.0*delta*random->uniform() - delta;
+ dy = 2.0*delta*random->uniform() - delta;
+ dz = 2.0*delta*random->uniform() - delta;
+
+ xnew[0] = xold[0] + dx;
+ xnew[1] = xold[1] + dx;
+ xnew[2] = xold[2] + dx;
+
+ // send atom ID and its new coords to MD
+ // recv new energy
+
+ cs->send(DISPLACE,2);
+ cs->pack_int(1,iatom+1);
+ cs->pack(2,4,3,xnew);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ pe_final = cs->unpack_double(1);
+
+ // decide whether to accept/reject MC event
+
+ if (pe_final <= pe_initial) accept = 1;
+ else if (temperature == 0.0) accept = 0;
+ else if (random->uniform() >
+ exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
+ else accept = 1;
+
+ nattempt++;
+ if (accept) naccept++;
+
+ // send accept (1) or reject (0) flag to MD
+
+ cs->send(ACCEPT,1);
+ cs->pack_int(1,accept);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // send dynamics timesteps
+
+ cs->send(RUN,1);
+ cs->pack_int(1,ndynamics);
+
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ }
+
+ // send exit message to MD
+
+ cs->send(-1,0);
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MC::options(char *filename)
+{
+ // default params
+
+ nsteps = 0;
+ ndynamics = 100;
+ delta = 0.1;
+ temperature = 1.0;
+ seed = 12345;
+
+ // read and parse file
+
+ FILE *fp = fopen(filename,"r");
+ if (fp == NULL) error("Could not open MC file");
+
+ char line[MAXLINE];
+ char *keyword,*value;
+ char *eof = fgets(line,MAXLINE,fp);
+
+ while (eof) {
+ if (line[0] == '#') { // comment line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ value = strtok(line," \t\n\r\f");
+ if (value == NULL) { // blank line
+ eof = fgets(line,MAXLINE,fp);
+ continue;
+ }
+
+ keyword = strtok(NULL," \t\n\r\f");
+ if (keyword == NULL) error("Missing keyword in MC file");
+
+ if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
+ else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
+ else if (strcmp(keyword,"delta") == 0) delta = atof(value);
+ else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
+ else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
+ else error("Unknown param in MC file");
+
+ eof = fgets(line,MAXLINE,fp);
+ }
+
+ // derived params
+
+ nloop = nsteps/ndynamics;
+}
diff --git a/examples/COUPLE/lammps_mc/mc.h b/examples/COUPLE/lammps_mc/mc.h
new file mode 100644
index 0000000000000000000000000000000000000000..e9d88523fcaec0a0d64c90735e9158d0a18ff031
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/mc.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+------------------------------------------------------------------------- */
+
+#ifndef MC_H
+#define MC_H
+
+/* ---------------------------------------------------------------------- */
+
+class MC {
+ public:
+ int naccept; // # of accepted MC events
+ int nattempt; // # of attempted MC events
+
+ MC(char *, void *);
+ ~MC();
+ void run();
+
+ private:
+ int nsteps; // total # of MD steps
+ int ndynamics; // steps in one short dynamics run
+ int nloop; // nsteps/ndynamics
+ int natoms; // # of MD atoms
+
+ double delta; // MC displacement distance
+ double temperature; // MC temperature for Boltzmann criterion
+ double *x; // atom coords as 3N 1d vector
+ double energy; // global potential energy
+
+ int seed; // RNG seed
+ class RanPark *random;
+
+ void *cs_void; // messaging library
+
+ void options(char *);
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_mc/random_park.cpp b/examples/COUPLE/lammps_mc/random_park.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..61ac18c6c00ac2984a692c8d13aca0303b48d5c3
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.cpp
@@ -0,0 +1,72 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+// Park/Miller RNG
+
+#include <math.h>
+#include "random_park.h"
+//#include "error.h"
+
+#define IA 16807
+#define IM 2147483647
+#define AM (1.0/IM)
+#define IQ 127773
+#define IR 2836
+
+/* ---------------------------------------------------------------------- */
+
+RanPark::RanPark(int seed_init)
+{
+ //if (seed_init <= 0)
+ // error->one(FLERR,"Invalid seed for Park random # generator");
+ seed = seed_init;
+ save = 0;
+}
+
+/* ----------------------------------------------------------------------
+ uniform RN
+------------------------------------------------------------------------- */
+
+double RanPark::uniform()
+{
+ int k = seed/IQ;
+ seed = IA*(seed-k*IQ) - IR*k;
+ if (seed < 0) seed += IM;
+ double ans = AM*seed;
+ return ans;
+}
+
+/* ----------------------------------------------------------------------
+ gaussian RN
+------------------------------------------------------------------------- */
+
+double RanPark::gaussian()
+{
+ double first,v1,v2,rsq,fac;
+
+ if (!save) {
+ do {
+ v1 = 2.0*uniform()-1.0;
+ v2 = 2.0*uniform()-1.0;
+ rsq = v1*v1 + v2*v2;
+ } while ((rsq >= 1.0) || (rsq == 0.0));
+ fac = sqrt(-2.0*log(rsq)/rsq);
+ second = v1*fac;
+ first = v2*fac;
+ save = 1;
+ } else {
+ first = second;
+ save = 0;
+ }
+ return first;
+}
diff --git a/examples/COUPLE/lammps_mc/random_park.h b/examples/COUPLE/lammps_mc/random_park.h
new file mode 100644
index 0000000000000000000000000000000000000000..0dc208176877708f1e6d19b20993da9c55a74f72
--- /dev/null
+++ b/examples/COUPLE/lammps_mc/random_park.h
@@ -0,0 +1,28 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef RANPARK_H
+#define RANPARK_H
+
+class RanPark {
+ public:
+ RanPark(int);
+ double uniform();
+ double gaussian();
+
+ private:
+ int seed,save;
+ double second;
+};
+
+#endif
diff --git a/examples/COUPLE/lammps_vasp/INCAR b/examples/COUPLE/lammps_vasp/INCAR
new file mode 100644
index 0000000000000000000000000000000000000000..ac2358e5fbdbfbd2c2f7ebe0d3b693c8376b8799
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/INCAR
@@ -0,0 +1,53 @@
+# Startparameter for this run:
+ NWRITE = 2 write-flag & timer
+ PREC = normal normal or accurate (medium, high low for compatibility)
+ ISTART = 0 job : 0-new 1-cont 2-samecut
+ ICHARG = 2 charge: 1-file 2-atom 10-const
+ ISPIN = 1 spin polarized calculation?
+ LSORBIT = F spin-orbit coupling
+ INIWAV = 1 electr: 0-lowe 1-rand 2-diag
+
+# Electronic Relaxation 1
+ ENCUT = 600.0 eV #Plane wave energy cutoff
+ ENINI = 600.0 initial cutoff
+ NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
+ EDIFF = 0.1E-05 stopping-criterion for ELM
+# Ionic relaxation
+ EDIFFG = 0.1E-02 stopping-criterion for IOM
+ NSW = 0 number of steps for IOM
+ NBLOCK = 1; KBLOCK = 1 inner block; outer block
+ IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
+ NFREE = 0 steps in history (QN), initial steepest desc. (CG)
+ ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
+ IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
+
+ POTIM = 0.5000 time-step for ionic-motion
+ TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
+ SMASS = -3.00 Nose mass-parameter (am)
+ estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
+ PSTRESS= 0.0 pullay stress
+
+# DOS related values:
+ EMIN = 10.00; EMAX =-10.00 energy-range for DOS
+ EFERMI = 0.00
+ ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
+
+# Electronic relaxation 2 (details)
+ IALGO = 48 algorithm
+
+# Write flags
+ LWAVE = T write WAVECAR
+ LCHARG = T write CHGCAR
+ LVTOT = F write LOCPOT, total local potential
+ LVHAR = F write LOCPOT, Hartree potential only
+ LELF = F write electronic localiz. function (ELF)
+
+# Dipole corrections
+ LMONO = F monopole corrections only (constant potential shift)
+ LDIPOL = F correct potential (dipole corrections)
+ IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
+ EPSILON= 1.0000000 bulk dielectric constant
+
+# Exchange correlation treatment:
+ GGA = -- GGA type
+
diff --git a/examples/COUPLE/lammps_vasp/KPOINTS b/examples/COUPLE/lammps_vasp/KPOINTS
new file mode 100644
index 0000000000000000000000000000000000000000..322509da300a773443eebe1019cc034df3eee02e
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/KPOINTS
@@ -0,0 +1,6 @@
+K-Points
+ 0
+Monkhorst Pack
+ 15 15 15
+ 0 0 0
+
diff --git a/examples/COUPLE/lammps_vasp/POSCAR_W b/examples/COUPLE/lammps_vasp/POSCAR_W
new file mode 100644
index 0000000000000000000000000000000000000000..aba5df54a02c631b807ece6f5f31f24992809025
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/POSCAR_W
@@ -0,0 +1,11 @@
+W unit cell
+1.0
+3.16 0.00000000 0.00000000
+0.00000000 3.16 0.00000000
+0.00000000 0.00000000 3.16
+W
+2
+Direct
+ 0.00000000 0.00000000 0.00000000
+ 0.50000000 0.50000000 0.50000000
+
diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README
new file mode 100644
index 0000000000000000000000000000000000000000..e942d52535d040a39f0b3076de64e7d47788ff65
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/README
@@ -0,0 +1,149 @@
+Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
+coupling
+
+See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
+Section_howto.html#howto10 for more details on how client/server
+coupling works in LAMMPS.
+
+In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
+code so it can work as a "server" code which LAMMPS drives as a
+"client" code to perform ab initio MD. LAMMPS performs the MD
+timestepping, sends VASP a current set of coordinates each timestep,
+VASP computes forces and energy and virial and returns that info to
+LAMMPS.
+
+Messages are exchanged between MC and LAMMPS via a client/server
+library (CSlib), which is included in the LAMMPS distribution in
+lib/message. As explained below you can choose to exchange data
+between the two programs either via files or sockets (ZMQ). If the
+vasp_wrap.py program became parallel, or the CSlib library calls were
+integrated into VASP directly, then data could also be exchanged via
+MPI.
+
+----------------
+
+Build LAMMPS with its MESSAGE package installed:
+
+See the Build extras doc page and its MESSAGE package
+section for details.
+
+CMake:
+
+-D PKG_MESSAGE=yes # include the MESSAGE package
+-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
+
+Traditional make:
+
+cd lammps/lib/message
+python Install.py -m -z # build CSlib with MPI and ZMQ support
+cd lammps/src
+make yes-message
+make mpi
+
+You can leave off the -z if you do not have ZMQ on your system.
+
+----------------
+
+Build the CSlib in a form usable by the vasp_wrapper.py script:
+
+% cd lammps/lib/message/cslib/src
+% make shlib # build serial and parallel shared lib with ZMQ support
+% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
+
+This will make a shared library versions of the CSlib, which Python
+requires. Python must be able to find both the cslib.py script and
+the libcsnompi.so library in your lammps/lib/message/cslib/src
+directory. If it is not able to do this, you will get an error when
+you run vasp_wrapper.py.
+
+You can do this by augmenting two environment variables, either
+from the command line, or in your shell start-up script.
+Here is the sample syntax for the csh or tcsh shells:
+
+setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
+
+----------------
+
+Prepare to use VASP and the vasp_wrapper.py script
+
+You can run the vasp_wrap.py script as-is to test that the coupling
+between it and LAMMPS is functional. This will use the included
+vasprun.xml file output by a previous VASP run.
+
+But note that the as-is version of vasp_wrap.py will not attempt to
+run VASP.
+
+To do this, you must edit the 1st vaspcmd line at the top of
+vasp_wrapper.py to be the launch command needed to run VASP on your
+system. It can be a command to run VASP in serial or in parallel,
+e.g. an mpirun command. Then comment out the 2nd vaspcmd line
+immediately following it.
+
+Insure you have the necessary VASP input files in this
+directory, suitable for the VASP calculation you want to perform:
+
+INCAR
+KPOINTS
+POSCAR_template
+POTCAR
+
+Examples of all but the POTCAR file are provided. As explained below,
+POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
+be used to test the LAMMPS/VASP coupling. The POTCAR file is a
+proprietary VASP file, so use one from your VASP installation.
+
+Note that the POSCAR_template file should be matched to the LAMMPS
+input script (# of atoms and atom types, box size, etc). The provided
+POSCAR_W matches in.client.W.
+
+Once you run VASP yourself, the vasprun.xml file will be overwritten.
+
+----------------
+
+To run in client/server mode:
+
+NOTE: The vasp_wrap.py script must be run with Python version 2, not
+3. This is because it used the CSlib python wrapper, which only
+supports version 2. We plan to upgrade CSlib to support Python 3.
+
+Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
+messaging mode, namely file or zmq. This is an argument to the
+vasp_wrap.py code; it can be selected by setting the "mode" variable
+when you run LAMMPS. The default mode = file.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means either of
+the messaging modes can be used and LAMMPS can be run in serial or
+parallel. The vasp_wrap.py code is always run in serial, but it
+launches VASP from Python via an mpirun command which can run VASP
+itself in parallel.
+
+When you run, the server should print out thermodynamic info every
+timestep which corresponds to the forces and virial computed by VASP.
+VASP will also generate output files each timestep. The vasp_wrapper.py
+script could be generalized to archive these.
+
+The examples below are commands you should use in two different
+terminal windows. The order of the two commands (client or server
+launch) does not matter. You can run them both in the same window if
+you append a "&" character to the first one to run it in the
+background.
+
+--------------
+
+File mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode file < in.client.W
+% python vasp_wrap.py file POSCAR_W
+
+ZMQ mode of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
+
+% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
+% python vasp_wrap.py zmq POSCAR_W
diff --git a/examples/COUPLE/lammps_vasp/data.W b/examples/COUPLE/lammps_vasp/data.W
new file mode 100644
index 0000000000000000000000000000000000000000..8accd9ca790422646d4fb9a671ef18387ee5457d
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/data.W
@@ -0,0 +1,15 @@
+LAMMPS W data file
+
+2 atoms
+
+1 atom types
+
+0.0 3.16 xlo xhi
+0.0 3.16 ylo yhi
+0.0 3.16 zlo zhi
+
+Atoms
+
+1 1 0.000 0.000 0.000
+2 1 1.58 1.58 1.58
+
diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W
new file mode 100644
index 0000000000000000000000000000000000000000..3eaf99dcbb121a342eea20b7a98f06c28c76f8a0
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/in.client.W
@@ -0,0 +1,34 @@
+# small W unit cell for use with VASP
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+mass 1 183.85
+
+replicate $x $y $z
+
+velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 1
+run 3
+
diff --git a/examples/COUPLE/lammps_vasp/log.client.output b/examples/COUPLE/lammps_vasp/log.client.output
new file mode 100644
index 0000000000000000000000000000000000000000..fa8f4f920ae90b5c72be06275bb4a76fcb028d1b
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/log.client.output
@@ -0,0 +1,76 @@
+LAMMPS (22 Aug 2018)
+# small W unit cell for use with VASP
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
+message client md zmq localhost:5555
+variable x index 1
+variable y index 1
+variable z index 1
+
+units metal
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+read_data data.W
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 2 atoms
+mass 1 183.85
+
+replicate $x $y $z
+replicate 1 $y $z
+replicate 1 1 $z
+replicate 1 1 1
+ orthogonal box = (0 0 0) to (3.16 3.16 3.16)
+ 1 by 1 by 2 MPI processor grid
+ 2 atoms
+ Time spent = 0.000148058 secs
+
+velocity all create 300.0 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 10 check no
+
+fix 1 all nve
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 1
+run 3
+Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 0 0 -48.030793 -78159.503
+ 1 298.24318 0 0 -48.03102 -78167.19
+ 2 296.85584 0 0 -48.031199 -78173.26
+ 3 295.83795 0 0 -48.031331 -78177.714
+Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
+
+Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
+Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
+Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
+Other | | 1.204e-05 | | | 0.00
+
+Nlocal: 1 ave 1 max 1 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 4 ave 4 max 4 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds not checked
+
+Total wall time: 0:01:21
diff --git a/examples/COUPLE/lammps_vasp/vasp_wrap.py b/examples/COUPLE/lammps_vasp/vasp_wrap.py
new file mode 100644
index 0000000000000000000000000000000000000000..1e2c52aa46d6d20d52ec656c3ab8889fd75aec05
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasp_wrap.py
@@ -0,0 +1,300 @@
+#!/usr/bin/env python
+
+# ----------------------------------------------------------------------
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+# ----------------------------------------------------------------------
+
+# Syntax: vasp_wrap.py file/zmq POSCARfile
+
+# wrapper on VASP to act as server program using CSlib
+# receives message with list of coords from client
+# creates VASP inputs
+# invokes VASP to calculate self-consistent energy of that config
+# reads VASP outputs
+# sends message with energy, forces, pressure to client
+
+# NOTES:
+# check to insure basic VASP input files are in place?
+# could archive VASP input/output in special filenames or dirs?
+# need to check that POTCAR file is consistent with atom ordering?
+# could make syntax for launching VASP more flexible
+# e.g. command-line arg for # of procs
+# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
+
+from __future__ import print_function
+import sys
+
+version = sys.version_info[0]
+if version == 3:
+ sys.exit("The CSlib python wrapper does not yet support python 3")
+
+import subprocess
+import xml.etree.ElementTree as ET
+from cslib import CSlib
+
+# comment out 2nd line once 1st line is correct for your system
+
+vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
+ "-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
+vaspcmd = "touch tmp"
+
+# enums matching FixClientMD class in LAMMPS
+
+SETUP,STEP = range(1,2+1)
+DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
+FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
+
+# -------------------------------------
+# functions
+
+# error message and exit
+
+def error(txt):
+ print("ERROR:",txt)
+ sys.exit(1)
+
+# -------------------------------------
+# read initial VASP POSCAR file to setup problem
+# return natoms,ntypes,box
+
+def vasp_setup(poscar):
+
+ ps = open(poscar,'r').readlines()
+
+ # box size
+
+ words = ps[2].split()
+ xbox = float(words[0])
+ words = ps[3].split()
+ ybox = float(words[1])
+ words = ps[4].split()
+ zbox = float(words[2])
+ box = [xbox,ybox,zbox]
+
+ ntypes = 0
+ natoms = 0
+ words = ps[6].split()
+ for word in words:
+ if word == '#': break
+ ntypes += 1
+ natoms += int(word)
+
+ return natoms,ntypes,box
+
+# -------------------------------------
+# write a new POSCAR file for VASP
+
+def poscar_write(poscar,natoms,ntypes,types,coords,box):
+
+ psold = open(poscar,'r').readlines()
+ psnew = open("POSCAR",'w')
+
+ # header, including box size
+
+ psnew.write(psold[0])
+ psnew.write(psold[1])
+ psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
+ psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
+ psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
+ psnew.write(psold[5])
+ psnew.write(psold[6])
+
+ # per-atom coords
+ # grouped by types
+
+ psnew.write("Cartesian\n")
+
+ for itype in range(1,ntypes+1):
+ for i in range(natoms):
+ if types[i] != itype: continue
+ x = coords[3*i+0]
+ y = coords[3*i+1]
+ z = coords[3*i+2]
+ aline = " %g %g %g\n" % (x,y,z)
+ psnew.write(aline)
+
+ psnew.close()
+
+# -------------------------------------
+# read a VASP output vasprun.xml file
+# uses ElementTree module
+# see https://docs.python.org/2/library/xml.etree.elementtree.html
+
+def vasprun_read():
+ tree = ET.parse('vasprun.xml')
+ root = tree.getroot()
+
+ #fp = open("vasprun.xml","r")
+ #root = ET.parse(fp)
+
+ scsteps = root.findall('calculation/scstep')
+ energy = scsteps[-1].find('energy')
+ for child in energy:
+ if child.attrib["name"] == "e_0_energy":
+ eout = float(child.text)
+
+ fout = []
+ sout = []
+
+ varrays = root.findall('calculation/varray')
+ for varray in varrays:
+ if varray.attrib["name"] == "forces":
+ forces = varray.findall("v")
+ for line in forces:
+ fxyz = line.text.split()
+ fxyz = [float(value) for value in fxyz]
+ fout += fxyz
+ if varray.attrib["name"] == "stress":
+ tensor = varray.findall("v")
+ stensor = []
+ for line in tensor:
+ sxyz = line.text.split()
+ sxyz = [float(value) for value in sxyz]
+ stensor.append(sxyz)
+ sxx = stensor[0][0]
+ syy = stensor[1][1]
+ szz = stensor[2][2]
+ # symmetrize off-diagonal components
+ sxy = 0.5 * (stensor[0][1] + stensor[1][0])
+ sxz = 0.5 * (stensor[0][2] + stensor[2][0])
+ syz = 0.5 * (stensor[1][2] + stensor[2][1])
+ sout = [sxx,syy,szz,sxy,sxz,syz]
+
+ #fp.close()
+
+ return eout,fout,sout
+
+# -------------------------------------
+# main program
+
+# command-line args
+
+if len(sys.argv) != 3:
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
+ sys.exit(1)
+
+mode = sys.argv[1]
+poscar_template = sys.argv[2]
+
+if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
+elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
+else:
+ print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
+ sys.exit(1)
+
+natoms,ntypes,box = vasp_setup(poscar_template)
+
+# initial message for MD protocol
+
+msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+if msgID != 0: error("Bad initial client/server handshake")
+protocol = cs.unpack_string(1)
+if protocol != "md": error("Mismatch in client/server protocol")
+cs.send(0,0)
+
+# endless server loop
+
+while 1:
+
+ # recv message from client
+ # msgID = 0 = all-done message
+
+ msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
+ if msgID < 0: break
+
+ # SETUP receive at beginning of each run
+ # required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ # NATOMS, NTYPES, TYPES, COORDS
+ # optional fields: others in enum above, but VASP ignores them
+
+ if msgID == SETUP:
+
+ origin = []
+ box = []
+ natoms_recv = ntypes_recv = 0
+ types = []
+ coords = []
+
+ for field in fieldID:
+ if field == DIM:
+ dim = cs.unpack_int(DIM)
+ if dim != 3: error("VASP only performs 3d simulations")
+ elif field == PERIODICITY:
+ periodicity = cs.unpack(PERIODICITY,1)
+ if not periodicity[0] or not periodicity[1] or not periodicity[2]:
+ error("VASP wrapper only currently supports fully periodic systems")
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+ elif field == NATOMS:
+ natoms_recv = cs.unpack_int(NATOMS)
+ if natoms != natoms_recv:
+ error("VASP wrapper mis-match in number of atoms")
+ elif field == NTYPES:
+ ntypes_recv = cs.unpack_int(NTYPES)
+ if ntypes != ntypes_recv:
+ error("VASP wrapper mis-match in number of atom types")
+ elif field == TYPES:
+ types = cs.unpack(TYPES,1)
+ elif field == COORDS:
+ coords = cs.unpack(COORDS,1)
+
+ if not origin or not box or not natoms or not ntypes or \
+ not types or not coords:
+ error("Required VASP wrapper setup field not received");
+
+ # STEP receive at each timestep of run or minimization
+ # required fields: COORDS
+ # optional fields: ORIGIN, BOX
+
+ elif msgID == STEP:
+
+ coords = []
+
+ for field in fieldID:
+ if field == COORDS:
+ coords = cs.unpack(COORDS,1)
+ elif field == ORIGIN:
+ origin = cs.unpack(ORIGIN,1)
+ elif field == BOX:
+ box = cs.unpack(BOX,1)
+
+ if not coords: error("Required VASP wrapper step field not received");
+
+ else: error("VASP wrapper received unrecognized message")
+
+ # create POSCAR file
+
+ poscar_write(poscar_template,natoms,ntypes,types,coords,box)
+
+ # invoke VASP
+
+ print("\nLaunching VASP ...")
+ print(vaspcmd)
+ subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
+
+ # process VASP output
+
+ energy,forces,virial = vasprun_read()
+
+ # convert VASP kilobars to bars
+
+ for i,value in enumerate(virial): virial[i] *= 1000.0
+
+ # return forces, energy, pressure to client
+
+ cs.send(msgID,3);
+ cs.pack(FORCES,4,3*natoms,forces)
+ cs.pack_double(ENERGY,energy)
+ cs.pack(VIRIAL,4,6,virial)
+
+# final reply to client
+
+cs.send(0,0)
+
+# clean-up
+
+del cs
diff --git a/examples/COUPLE/lammps_vasp/vasprun.xml b/examples/COUPLE/lammps_vasp/vasprun.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0f15c871b4136496c82e3a03700d33b8939492d5
--- /dev/null
+++ b/examples/COUPLE/lammps_vasp/vasprun.xml
@@ -0,0 +1,12329 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<modeling>
+ <generator>
+ <i name="program" type="string">vasp </i>
+ <i name="version" type="string">5.4.4.18Apr17-6-g9f103f2a35 </i>
+ <i name="subversion" type="string">(build Aug 01 2017 10:32:50) complex parallel </i>
+ <i name="platform" type="string">LinuxIFC </i>
+ <i name="date" type="string">2017 12 19 </i>
+ <i name="time" type="string">15:22:45 </i>
+ </generator>
+ <incar>
+ <i type="int" name="ISTART"> 0</i>
+ <i type="string" name="PREC">normal normal or accurate (medium, h</i>
+ <i type="int" name="IALGO"> 48</i>
+ <i type="logical" name="LSORBIT"> F </i>
+ <i type="int" name="ISPIN"> 1</i>
+ <i type="int" name="ICHARG"> 2</i>
+ <i type="int" name="INIWAV"> 1</i>
+ <i type="int" name="NELM"> 100</i>
+ <i type="int" name="NELMDL"> -5</i>
+ <i type="int" name="NELMIN"> 2</i>
+ <i type="int" name="IBRION"> -1</i>
+ <i type="int" name="NFREE"> 0</i>
+ <i name="EDIFF"> 0.00000100</i>
+ <i name="EDIFFG"> 0.00100000</i>
+ <i type="int" name="NSW"> 0</i>
+ <i type="int" name="ISIF"> 2</i>
+ <i type="int" name="IWAVPR"> 10</i>
+ <i type="int" name="NBLOCK"> 1</i>
+ <i type="int" name="KBLOCK"> 1</i>
+ <i name="ENCUT"> 600.00000000</i>
+ <i name="ENINI"> 600.00000000</i>
+ <i name="POTIM"> 0.50000000</i>
+ <i name="TEBEG"> 3500.00000000</i>
+ <i name="TEEND"> 3500.00000000</i>
+ <i name="SMASS"> -3.00000000</i>
+ <i name="EMIN"> 10.00000000</i>
+ <i name="EMAX"> -10.00000000</i>
+ <i name="EFERMI"> 0.00000000</i>
+ <i type="int" name="ISMEAR"> 0</i>
+ <i name="SIGMA"> 0.10000000</i>
+ <i type="int" name="NWRITE"> 2</i>
+ <i name="PSTRESS"> 0.00000000</i>
+ <i type="logical" name="LWAVE"> T </i>
+ <i type="logical" name="LCHARG"> T </i>
+ <i type="logical" name="LVTOT"> F </i>
+ <i type="logical" name="LVHAR"> F </i>
+ <i type="logical" name="LELF"> F </i>
+ <v type="int" name="KPOINT_BSE"> -1 0 0 0</v>
+ <i type="int" name="NELM"> 100</i>
+ <i type="string" name="GGA"> -- GGA type</i>
+ <i type="logical" name="LDIPOL"> F </i>
+ <i type="logical" name="LMONO"> F </i>
+ <i type="int" name="IDIPOL"> 0</i>
+ <i name="EPSILON"> 1.00000000</i>
+ </incar>
+ <structure name="primitive_cell" >
+ <crystal>
+ <varray name="basis" >
+ <v> 3.66961100 0.00000000 0.00000000 </v>
+ <v> 0.00000000 3.55744000 0.00000000 </v>
+ <v> 0.00000000 0.00000000 3.17678100 </v>
+ </varray>
+ <i name="volume"> 41.47103646 </i>
+ <varray name="rec_basis" >
+ <v> 0.27250845 0.00000000 0.00000000 </v>
+ <v> 0.00000000 0.28110102 0.00000000 </v>
+ <v> 0.00000000 0.00000000 0.31478405 </v>
+ </varray>
+ </crystal>
+ <varray name="positions" >
+ <v> 0.00000000 0.00000000 0.00000000 </v>
+ <v> 0.00000000 -0.50000000 -0.50000000 </v>
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+ </varray>
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+ </varray>
+ </structure>
+</modeling>
diff --git a/examples/README b/examples/README
index a8dfe63d923f211598141b76a5ec892ea4e48d60..3c9c299819db13b27f3152cc8496e9ed2f90aaa1 100644
--- a/examples/README
+++ b/examples/README
@@ -59,6 +59,7 @@ sub-directories:
accelerate: use of all the various accelerator packages
airebo: polyethylene with AIREBO potential
+atm: Axilrod-Teller-Muto potential
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
@@ -82,6 +83,7 @@ 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
+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
mscg: parameterize a multi-scale coarse-graining (MSCG) model
diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in
index 0fa9c1b74c2c41d9917d21b7167d4761403a2c2b..8315e57750b021c691ade481caccb1f727a44b3c 100644
--- a/examples/USER/diffraction/BulkNi.in
+++ b/examples/USER/diffraction/BulkNi.in
@@ -17,8 +17,9 @@ atom_modify sort 0 0
compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.05 echo manual
+compute SAED all saed 0.0251 Ni Kmax 0.85 &
+ Zone 0 0 0 c 0.025 0.025 0.025 &
+ dR_Ewald 0.01 echo manual
fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
mode vector file $A.hist.xrd
diff --git a/examples/USER/diffraction/Output/BulkNi.in b/examples/USER/diffraction/Output/BulkNi.in
deleted file mode 100644
index 8315e57750b021c691ade481caccb1f727a44b3c..0000000000000000000000000000000000000000
--- a/examples/USER/diffraction/Output/BulkNi.in
+++ /dev/null
@@ -1,35 +0,0 @@
-variable A string bulkNi
-log $A.log
-
-boundary p p p
-
-units metal
-timestep 0.001
-
-lattice fcc 3.52
-region box block 0 20 0 20 0 20
-create_box 1 box
-create_atoms 1 box
-
-pair_style none
-mass * 58.71
-atom_modify sort 0 0
-
-compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo
-
-compute SAED all saed 0.0251 Ni Kmax 0.85 &
- Zone 0 0 0 c 0.025 0.025 0.025 &
- dR_Ewald 0.01 echo manual
-
-fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] &
- mode vector file $A.hist.xrd
-
-fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed
-
-dump 1 all custom 1 $A.dump id x y z
-run 0
-
-unfix 1
-unfix 2
-uncompute XRD
-uncompute SAED
diff --git a/examples/atm/in.atm b/examples/atm/in.atm
new file mode 100644
index 0000000000000000000000000000000000000000..131528dce396b528943fc6ae1e0abf62702dd7df
--- /dev/null
+++ b/examples/atm/in.atm
@@ -0,0 +1,31 @@
+# Axilrod-Teller-Muto potential example
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable yy equal 10*$y
+variable zz equal 10*$z
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box 1 box
+create_atoms 1 box
+
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 5
+
+run 25
diff --git a/examples/atm/log.27Aug18.g++.1 b/examples/atm/log.27Aug18.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..46215e108c0be7ce2f3e6587cec0e05f396061ee
--- /dev/null
+++ b/examples/atm/log.27Aug18.g++.1
@@ -0,0 +1,100 @@
+LAMMPS (22 Aug 2018)
+# Axilrod-Teller-Muto potential example
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable xx equal 10*1
+variable yy equal 10*$y
+variable yy equal 10*1
+variable zz equal 10*$z
+variable zz equal 10*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+Lattice spacing in x,y,z = 1.83252 1.83252 1.83252
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 10 0 ${yy} 0 ${zz}
+region box block 0 10 0 10 0 ${zz}
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+ Time spent = 0.00139618 secs
+
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 5
+
+run 25
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4, bins = 8 8 8
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair atm, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms
+
+Performance: 270.846 tau/day, 1.567 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01
+Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00
+Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01
+Other | | 0.0006771 | | | 0.00
+
+Nlocal: 4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10895 ave 10895 max 10895 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 640000 ave 640000 max 640000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 1.28e+06 ave 1.28e+06 max 1.28e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1280000
+Ave neighs/atom = 320
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:16
diff --git a/examples/atm/log.27Aug18.g++.4 b/examples/atm/log.27Aug18.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..d84f17ee2b5562b5c9e22a0d2a6e8722bb974c6b
--- /dev/null
+++ b/examples/atm/log.27Aug18.g++.4
@@ -0,0 +1,100 @@
+LAMMPS (22 Aug 2018)
+# Axilrod-Teller-Muto potential example
+
+variable x index 1
+variable y index 1
+variable z index 1
+
+variable xx equal 10*$x
+variable xx equal 10*1
+variable yy equal 10*$y
+variable yy equal 10*1
+variable zz equal 10*$z
+variable zz equal 10*1
+
+units lj
+atom_style atomic
+
+lattice fcc 0.65
+Lattice spacing in x,y,z = 1.83252 1.83252 1.83252
+region box block 0 ${xx} 0 ${yy} 0 ${zz}
+region box block 0 10 0 ${yy} 0 ${zz}
+region box block 0 10 0 10 0 ${zz}
+region box block 0 10 0 10 0 10
+create_box 1 box
+Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 4000 atoms
+ Time spent = 0.000900984 secs
+
+pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * atm * 0.072
+
+mass * 1.0
+velocity all create 1.033 12345678 loop geom
+
+fix 1 all nvt temp 1.033 1.033 0.05
+
+timestep 0.002
+thermo 5
+
+run 25
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 4.8
+ ghost atom cutoff = 4.8
+ binsize = 2.4, bins = 8 8 8
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair lj/cut, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair atm, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.033 -4.8404387 0 -3.291326 -4.1332095
+ 5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
+ 10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
+ 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
+ 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
+ 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
+Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms
+
+Performance: 993.935 tau/day, 5.752 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55
+Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00
+Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02
+Other | | 0.0003656 | | | 0.01
+
+Nlocal: 1000 ave 1000 max 1000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5835 ave 5835 max 5835 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 160000 ave 160000 max 160000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 320000 ave 320000 max 320000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1280000
+Ave neighs/atom = 320
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
diff --git a/examples/message/README b/examples/message/README
new file mode 100644
index 0000000000000000000000000000000000000000..6cd99d5c097fffb8e5c09bba4fefa5dad5bb7c94
--- /dev/null
+++ b/examples/message/README
@@ -0,0 +1,117 @@
+This dir contains scripts that demonstrate how to use LAMMPS as both a
+client and server code to run a simple MD simulation. LAMMPS as a
+client performs the MD timestepping. LAMMPS as a server provides the
+energy and forces between interacting particles. Every timestep the
+LAMMPS client sends a message to the LAMMPS server and receives a
+response message in return.
+
+Another code could replace LAMMPS as the client, e.g. another MD code
+which wants to use a LAMMPS potential. Another code could replace
+LAMMPS as the server, e.g. a quantum code computing quantum forces, so
+that ab initio MD could be performed. See an example of the latter in
+examples/COUPLE/lammps_vasp.
+
+See the doc pages for the "MESSAGE package"
+(Package_details.html#PKG-MESSAGE) and "Howto client/server"
+(Howto_client_server.html) for more details on how client/server
+coupling works in LAMMPS.
+
+--------------
+
+Note that you can adjust the problem size run by these scripts by
+setting "x,y,z" variables when you run LAMMPS. The default problem size
+is x = y = z = 5, which is 500 particles.
+
+lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
+
+This applies to either in.message or in.message.client
+
+You can also run the in.message scripts with an NPT integrator
+instead of NVE, if you comment/uncomment the correct lines.
+
+The client and server script define a "mode" variable
+which can be set to file, zmq, mpi/one, or mpi/two,
+as illustrated below.
+
+--------------
+
+To run this problem in the traditional way (no client/server coupling)
+do one of these:
+
+% lmp_serial < in.message
+% mpirun -np 4 lmp_mpi < in.message
+
+Or run with in.message.tilt.
+
+--------------
+
+To run in client/server mode:
+
+Both the client and server script must use the same messaging mode.
+This can be selected by setting the "mode" variable when you run
+LAMMPS. The default mode = file. The other options for the mode
+variable are zmq, mpione, mpitwo.
+
+Here we assume LAMMPS was built to run in parallel, and the MESSAGE
+package was installed with socket (ZMQ) support. This means any of
+the 4 messaging modes can be used.
+
+The next sections illustrate how to launch LAMMPS twice, once as a
+client, once as a server, for each of the messaging modes.
+
+In all cases, the client should print out thermodynamic info for 50
+steps. The server should print out setup info, print nothing until
+the client exits, at which point the server should also exit.
+
+The examples below show launching LAMMPS twice from the same window
+(or batch script), using the "&" character to launch the first time in
+the background. For all modes except {mpi/one}, you could also launch
+twice in separate windows on your desktop machine. It does not matter
+whether you launch the client or server first.
+
+In these examples either the client or server can be run on one or
+more processors. If running in a non-MPI mode (file or zmq) you can
+launch LAMMPS on a single processor without using mpirun.
+
+IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both
+times via mpirun, even if one or both of them runs on a single
+processor. This is so that MPI can figure out how to connect both MPI
+processes together to exchange MPI messages between them.
+
+--------------
+
+NOTE: the Script.sh file has comands to perform all the
+runs listed below.
+
+--------------
+
+File or ZMQ or mpi/two modes of messaging:
+
+% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
+% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
+
+% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client &
+% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server
+
+% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
+% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
+
+Or run with in.message.tilt.client/server.
+Don't run the tilt files with the "file" mode; they run too slow.
+
+--------------
+
+Mpi/one mode of messaging:
+
+Launch LAMMPS twice in a single mpirun command:
+
+% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server
+
+Or run with in.message.tilt.client/server.
+
+The two -np values determine how many procs the client and the server
+run on.
+
+A LAMMPS executable run in this manner must use the -mpicolor color
+command-line option as its first option, where color is set to one
+integer value for the 1st app, and another value for the 2nd app.
diff --git a/examples/message/Script.sh b/examples/message/Script.sh
new file mode 100644
index 0000000000000000000000000000000000000000..fdcd6f11888448eb40e9425873257a7a9773b0b6
--- /dev/null
+++ b/examples/message/Script.sh
@@ -0,0 +1,55 @@
+# sample launch script
+
+# message on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message
+
+mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
+
+mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
+
+# message on 2/4 procs each
+
+mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message
+
+mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
+
+mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
+
+# message.tilt on 1 proc each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt
+
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
+mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
+
+mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
+
+# message.tilt on 2/4 procs each
+
+mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt
+
+mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
+mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
+
+mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
diff --git a/examples/message/in.message b/examples/message/in.message
new file mode 100644
index 0000000000000000000000000000000000000000..7fbbffc355cf82402ed7fc3975ffa9136f56ceec
--- /dev/null
+++ b/examples/message/in.message
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.client b/examples/message/in.message.client
new file mode 100644
index 0000000000000000000000000000000000000000..f1ec644a8005fae80cdbd41657bc146482c9b128
--- /dev/null
+++ b/examples/message/in.message.client
@@ -0,0 +1,41 @@
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+region box block 0 $x 0 $y 0 $z
+create_box 1 box
+create_atoms 1 box
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
diff --git a/examples/message/in.message.server b/examples/message/in.message.server
new file mode 100644
index 0000000000000000000000000000000000000000..2fedd2ae0061329741a5a1abbbc0694ef3ef2d9b
--- /dev/null
+++ b/examples/message/in.message.server
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+region box block 0 1 0 1 0 1
+create_box 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/in.message.tilt b/examples/message/in.message.tilt
new file mode 100644
index 0000000000000000000000000000000000000000..51126eae1ef14b8c0b8ebb93b9ea90a910a33dc3
--- /dev/null
+++ b/examples/message/in.message.tilt
@@ -0,0 +1,30 @@
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client
new file mode 100644
index 0000000000000000000000000000000000000000..b55bc6585b07bca4607673b080700c963fdc6a6a
--- /dev/null
+++ b/examples/message/in.message.tilt.client
@@ -0,0 +1,42 @@
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message client md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message client md zmq localhost:5555" &
+elif "${mode} == mpione" &
+ "message client md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message client md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
diff --git a/examples/message/in.message.tilt.server b/examples/message/in.message.tilt.server
new file mode 100644
index 0000000000000000000000000000000000000000..ba211ed15fce9030032b5e9bc2eed3ecdee6d766
--- /dev/null
+++ b/examples/message/in.message.tilt.server
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then &
+ "message server md file tmp.couple" &
+elif "${mode} == zmq" &
+ "message server md zmq *:5555" &
+elif "${mode} == mpione" &
+ "message server md mpi/one" &
+elif "${mode} == mpitwo" &
+ "message server md mpi/two tmp.couple"
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+create_atoms 1 box
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
diff --git a/examples/message/log.28Aug18.message.client.file.g++.1 b/examples/message/log.28Aug18.message.client.file.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..bca1d37dd5022f93df73ed80a0dc6fb62db40deb
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.file.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000752926 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms
+
+Performance: 4298.421 tau/day, 9.950 timesteps/s
+0.1% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
+Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00
+Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
+Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98
+Other | | 0.0004668 | | | 0.01
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.client.file.g++.2 b/examples/message/log.28Aug18.message.client.file.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..1c868dde37cf3e7fcca7555b1babca1b9f16bfd7
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.file.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md file tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000613928 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms
+
+Performance: 4299.499 tau/day, 9.953 timesteps/s
+50.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00
+Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00
+Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01
+Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92
+Other | | 0.003203 | | | 0.06
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.1 b/examples/message/log.28Aug18.message.client.mpione.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..78bee72fdf5e2a4cd364be6f149f80a2cf02c778
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000540018 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms
+
+Performance: 534798.272 tau/day, 1237.959 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01
+Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16
+Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24
+Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17
+Other | | 0.0001726 | | | 0.43
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpione.g++.2 b/examples/message/log.28Aug18.message.client.mpione.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..7d7af866e39cc806e48c87d22d55cdbc5fe8aff0
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpione.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000475883 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms
+
+Performance: 1035997.740 tau/day, 2398.143 timesteps/s
+99.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02
+Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60
+Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38
+Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15
+Other | | 0.0001761 | | | 0.84
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..ee97e7bd1a30cada0045240d6458cd7d4a88fcf4
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000603914 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms
+
+Performance: 312504.627 tau/day, 723.390 timesteps/s
+42.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01
+Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15
+Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20
+Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25
+Other | | 0.0002651 | | | 0.38
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..72db0198d582ac4fce9fee22a85c687369186cd8
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.mpitwo.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000667095 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms
+
+Performance: 1135563.588 tau/day, 2628.619 timesteps/s
+58.5% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02
+Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95
+Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81
+Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58
+Other | | 0.0005029 | | | 2.64
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.1 b/examples/message/log.28Aug18.message.client.zmq.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..23fa70c1be67ea310f6271eeb9f8977def4aecfa
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.1
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000734091 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms
+
+Performance: 277513.222 tau/day, 642.392 timesteps/s
+11.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01
+Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11
+Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15
+Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37
+Other | | 0.0002885 | | | 0.37
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.client.zmq.g++.2 b/examples/message/log.28Aug18.message.client.zmq.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..7833befd211aab1fcbf01e8a7a57ad39ef136e03
--- /dev/null
+++ b/examples/message/log.28Aug18.message.client.zmq.g++.2
@@ -0,0 +1,79 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+atom_modify sort 0 0.0 map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000570059 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+fix 2 all client/md
+fix_modify 2 energy yes
+
+thermo 10
+run 50
+Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 0 0 -4.6176881 -5.0221006
+ 10 1.1347688 0 0 -4.6166043 -2.6072847
+ 20 0.628166 0 0 -4.62213 1.0186262
+ 30 0.73767593 0 0 -4.6254647 0.49629637
+ 40 0.69517962 0 0 -4.6253506 0.69303877
+ 50 0.70150496 0 0 -4.6259832 0.59551518
+Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms
+
+Performance: 518489.499 tau/day, 1200.207 timesteps/s
+56.5% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01
+Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33
+Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27
+Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49
+Other | | 0.0003769 | | | 0.90
+
+Nlocal: 250 ave 255 max 245 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.g++.1 b/examples/message/log.28Aug18.message.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c06af4e0d1584a740ee3ed501bb9c0185c7e9444
--- /dev/null
+++ b/examples/message/log.28Aug18.message.g++.1
@@ -0,0 +1,85 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000682831 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms
+
+Performance: 544341.699 tau/day, 1260.050 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59
+Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41
+Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21
+Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32
+Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34
+Other | | 0.000448 | | | 1.13
+
+Nlocal: 500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1946 ave 1946 max 1946 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 18820 ave 18820 max 18820 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.g++.4 b/examples/message/log.28Aug18.message.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..695b51f166e463afc9bb4136d57e91f4fa676143
--- /dev/null
+++ b/examples/message/log.28Aug18.message.g++.4
@@ -0,0 +1,85 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - no client/server mode
+
+variable x index 5
+variable y index 5
+variable z index 5
+
+units lj
+atom_style atomic
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 $x 0 $y 0 $z
+region box block 0 5 0 $y 0 $z
+region box block 0 5 0 5 0 $z
+region box block 0 5 0 5 0 5
+create_box 1 box
+Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 500 atoms
+ Time spent = 0.000656843 secs
+mass 1 1.0
+
+velocity all create 1.44 87287 loop geom
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nve
+# same with NPT
+#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
+
+thermo 10
+run 50
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 1.44 -6.7733681 0 -4.6176881 -5.0221006
+ 10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
+ 20 0.628166 -5.5624945 0 -4.62213 1.0186262
+ 30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
+ 40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
+ 50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
+Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms
+
+Performance: 1642350.242 tau/day, 3801.737 timesteps/s
+97.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71
+Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82
+Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41
+Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98
+Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14
+Other | | 0.0003865 | | | 2.94
+
+Nlocal: 125 ave 128 max 121 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 1091 ave 1094 max 1089 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs: 4705 ave 4849 max 4648 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 18820
+Ave neighs/atom = 37.64
+Neighbor list builds = 4
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.file.g++.1 b/examples/message/log.28Aug18.message.server.file.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..cf1418d3c5fdd5b4006470b353fe8e3c9609dd49
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.file.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.server.file.g++.4 b/examples/message/log.28Aug18.message.server.file.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c233bad692592ba370b9086626b156829951f81d
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.file.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md file tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:05
diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.1 b/examples/message/log.28Aug18.message.server.mpione.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..81e04aa9230b6e222d85ca8c0dbd6b71453d7ea3
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpione.g++.4 b/examples/message/log.28Aug18.message.server.mpione.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..a185cb1c29ff902ace0735a4da657dbb045bdb17
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpione.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..973a08eb6a571594b94d22efe5762097f651abb8
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..9e76e52d9034adf4826220aee6d95a94fbc85eae
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.mpitwo.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.1 b/examples/message/log.28Aug18.message.server.zmq.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..ce5729878b3cd2fd89b5638a1c1e317052b48151
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.1
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 1 by 1 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.server.zmq.g++.4 b/examples/message/log.28Aug18.message.server.zmq.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..b3201da4dad91007fea1224051d0938feccd08f9
--- /dev/null
+++ b/examples/message/log.28Aug18.message.server.zmq.g++.4
@@ -0,0 +1,44 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+atom_modify map yes
+
+lattice fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region box block 0 1 0 1 0 1
+create_box 1 box
+Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
+ 1 by 2 by 2 MPI processor grid
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 2.5
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 2 by 2 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Server MD calls = 51
+Server MD reneighborings 5
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a290ec307bb6a101348b023f9995f81fb9e2d740
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000485897 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 12374053.445 tau/day, 28643.642 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12
+Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89
+Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03
+Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15
+Other | | 0.04905 | | | 2.81
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..0089732355cd35c3dd08ace88fdec38404630670
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000453949 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 7638300.565 tau/day, 17681.251 timesteps/s
+100.0% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04
+Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89
+Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02
+Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41
+Other | | 0.07465 | | | 2.64
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..814b3df1aa8daaaf6fcb260f1e7bda9f1d7505b0
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000543118 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 4497356.047 tau/day, 10410.546 timesteps/s
+50.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07
+Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70
+Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02
+Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25
+Other | | 0.09449 | | | 1.97
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2 b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..7c172d3727935fe6fe3b3b73178f84e11823d64b
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000574827 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 3812643.232 tau/day, 8825.563 timesteps/s
+48.1% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03
+Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67
+Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01
+Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27
+Other | | 0.1146 | | | 2.02
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..f5e2f220cd852a8c70cd8a04e8585918656e6f17
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000530005 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0086399 0 1.3760711 6.8772078 0.61567613
+ 2000 1.0707188 0 1.3744107 6.628097 1.2313523
+ 3000 1.0627515 0 1.310096 6.1647179 1.8470284
+ 4000 0.94091054 0 1.268976 6.4723215 2.4627045
+ 5000 1.0218949 0 1.2430242 5.6945977 3.0783806
+ 6000 0.98649481 0 1.1997565 5.2870413 3.6940568
+ 7000 0.9047957 0 1.1461262 5.9291636 4.3097329
+ 8000 0.85697614 0 1.0437412 5.0652097 4.925409
+ 9000 0.84208329 0 1.109218 6.1749808 5.5410852
+ 10000 0.86418108 0 1.1594773 6.2581867 6.1567613
+ 11000 0.95136356 0 1.1650901 5.8389085 6.7724374
+ 12000 0.94571583 0 1.2210342 6.2498816 7.3881135
+ 13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
+ 14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
+ 15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
+ 16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
+ 17000 1.0306843 0 1.3101457 6.4750102 -4.925409
+ 18000 1.071154 0 1.2947547 5.695888 -4.3097329
+ 19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
+ 20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
+ 21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
+ 22000 0.98550707 0 1.1768148 5.019967 -1.8470284
+ 23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
+ 24000 0.94069959 0 1.184119 5.8434876 -0.61567613
+ 25000 0.91569312 0 1.1642118 5.668997 0
+ 26000 0.98882932 0 1.1999248 5.0115507 0.61567613
+ 27000 0.8972608 0 1.2556546 7.0837158 1.2313523
+ 28000 0.93554756 0 1.2221911 5.9302841 1.8470284
+ 29000 0.97894608 0 1.2168736 5.5766766 2.4627045
+ 30000 0.97877055 0 1.2575839 6.4308887 3.0783806
+ 31000 1.0002387 0 1.2338069 5.3873124 3.6940568
+ 32000 0.89608618 0 1.2382021 6.7892204 4.3097329
+ 33000 0.87439302 0 1.2252635 7.078134 4.925409
+ 34000 1.076102 0 1.2991393 5.5556892 5.5410852
+ 35000 1.0018689 0 1.272105 6.1320483 6.1567613
+ 36000 0.93327214 0 1.2428039 7.0030867 6.7724374
+ 37000 1.0770236 0 1.3002931 5.4996076 7.3881135
+ 38000 0.98715132 0 1.215562 5.5958335 -7.3881135
+ 39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
+ 40000 1.0445585 0 1.241151 5.3589806 -6.1567613
+ 41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
+ 42000 0.99231038 0 1.2228781 5.9363471 -4.925409
+ 43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
+ 44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
+ 45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
+ 46000 0.98701623 0 1.170581 4.9719567 -2.4627045
+ 47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
+ 48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
+ 49000 1.0187472 0 1.271608 5.3355092 -0.61567613
+ 50000 1.0194881 0 1.2831094 6.2449759 0
+Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 1666000.147 tau/day, 3856.482 timesteps/s
+23.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01
+Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16
+Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00
+Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28
+Other | | 0.07062 | | | 0.54
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5270
+Dangerous builds = 0
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2 b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
new file mode 100644
index 0000000000000000000000000000000000000000..8fc570f5da7b96a857715bbff46374cb4cd4ef1f
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
@@ -0,0 +1,130 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - client script
+
+variable mode index file
+
+if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
+message client md zmq localhost:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify sort 0 0.0 map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000673056 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+fix 3 all client/md
+fix_modify 3 energy yes
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 0
+ ghost atom cutoff = 0
+ binsize = 15.3919, bins = 1 1 1
+ 0 neighbor lists, perpetual/occasional/extra = 0 0 0
+Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.0876599 0 1.3637783 6.063363 0.61567613
+ 2000 1.0722996 0 1.4108622 7.0518942 1.2313523
+ 3000 1.0580774 0 1.3845895 6.0395275 1.8470284
+ 4000 1.0068006 0 1.3804387 7.0944598 2.4627045
+ 5000 0.95391814 0 1.2578438 6.1878831 3.0783806
+ 6000 0.93492945 0 1.2711287 7.0440517 3.6940568
+ 7000 0.94107853 0 1.2384371 6.1438077 4.3097329
+ 8000 0.89711744 0 1.145748 6.3558305 4.925409
+ 9000 0.90190304 0 1.0860684 4.957098 5.5410852
+ 10000 0.84255749 0 1.0376892 5.2351795 6.1567613
+ 11000 0.90250882 0 1.0497695 4.3844838 6.7724374
+ 12000 0.83461274 0 1.0281949 5.1534361 7.3881135
+ 13000 0.80315331 0 1.0226333 5.757222 -7.3881135
+ 14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
+ 15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
+ 16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
+ 17000 0.98268136 0 1.2086981 5.6302847 -4.925409
+ 18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
+ 19000 1.0795086 0 1.4562691 7.639418 -3.6940568
+ 20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
+ 21000 1.2424296 0 1.6048792 7.959585 -2.4627045
+ 22000 1.297169 0 1.7421262 8.9432388 -1.8470284
+ 23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
+ 24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
+ 25000 1.3339728 0 1.6883255 7.529098 0
+ 26000 1.1483243 0 1.5155578 7.3869994 0.61567613
+ 27000 1.1372606 0 1.4368323 7.0580136 1.2313523
+ 28000 1.0518579 0 1.355311 6.478857 1.8470284
+ 29000 1.0581145 0 1.2535509 5.3697479 2.4627045
+ 30000 0.93612564 0 1.185532 5.5520142 3.0783806
+ 31000 0.94387516 0 1.1716454 5.8655485 3.6940568
+ 32000 0.83953515 0 1.0737746 5.5551953 4.3097329
+ 33000 0.84862926 0 1.0564042 5.7795428 4.925409
+ 34000 0.83621877 0 1.079387 5.7514243 5.5410852
+ 35000 0.86938506 0 1.031783 4.5897825 6.1567613
+ 36000 0.88990609 0 1.0807597 5.3751744 6.7724374
+ 37000 0.89534631 0 1.1238882 5.2400355 7.3881135
+ 38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
+ 39000 0.96737778 0 1.2472934 6.1139 -6.7724374
+ 40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
+ 41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
+ 42000 1.0875422 0 1.3963739 7.1208066 -4.925409
+ 43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
+ 44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
+ 45000 1.1243261 0 1.432186 6.884782 -3.0783806
+ 46000 1.039713 0 1.4389721 7.5585257 -2.4627045
+ 47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
+ 48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
+ 49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
+ 50000 0.92367087 0 1.1875669 6.4685214 0
+Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms
+
+Performance: 1586733.497 tau/day, 3672.994 timesteps/s
+59.3% CPU use with 2 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0 | 0 | 0 | 0.0 | 0.00
+Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01
+Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21
+Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00
+Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04
+Other | | 0.0994 | | | 0.73
+
+Nlocal: 80 ave 80 max 80 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Nghost: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 5257
+Dangerous builds = 0
+Total wall time: 0:00:13
diff --git a/examples/message/log.28Aug18.message.tilt.g++.1 b/examples/message/log.28Aug18.message.tilt.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..3f7cfc9da01d9b125b581c2a6ef7cf74aa7242a0
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.1
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000437021 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 18673426.371 tau/day, 43225.524 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66
+Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10
+Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85
+Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05
+Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42
+Other | | 0.05684 | | | 4.91
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.g++.4 b/examples/message/log.28Aug18.message.tilt.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..74061463f6bdb67be6356b4ec7d0a66635aef989
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.g++.4
@@ -0,0 +1,129 @@
+LAMMPS (22 Aug 2018)
+# 2d NEMD simulation - no client/server mode
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000396967 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+thermo_style custom step temp epair etotal press xy
+
+thermo 1000
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair TotEng Press Xy
+ 0 1.44 0 1.431 1.2080502 0
+ 1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
+ 2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
+ 3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
+ 4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
+ 5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
+ 6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
+ 7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
+ 8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
+ 9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
+ 10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
+ 11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
+ 12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
+ 13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
+ 14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
+ 15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
+ 16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
+ 17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
+ 18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
+ 19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
+ 20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
+ 21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
+ 22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
+ 23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
+ 24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
+ 25000 1.0946409 0.33366032 1.4214597 7.1907559 0
+ 26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
+ 27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
+ 28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
+ 29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
+ 30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
+ 31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
+ 32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
+ 33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
+ 34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
+ 35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
+ 36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
+ 37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
+ 38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
+ 39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
+ 40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
+ 41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
+ 42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
+ 43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
+ 44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
+ 45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
+ 46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
+ 47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
+ 48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
+ 49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
+ 50000 1.0566272 0.28657142 1.3365947 6.261203 0
+Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 23312793.646 tau/day, 53964.800 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26
+Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81
+Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87
+Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07
+Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98
+Other | | 0.0465 | | | 5.02
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 362 ave 362 max 362 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 362
+Ave neighs/atom = 2.2625
+Neighbor list builds = 5256
+Dangerous builds = 0
+Total wall time: 0:00:00
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..428ff346ad47e960e6cd188a3a4dc9e42d8d14a6
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000438929 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:01
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..3da50163eda27b4109997a41f08feacacce43bfe
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpione.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/one
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000455141 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:02
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..fc29a6da63fcce1e90b225802b48be7f2468ab46
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000521898 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:04
diff --git a/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4 b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..758b84fe9d45d811eb7051aae852e49eb5ab9ffc
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.mpitwo.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md mpi/two tmp.couple
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000378847 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:06
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..78526ba74895f2ea873ece689faa73da78e984a8
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000557184 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 1 by 1 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5073
+Total wall time: 0:00:12
diff --git a/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4 b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..b1ad7684708ceaad098d090f58985756ba4adc90
--- /dev/null
+++ b/examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
@@ -0,0 +1,48 @@
+LAMMPS (22 Aug 2018)
+# 3d Lennard-Jones melt - server script
+
+variable mode index file
+
+if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
+message server md zmq *:5555
+
+units lj
+atom_style atomic
+dimension 2
+atom_modify map yes
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000586987 secs
+mass * 1.0 # masses not used by server
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1 check yes
+
+server md
+ 2 by 2 by 1 MPI processor grid
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.3
+ ghost atom cutoff = 1.3
+ binsize = 0.65, bins = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Server MD calls = 50001
+Server MD reneighborings 5066
+Total wall time: 0:00:13
diff --git a/lib/README b/lib/README
index 3c8f46dd0a957162660045fc76caeafceb03adec..12c27b2a397d7b0fd9c7f90819774615e5900deb 100644
--- a/lib/README
+++ b/lib/README
@@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package
from Axel Kohlmeyer (Temple U)
meam modified embedded atom method (MEAM) potential, MEAM package
from Greg Wagner (Sandia)
+message client/server communication library via MPI, sockets, files
+ from Steve Plimpton (Sandia)
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
from Axel Kohlmeyer (Temple U) and the VMD development team
mscg hooks to the MSCG library, used by fix_mscg command
diff --git a/lib/message/Install.py b/lib/message/Install.py
new file mode 100644
index 0000000000000000000000000000000000000000..d3f31c986fba19e9d3fd476ad71c0e14c6616c0f
--- /dev/null
+++ b/lib/message/Install.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+# Install.py tool to build the CSlib library
+# used to automate the steps described in the README file in this dir
+
+from __future__ import print_function
+import sys,os,re,subprocess
+
+# help message
+
+help = """
+Syntax from src dir: make lib-message args="-m"
+ or: make lib-message args="-s -z"
+Syntax from lib dir: python Install.py -m
+ or: python Install.py -s -z
+
+specify zero or more options, order does not matter
+
+ -m = parallel build of CSlib library
+ -s = serial build of CSlib library
+ -z = build CSlib library with ZMQ socket support, default = no ZMQ support
+
+Example:
+
+make lib-message args="-m -z" # build parallel CSlib with ZMQ support
+make lib-message args="-s" # build serial CSlib with no ZMQ support
+"""
+
+# print error message or help
+
+def error(str=None):
+ if not str: print(help)
+ else: print("ERROR",str)
+ sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+
+def fullpath(path):
+ return os.path.abspath(os.path.expanduser(path))
+
+def which(program):
+ def is_exe(fpath):
+ return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+ fpath, fname = os.path.split(program)
+ if fpath:
+ if is_exe(program):
+ return program
+ else:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ exe_file = os.path.join(path, program)
+ if is_exe(exe_file):
+ return exe_file
+
+ return None
+
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+mpiflag = False
+serialflag = False
+zmqflag = False
+
+iarg = 0
+while iarg < nargs:
+ if args[iarg] == "-m":
+ mpiflag = True
+ iarg += 1
+ elif args[iarg] == "-s":
+ serialflag = True
+ iarg += 1
+ elif args[iarg] == "-z":
+ zmqflag = True
+ iarg += 1
+ else: error()
+
+if (not mpiflag and not serialflag):
+ error("Must use either -m or -s flag")
+
+if (mpiflag and serialflag):
+ error("Cannot use -m and -s flag at the same time")
+
+# build CSlib
+# copy resulting lib to cslib/src/libmessage.a
+# copy appropriate Makefile.lammps.* to Makefile.lammps
+
+print("Building CSlib ...")
+srcdir = fullpath("./cslib/src")
+
+if mpiflag and zmqflag:
+ cmd = "cd %s; make lib_parallel" % srcdir
+elif mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_parallel zmq=no" % srcdir
+elif not mpiflag and zmqflag:
+ cmd = "cd %s; make lib_serial" % srcdir
+elif not mpiflag and not zmqflag:
+ cmd = "cd %s; make lib_serial zmq=no" % srcdir
+
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir
+else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
+
+if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps"
+else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps"
+print(cmd)
+txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+print(txt.decode('UTF-8'))
diff --git a/lib/message/Makefile.lammps.nozmq b/lib/message/Makefile.lammps.nozmq
new file mode 100644
index 0000000000000000000000000000000000000000..1bb10cc98876d90ca1e34941451165fab7a51573
--- /dev/null
+++ b/lib/message/Makefile.lammps.nozmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB =
+message_SYSPATH =
diff --git a/lib/message/Makefile.lammps.zmq b/lib/message/Makefile.lammps.zmq
new file mode 100644
index 0000000000000000000000000000000000000000..759f2ce04b9ac229beb590d4fad8e861585591e8
--- /dev/null
+++ b/lib/message/Makefile.lammps.zmq
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+message_SYSINC =
+message_SYSLIB = -lzmq
+message_SYSPATH =
diff --git a/lib/message/README b/lib/message/README
new file mode 100644
index 0000000000000000000000000000000000000000..dafb94e9eff621f0b7a7782751f0bc91296d33b0
--- /dev/null
+++ b/lib/message/README
@@ -0,0 +1,51 @@
+This directory contains the CSlib library which is required
+to use the MESSAGE package and its client/server commands
+in a LAMMPS input script.
+
+The CSlib libary is included in the LAMMPS distribution. A fuller
+version including documentation and test programs is available at
+http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia
+National Laboratories.
+
+You can type "make lib-message" from the src directory to see help on
+how to build this library via make commands, or you can do the same
+thing by typing "python Install.py" from within this directory, or you
+can do it manually by following the instructions below.
+
+The CSlib can be optionally built with support for sockets using
+the open-source ZeroMQ (ZMQ) library. If it is not installed
+on your system, it is easy to download and install.
+
+Go to the ZMQ website for details: http://zeromq.org
+
+-----------------
+
+Instructions:
+
+1. Compile CSlib from within cslib/src with one of the following:
+ % make lib_parallel # build parallel library with ZMQ socket support
+ % make lib_serial # build serial library with ZMQ support
+ % make lib_parallel zmq=no # build parallel lib with no ZMQ support
+ % make lib_serial zmq=no # build serial lib with no ZMQ support
+
+2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to
+ cslib/src/libmessage.a
+
+3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq
+ to lib/message/Makefile.lammps, depending on whether you
+ build the library with ZMQ support or not.
+ If your ZMQ library is not in a place your shell path finds,
+ you can set the INCLUDE and PATH variables in Makefile.lammps
+ to point to the dirs where the ZMQ include and library files are.
+
+-----------------
+
+When these steps are complete you can build LAMMPS
+with the MESSAGAE package installed:
+
+% cd lammps/src
+% make yes-message
+% make mpi (or whatever target you wish)
+
+Note that if you download and unpack a new LAMMPS tarball, you will
+need to re-build the CSlib in this dir.
diff --git a/lib/message/cslib/LICENSE b/lib/message/cslib/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..7a36e21daf9120d3f5f49b25d70321cdd28a73c6
--- /dev/null
+++ b/lib/message/cslib/LICENSE
@@ -0,0 +1,32 @@
+Program: CSlib client/server coupling library
+
+Copyright 2018 National Technology & Engineering Solutions of Sandia,
+LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
+U.S. Government retains certain rights in this software. This
+software is distributed under the modified Berkeley Software
+Distribution (BSD) License.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+* Neither the name of Sandia Corporation nor the names of contributors
+ to this software may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/lib/message/cslib/README b/lib/message/cslib/README
new file mode 100644
index 0000000000000000000000000000000000000000..37f4a97d54b3293c64f94bc09969256bee5a6015
--- /dev/null
+++ b/lib/message/cslib/README
@@ -0,0 +1,23 @@
+This is the the Client/Server messaging library (CSlib).
+
+Only the source directory and license file are included here as part
+of the LAMMPS distribution. The full CSlib distribution, including
+documentation and test codes, can be found at the website:
+http://cslib.sandia.gov (as of Aug 2018).
+
+The contact author is
+
+Steve Plimpton
+Sandia National Laboratories
+sjplimp@sandia.gov
+http://www.sandia.gov/~sjplimp
+
+The CSlib is distributed as open-source code under the modified
+Berkeley Software Distribution (BSD) License. See the accompanying
+LICENSE file.
+
+This directory contains the following:
+
+README this file
+LICENSE GNU LGPL license
+src source files for library
diff --git a/lib/message/cslib/src/Makefile b/lib/message/cslib/src/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..83cf902220da9e68240bbf72b5e48423d5756f1a
--- /dev/null
+++ b/lib/message/cslib/src/Makefile
@@ -0,0 +1,107 @@
+# Makefile for CSlib = client/server messaging library
+# type "make help" for options
+
+SHELL = /bin/sh
+
+# ----------------------------------------
+# should only need to change this section
+# compiler/linker settings
+# ----------------------------------------
+
+CC = g++
+CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI)
+SHFLAGS = -fPIC
+ARCHIVE = ar
+ARCHFLAGS = -rc
+SHLIBFLAGS = -shared
+
+# files
+
+LIB = libcsmpi.a
+SHLIB = libcsmpi.so
+SRC = $(wildcard *.cpp)
+INC = $(wildcard *.h)
+OBJ = $(SRC:.cpp=.o)
+
+# build with ZMQ support or not
+
+zmq = yes
+ZMQ = $(shell echo $(zmq) | tr a-z A-Z)
+
+ifeq ($(ZMQ),YES)
+ ZMQLIB = -lzmq
+else
+ CCFLAGS += -I./STUBS_ZMQ
+endif
+
+# build with MPI support or not
+
+mpi = yes
+MPI = $(shell echo $(mpi) | tr a-z A-Z)
+
+ifeq ($(MPI),YES)
+ CC = mpicxx
+else
+ CCFLAGS += -I./STUBS_MPI
+ LIB = libcsnompi.a
+ SHLIB = libcsnompi.so
+endif
+
+# targets
+
+shlib: shlib_parallel shlib_serial
+
+lib: lib_parallel lib_serial
+
+all: shlib lib
+
+help:
+ @echo 'make default = shlib'
+ @echo 'make shlib build 2 shared CSlibs: parallel & serial'
+ @echo 'make lib build 2 static CSlibs: parallel & serial'
+ @echo 'make all build 4 CSlibs: shlib and lib'
+ @echo 'make shlib_parallel build shared parallel CSlib'
+ @echo 'make shlib_serial build shared serial CSlib'
+ @echo 'make lib_parallel build static parallel CSlib'
+ @echo 'make lib_serial build static serial CSlib'
+ @echo 'make ... zmq=no build w/out ZMQ support'
+ @echo 'make clean remove all *.o files'
+ @echo 'make clean-all remove *.o and lib files'
+ @echo 'make tar create a tarball, 2 levels up'
+
+shlib_parallel:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=yes
+
+shlib_serial:
+ $(MAKE) clean
+ $(MAKE) shared zmq=$(zmq) mpi=no
+
+lib_parallel:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=yes
+
+lib_serial:
+ $(MAKE) clean
+ $(MAKE) static zmq=$(zmq) mpi=no
+
+static: $(OBJ)
+ $(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ)
+
+shared: $(OBJ)
+ $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB)
+
+clean:
+ @rm -f *.o *.pyc
+
+clean-all:
+ @rm -f *.o *.pyc lib*.a lib*.so
+
+tar:
+ cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \
+ cslib/doc cslib/src cslib/test
+
+# rules
+
+%.o:%.cpp
+ $(CC) $(CCFLAGS) $(SHFLAGS) -c $<
diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi.h
new file mode 100644
index 0000000000000000000000000000000000000000..2919e4c3a2f8810ba99c303e6748271b0dae229c
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_MPI/mpi.h
@@ -0,0 +1,96 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// MPI constants and dummy functions
+
+#ifndef MPI_DUMMY_H
+#define MPI_DUMMY_H
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+
+namespace CSLIB_NS {
+
+typedef int MPI_Comm;
+typedef int MPI_Fint;
+typedef int MPI_Datatype;
+typedef int MPI_Status;
+typedef int MPI_Op;
+typedef int MPI_Info;
+
+#define MPI_COMM_WORLD 0
+#define MPI_MAX_PORT_NAME 0
+#define MPI_INFO_NULL 0
+#define MPI_INT 1
+#define MPI_LONG_LONG 2
+#define MPI_FLOAT 3
+#define MPI_DOUBLE 4
+#define MPI_CHAR 5
+#define MPI_SUM 0
+
+static void MPI_Init(int *, char ***) {}
+static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;}
+static void MPI_Comm_rank(MPI_Comm, int *) {}
+static void MPI_Comm_size(MPI_Comm, int *) {}
+
+static void MPI_Open_port(MPI_Info, char *) {}
+static void MPI_Close_port(const char *) {}
+static void MPI_Comm_accept(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+static void MPI_Comm_connect(const char *, MPI_Info, int,
+ MPI_Comm, MPI_Comm *) {}
+
+static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {}
+static void MPI_Comm_free(MPI_Comm *) {}
+
+static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {}
+static void MPI_Recv(void *, int, MPI_Datatype, int, int,
+ MPI_Comm, MPI_Status *) {}
+
+static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type,
+ MPI_Op op, MPI_Comm)
+{
+ if (type == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype,
+ MPI_Op op,MPI_Comm)
+{
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+
+static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {}
+static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype,
+ void *out, int, MPI_Datatype, MPI_Comm)
+{
+ // assuming incount = 1
+ if (intype == MPI_INT) *((int *) out) = *((int *) in);
+}
+static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype,
+ void *out, const int *, const int *,
+ MPI_Datatype, MPI_Comm)
+{
+ if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int));
+ else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t));
+ else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float));
+ else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double));
+ else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char));
+}
+
+static void MPI_Abort(MPI_Comm, int) {exit(1);}
+static void MPI_Finalize() {}
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/STUBS_ZMQ/zmq.h b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
new file mode 100644
index 0000000000000000000000000000000000000000..2f02eb4035c75cab753f430c3a31810c961d4702
--- /dev/null
+++ b/lib/message/cslib/src/STUBS_ZMQ/zmq.h
@@ -0,0 +1,36 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// ZMQ constants and dummy functions
+
+#ifndef ZMQ_DUMMY_H
+#define ZMQ_DUMMY_H
+
+namespace CSLIB_NS {
+
+#define ZMQ_REQ 0
+#define ZMQ_REP 0
+
+static void *zmq_ctx_new() {return NULL;}
+static void *zmq_connect(void *, char *) {return NULL;}
+static int zmq_bind(void *, char *) {return 0;}
+static void *zmq_socket(void *,int) {return NULL;}
+static void zmq_close(void *) {}
+static void zmq_ctx_destroy(void *) {}
+static void zmq_send(void *, void *, int, int) {}
+static void zmq_recv(void *, void *, int, int) {}
+
+};
+
+#endif
diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..874333607e5af076a4b6c73959127bbc7f2c9653
--- /dev/null
+++ b/lib/message/cslib/src/cslib.cpp
@@ -0,0 +1,768 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include "cslib.h"
+#include "msg_file.h"
+#include "msg_zmq.h"
+#include "msg_mpi_one.h"
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+#define MAXTYPE 5 // # of defined field data types
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm)
+{
+ if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm);
+ else myworld = 0;
+
+#ifdef MPI_NO
+ if (pcomm)
+ error_all("constructor(): CSlib invoked with MPI_Comm "
+ "but built w/out MPI support");
+#endif
+#ifdef MPI_YES // NOTE: this could be OK to allow ??
+ // would allow a parallel app to invoke CSlib
+ // in parallel and/or in serial
+ if (!pcomm)
+ error_all("constructor(): CSlib invoked w/out MPI_Comm "
+ "but built with MPI support");
+#endif
+
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+ else error_all("constructor(): Invalid client/server arg");
+
+ if (pcomm == NULL) {
+ me = 0;
+ nprocs = 1;
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr);
+ else if (strcmp(mode,"mpi/one") == 0)
+ error_all("constructor(): No mpi/one mode for serial lib usage");
+ else if (strcmp(mode,"mpi/two") == 0)
+ error_all("constructor(): No mpi/two mode for serial lib usage");
+ else error_all("constructor(): Unknown mode");
+
+ } else if (pcomm) {
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world);
+ else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world);
+ else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world);
+ else error_all("constructor(): Unknown mode");
+ }
+
+ maxfield = 0;
+ fieldID = fieldtype = fieldlen = fieldoffset = NULL;
+ maxheader = 0;
+ header = NULL;
+ maxbuf = 0;
+ buf = NULL;
+
+ recvcounts = displs = NULL;
+ maxglobal = 0;
+ allids = NULL;
+ maxfieldbytes = 0;
+ fielddata = NULL;
+
+ pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+CSlib::~CSlib()
+{
+ deallocate_fields();
+ sfree(header);
+ sfree(buf);
+
+ sfree(recvcounts);
+ sfree(displs);
+ sfree(allids);
+ sfree(fielddata);
+
+ delete msg;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send(int msgID_caller, int nfield_caller)
+{
+ if (nfield_caller < 0) error_all("send(): Invalid nfield");
+
+ msgID = msgID_caller;
+ nfield = nfield_caller;
+ allocate_fields();
+
+ fieldcount = 0;
+ nbuf = 0;
+
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int(int id, int value)
+{
+ pack(id,1,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_int64(int id, int64_t value)
+{
+ pack(id,2,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_float(int id, float value)
+{
+ pack(id,3,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_double(int id, double value)
+{
+ pack(id,4,1,&value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_string(int id, char *value)
+{
+ pack(id,5,strlen(value)+1,value);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack(int id, int ftype, int flen, void *data)
+{
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype");
+ if (flen < 0) error_all("pack(): Invalid flen");
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ memcpy(&buf[nbuf],data,nbytes);
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::pack_parallel(int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ if (find_field(id,fieldcount) >= 0)
+ error_all("pack_parallel(): Reuse of field ID");
+ if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype");
+ if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ // NOTE: check for overflow of maxglobal and flen
+
+ int nglobal;
+ MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world);
+ int flen = nper*nglobal;
+
+ fieldID[fieldcount] = id;
+ fieldtype[fieldcount] = ftype;
+ fieldlen[fieldcount] = flen;
+
+ // nlocal datums, each of nper length, from all procs
+ // final data in buf = datums for all natoms, ordered by ids
+
+ if (recvcounts == NULL) {
+ recvcounts = (int *) smalloc(nprocs*sizeof(int));
+ displs = (int *) smalloc(nprocs*sizeof(int));
+ }
+
+ MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ if (ids && nglobal > maxglobal) {
+ sfree(allids);
+ maxglobal = nglobal;
+ // NOTE: maxglobal*sizeof(int) could overflow int
+ allids = (int *) smalloc(maxglobal*sizeof(int));
+ }
+
+ MPI_Allgatherv(ids,nlocal,MPI_INT,allids,
+ recvcounts,displs,MPI_INT,world);
+
+ int nlocalsize = nper*nlocal;
+ MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world);
+
+ displs[0] = 0;
+ for (int iproc = 1; iproc < nprocs; iproc++)
+ displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
+
+ int nbytes,nbytesround;
+ onefield(ftype,flen,nbytes,nbytesround);
+
+ if (ftype == 1) {
+ int *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int *) fielddata;
+ } else alldata = (int *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata,
+ recvcounts,displs,MPI_INT,world);
+ if (ids) {
+ int *bufptr = (int *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 2) {
+ int64_t *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (int64_t *) fielddata;
+ } else alldata = (int64_t *) &buf[nbuf];
+ // NOTE: may be just MPI_LONG on some machines
+ MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata,
+ recvcounts,displs,MPI_LONG_LONG,world);
+ if (ids) {
+ int64_t *bufptr = (int64_t *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 3) {
+ float *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (float *) fielddata;
+ } else alldata = (float *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata,
+ recvcounts,displs,MPI_FLOAT,world);
+ if (ids) {
+ float *bufptr = (float *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ } else if (ftype == 4) {
+ double *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (double *) fielddata;
+ } else alldata = (double *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata,
+ recvcounts,displs,MPI_DOUBLE,world);
+ if (ids) {
+ double *bufptr = (double *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ if (nper == 1) bufptr[j] = alldata[m++];
+ else
+ for (k = 0; k < nper; k++)
+ bufptr[j++] = alldata[m++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (ftype == 5) {
+ char *alldata;
+ if (ids) {
+ if (nbytes > maxfieldbytes) {
+ sfree(fielddata);
+ maxfieldbytes = nbytes;
+ fielddata = (char *) smalloc(maxfieldbytes);
+ }
+ alldata = (char *) fielddata;
+ } else alldata = (char *) &buf[nbuf];
+ MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata,
+ recvcounts,displs,MPI_CHAR,world);
+ if (ids) {
+ char *bufptr = (char *) &buf[nbuf];
+ m = 0;
+ for (i = 0; i < nglobal; i++) {
+ j = (allids[i]-1) * nper;
+ memcpy(&bufptr[j],&alldata[m],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+
+ memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
+ nbuf += nbytesround;
+
+ fieldcount++;
+ if (fieldcount == nfield) send_message();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::send_message()
+{
+ // setup header message
+
+ int m = 0;
+ header[m++] = msgID;
+ header[m++] = nfield;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ header[m++] = fieldID[ifield];
+ header[m++] = fieldtype[ifield];
+ header[m++] = fieldlen[ifield];
+ }
+
+ msg->send(nheader,header,nbuf,buf);
+ nsend++;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::recv(int &nfield_caller, int *&fieldID_caller,
+ int *&fieldtype_caller, int *&fieldlen_caller)
+{
+ msg->recv(maxheader,header,maxbuf,buf);
+ nrecv++;
+
+ // unpack header message
+
+ int m = 0;
+ msgID = header[m++];
+ nfield = header[m++];
+ allocate_fields();
+
+ int nbytes,nbytesround;
+
+ nbuf = 0;
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ fieldID[ifield] = header[m++];
+ fieldtype[ifield] = header[m++];
+ fieldlen[ifield] = header[m++];
+ fieldoffset[ifield] = nbuf;
+ onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround);
+ nbuf += nbytesround;
+ }
+
+ // return message parameters
+
+ nfield_caller = nfield;
+ fieldID_caller = fieldID;
+ fieldtype_caller = fieldtype;
+ fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::unpack_int(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int(): Unknown field ID");
+ if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1");
+
+ int *ptr = (int *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int64_t CSlib::unpack_int64(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_int64(): Unknown field ID");
+ if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1");
+
+ int64_t *ptr = (int64_t *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+float CSlib::unpack_float(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_float(): Unknown field ID");
+ if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1");
+
+ float *ptr = (float *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double CSlib::unpack_double(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_double(): Unknown field ID");
+ if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype");
+ if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1");
+
+ double *ptr = (double *) unpack(id);
+ return *ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+char *CSlib::unpack_string(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_string(): Unknown field ID");
+ if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype");
+
+ char *ptr = (char *) unpack(id);
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::unpack(int id)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+ return &buf[fieldoffset[ifield]];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack(int id, void *data)
+{
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack(): Unknown field ID");
+
+ int ftype = fieldtype[ifield];
+ int nbytes = fieldlen[ifield];
+ if (ftype == 1) nbytes *= sizeof(int);
+ else if (ftype == 2) nbytes *= sizeof(int64_t);
+ else if (ftype == 3) nbytes *= sizeof(float);
+ else if (ftype == 4) nbytes *= sizeof(double);
+ memcpy(data,&buf[fieldoffset[ifield]],nbytes);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data)
+{
+ int i,j,k,m;
+
+ int ifield = find_field(id,nfield);
+ if (ifield < 0) error_all("unpack_parallel(): Unknown field ID");
+ if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal");
+ if (nper < 1) error_all("pack_parallel(): Invalid nper");
+
+ MPI_Comm world = (MPI_Comm) myworld;
+
+ int upto;
+ if (!ids) {
+ MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world);
+ upto -= nlocal;
+ }
+
+ if (fieldtype[ifield] == 1) {
+ int *local = (int *) data;
+ int *global = (int *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 2) {
+ int64_t *local = (int64_t *) data;
+ int64_t *global = (int64_t *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 3) {
+ float *local = (float *) data;
+ float *global = (float *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ } else if (fieldtype[ifield] == 4) {
+ double *local = (double *) data;
+ double *global = (double *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ if (nper == 1) local[m++] = global[j];
+ else
+ for (k = 0; k < nper; k++)
+ local[m++] = global[j++];
+ }
+ }
+
+ /* eventually ftype = BYTE, but not yet
+ } else if (fieldtype[ifield] == 5) {
+ char *local = (char *) data;
+ char *global = (char *) &buf[fieldoffset[ifield]];
+ if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char));
+ else {
+ m = 0;
+ for (i = 0; i < nlocal; i++) {
+ j = (ids[i]-1) * nper;
+ memcpy(&local[m],&global[j],nper);
+ m += nper;
+ }
+ }
+ */
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::extract(int flag)
+{
+ if (flag == 1) return nsend;
+ if (flag == 2) return nrecv;
+ error_all("extract(): Invalid flag");
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround)
+{
+ int64_t bigbytes,bigbytesround;
+ int64_t biglen = flen;
+
+ if (ftype == 1) bigbytes = biglen * sizeof(int);
+ else if (ftype == 2) bigbytes = biglen * sizeof(int64_t);
+ else if (ftype == 3) bigbytes = biglen * sizeof(float);
+ else if (ftype == 4) bigbytes = biglen * sizeof(double);
+ else if (ftype == 5) bigbytes = biglen * sizeof(char);
+ bigbytesround = roundup(bigbytes,8);
+
+ if (nbuf + bigbytesround > INT_MAX)
+ error_all("pack(): Message size exceeds 32-bit integer limit");
+
+ nbytes = (int) bigbytes;
+ nbytesround = (int) bigbytesround;
+ if (nbuf + nbytesround > maxbuf) {
+ maxbuf = nbuf + nbytesround;
+ buf = (char *) srealloc(buf,maxbuf);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int CSlib::find_field(int id, int n)
+{
+ int ifield;
+ for (ifield = 0; ifield < n; ifield++)
+ if (id == fieldID[ifield]) return ifield;
+ return -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::allocate_fields()
+{
+ int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int);
+ if (bigbytes > INT_MAX)
+ error_all("send(): Message header size exceeds 32-bit integer limit");
+
+ nheader = 2;
+ nheader += 3 * nfield;
+
+ if (nfield > maxfield) {
+ deallocate_fields();
+ maxfield = nfield;
+ fieldID = new int[maxfield];
+ fieldtype = new int[maxfield];
+ fieldlen = new int[maxfield];
+ fieldoffset = new int[maxfield];
+ }
+
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::deallocate_fields()
+{
+ delete [] fieldID;
+ delete [] fieldtype;
+ delete [] fieldlen;
+ delete [] fieldoffset;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *CSlib::srealloc(void *ptr, int nbytes)
+{
+ if (nbytes == 0) {
+ sfree(ptr);
+ return NULL;
+ }
+
+ ptr = realloc(ptr,nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes);
+ error_one(str);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CSlib::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Comm world = (MPI_Comm) myworld;
+ MPI_Abort(world,1);
+}
+
+/* ----------------------------------------------------------------------
+ round N up to multiple of nalign and return it
+ NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t
+------------------------------------------------------------------------- */
+
+int64_t CSlib::roundup(int64_t n, int nalign)
+{
+ if (n % nalign == 0) return n;
+ n = (n/nalign + 1) * nalign;
+ return n;
+}
diff --git a/lib/message/cslib/src/cslib.h b/lib/message/cslib/src/cslib.h
new file mode 100644
index 0000000000000000000000000000000000000000..b4da9680268729c9ca75e29ebe73eac1c5b0522c
--- /dev/null
+++ b/lib/message/cslib/src/cslib.h
@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef CSLIB_H
+#define CSLIB_H
+
+#include <stdint.h>
+
+namespace CSLIB_NS {
+
+class CSlib {
+ public:
+ int nsend,nrecv;
+
+ CSlib(int, const char *, const void *, const void *);
+ ~CSlib();
+
+ void send(int, int);
+
+ void pack_int(int, int);
+ void pack_int64(int, int64_t);
+ void pack_float(int, float);
+ void pack_double(int, double);
+ void pack_string(int, char *);
+ void pack(int, int, int, void *);
+ void pack_parallel(int, int, int, int *, int, void *);
+
+ int recv(int &, int *&, int *&, int *&);
+
+ int unpack_int(int);
+ int64_t unpack_int64(int);
+ float unpack_float(int);
+ double unpack_double(int);
+ char *unpack_string(int);
+ void *unpack(int);
+ void unpack(int, void *);
+ void unpack_parallel(int, int, int *, int, void *);
+
+ int extract(int);
+
+ private:
+ uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file
+ // so apps can include this file w/ no MPI on system
+ int me,nprocs;
+ int client,server;
+ int nfield,maxfield;
+ int msgID,fieldcount;
+ int nheader,maxheader;
+ int nbuf,maxbuf;
+ int maxglobal,maxfieldbytes;
+ int *fieldID,*fieldtype,*fieldlen,*fieldoffset;
+ int *header;
+ int *recvcounts,*displs; // nprocs size for Allgathers
+ int *allids; // nglobal size for pack_parallel()
+ char *buf; // maxbuf size for msg with all fields
+ char *fielddata; // maxfieldbytes size for one global field
+ const char *pad;
+
+ class Msg *msg;
+
+ void send_message();
+ void onefield(int, int, int &, int &);
+ int find_field(int, int);
+ void allocate_fields();
+ void deallocate_fields();
+ int64_t roundup(int64_t, int);
+ void *smalloc(int);
+ void *srealloc(void *, int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/cslib.py b/lib/message/cslib/src/cslib.py
new file mode 100644
index 0000000000000000000000000000000000000000..0ba3516255a4f7f3f54d98dc02279db29a91698a
--- /dev/null
+++ b/lib/message/cslib/src/cslib.py
@@ -0,0 +1,362 @@
+# ------------------------------------------------------------------------
+# CSlib - Client/server library for code coupling
+# http://cslib.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright 2018 National Technology & Engineering Solutions of
+# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+# NTESS, the U.S. Government retains certain rights in this software.
+# This software is distributed under the modified Berkeley Software
+# Distribution (BSD) License.
+#
+# See the README file in the top-level CSlib directory.
+# -------------------------------------------------------------------------
+
+# Python wrapper on CSlib library via ctypes
+
+# ctypes and Numpy data types:
+# 32-bit int = c_int = np.intc = np.int32
+# 64-bit int = c_longlong = np.int64
+# 32-bit floating point = c_float = np.float32
+# 64-bit floating point = c_double = np.float = np.float64
+
+import sys,traceback
+from ctypes import *
+
+# Numpy and mpi4py packages may not exist
+
+try:
+ import numpy as np
+ numpyflag = 1
+except:
+ numpyflag = 0
+
+try:
+ from mpi4py import MPI
+ mpi4pyflag = 1
+except:
+ mpi4pyflag = 0
+
+# wrapper class
+
+class CSlib:
+
+ # instantiate CSlib thru its C-interface
+
+ def __init__(self,csflag,mode,ptr,comm):
+
+ # load libcslib.so
+
+ try:
+ if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL)
+ else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL)
+ except:
+ etype,value,tb = sys.exc_info()
+ traceback.print_exception(etype,value,tb)
+ raise OSError,"Could not load CSlib dynamic library"
+
+ # define ctypes API for each library method
+
+ self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p,
+ POINTER(c_void_p)]
+ self.lib.cslib_open.restype = None
+
+ self.lib.cslib_close.argtypes = [c_void_p]
+ self.lib.cslib_close.restype = None
+
+ self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_send.restype = None
+
+ self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int]
+ self.lib.cslib_pack_int.restype = None
+
+ self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong]
+ self.lib.cslib_pack_int64.restype = None
+
+ self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float]
+ self.lib.cslib_pack_float.restype = None
+
+ self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double]
+ self.lib.cslib_pack_double.restype = None
+
+ self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p]
+ self.lib.cslib_pack_string.restype = None
+
+ self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p]
+ self.lib.cslib_pack.restype = None
+
+ self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_pack_parallel.restype = None
+
+ self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int)),
+ POINTER(POINTER(c_int))]
+ self.lib.cslib_recv.restype = c_int
+
+ self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int.restype = c_int
+
+ self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_int64.restype = c_longlong
+
+ self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_float.restype = c_float
+
+ self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_double.restype = c_double
+
+ self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack_string.restype = c_char_p
+
+ # override return in unpack()
+ self.lib.cslib_unpack.argtypes = [c_void_p,c_int]
+ self.lib.cslib_unpack.restype = c_void_p
+
+ self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p]
+ self.lib.cslib_unpack_data.restype = None
+
+ # override last arg in unpack_parallel()
+ self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int,
+ POINTER(c_int),c_int,c_void_p]
+ self.lib.cslib_unpack_parallel.restype = None
+
+ self.lib.cslib_extract.argtypes = [c_void_p,c_int]
+ self.lib.cslib_extract.restype = c_int
+
+ # create an instance of CSlib with or w/out MPI communicator
+
+ self.cs = c_void_p()
+
+ if not comm:
+ self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs))
+ elif not mpi4pyflag:
+ print "Cannot pass MPI communicator to CSlib w/out mpi4py package"
+ sys.exit()
+ else:
+ address = MPI._addressof(comm)
+ comm_ptr = c_void_p(address)
+ if mode == "mpi/one":
+ address = MPI._addressof(ptr)
+ ptrcopy = c_void_p(address)
+ else: ptrcopy = ptr
+ self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs))
+
+ # destroy instance of CSlib
+
+ def __del__(self):
+ if self.cs: self.lib.cslib_close(self.cs)
+
+ def close(self):
+ self.lib.cslib_close(self.cs)
+ self.lib = None
+
+ # send a message
+
+ def send(self,msgID,nfield):
+ self.nfield = nfield
+ self.lib.cslib_send(self.cs,msgID,nfield)
+
+ # pack one field of message
+
+ def pack_int(self,id,value):
+ self.lib.cslib_pack_int(self.cs,id,value)
+
+ def pack_int64(self,id,value):
+ self.lib.cslib_pack_int64(self.cs,id,value)
+
+ def pack_float(self,id,value):
+ self.lib.cslib_pack_float(self.cs,id,value)
+
+ def pack_double(self,id,value):
+ self.lib.cslib_pack_double(self.cs,id,value)
+
+ def pack_string(self,id,value):
+ self.lib.cslib_pack_string(self.cs,id,value)
+
+ def pack(self,id,ftype,flen,data):
+ cdata = self.data_convert(ftype,flen,data)
+ self.lib.cslib_pack(self.cs,id,ftype,flen,cdata)
+
+ def pack_parallel(self,id,ftype,nlocal,ids,nper,data):
+ cids = self.data_convert(1,nlocal,ids)
+ cdata = self.data_convert(ftype,nper*nlocal,data)
+ self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata)
+
+ # convert input data to a ctypes vector to pass to CSlib
+
+ def data_convert(self,ftype,flen,data):
+
+ # tflag = type of data
+ # tflag = 1 if data is list or tuple
+ # tflag = 2 if data is Numpy array
+ # tflag = 3 if data is ctypes vector
+ # same usage of tflag as in unpack function
+
+ txttype = str(type(data))
+ if "numpy" in txttype: tflag = 2
+ elif "c_" in txttype: tflag = 3
+ else: tflag = 1
+
+ # create ctypes vector out of data to pass to lib
+ # cdata = ctypes vector to return
+ # NOTE: error check on ftype and tflag everywhere, also flen
+
+ if ftype == 1:
+ if tflag == 1: cdata = (flen * c_int)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int))
+ elif tflag == 3: cdata = data
+ elif ftype == 2:
+ if tflag == 1: cdata = (flen * c_longlong)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong))
+ elif tflag == 3: cdata = data
+ elif ftype == 3:
+ if tflag == 1: cdata = (flen * c_float)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float))
+ elif tflag == 3: cdata = data
+ elif ftype == 4:
+ if tflag == 1: cdata = (flen * c_double)(*data)
+ elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double))
+ elif tflag == 3: cdata = data
+
+ return cdata
+
+ # receive a message
+
+ def recv(self):
+ self.lib.cslib_recv.restype = c_int
+ nfield = c_int()
+ fieldID = POINTER(c_int)()
+ fieldtype = POINTER(c_int)()
+ fieldlen = POINTER(c_int)()
+ msgID = self.lib.cslib_recv(self.cs,byref(nfield),
+ byref(fieldID),byref(fieldtype),byref(fieldlen))
+
+ # copy returned C args to native Python int and lists
+ # store them in class so unpack() methods can access the info
+
+ self.nfield = nfield = nfield.value
+ self.fieldID = fieldID[:nfield]
+ self.fieldtype = fieldtype[:nfield]
+ self.fieldlen = fieldlen[:nfield]
+
+ return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen
+
+ # unpack one field of message
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+
+ def unpack_int(self,id):
+ return self.lib.cslib_unpack_int(self.cs,id)
+
+ def unpack_int64(self,id):
+ return self.lib.cslib_unpack_int64(self.cs,id)
+
+ def unpack_float(self,id):
+ return self.lib.cslib_unpack_float(self.cs,id)
+
+ def unpack_double(self,id):
+ return self.lib.cslib_unpack_double(self.cs,id)
+
+ def unpack_string(self,id):
+ return self.lib.cslib_unpack_string(self.cs,id)
+
+ def unpack(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # reset data type of return so can morph by tflag
+ # cannot do this for the generic c_void_p returned by CSlib
+
+ if self.fieldtype[index] == 1:
+ self.lib.cslib_unpack.restype = POINTER(c_int)
+ elif self.fieldtype[index] == 2:
+ self.lib.cslib_unpack.restype = POINTER(c_longlong)
+ elif self.fieldtype[index] == 3:
+ self.lib.cslib_unpack.restype = POINTER(c_float)
+ elif self.fieldtype[index] == 4:
+ self.lib.cslib_unpack.restype = POINTER(c_double)
+ #elif self.fieldtype[index] == 5:
+ # self.lib.cslib_unpack.restype = POINTER(c_char)
+
+ cdata = self.lib.cslib_unpack(self.cs,id)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+ # tflag = 2,3 should NOT perform a data copy
+
+ if tflag == 1:
+ data = cdata[:self.fieldlen[index]]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # handle data array like pack() or unpack_parallel() ??
+
+ def unpack_data(self,id,tflag=3):
+ index = self.fieldID.index(id)
+
+ # unpack one field of message in parallel
+ # tflag = type of data to return
+ # 3 = ctypes vector is default, since no conversion required
+ # NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg?
+ # as opposed to creating this cdata
+ # does that make any performance difference ?
+ # e.g. should we allow CSlib to populate an existing Numpy array's memory
+
+ def unpack_parallel(self,id,nlocal,ids,nper,tflag=3):
+ cids = self.data_convert(1,nlocal,ids)
+
+ # allocate memory for the returned data
+ # pass cdata ptr to the memory to CSlib unpack_parallel()
+ # this resets data type of last unpack_parallel() arg
+
+ index = self.fieldID.index(id)
+ if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)()
+ elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)()
+ elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)()
+ elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)()
+ #elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)()
+
+ self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata)
+
+ # tflag = user-requested type of data to return
+ # tflag = 1 to return data as list
+ # tflag = 2 to return data as Numpy array
+ # tflag = 3 to return data as ctypes vector
+ # same usage of tflag as in pack functions
+
+ if tflag == 1:
+ data = cdata[:nper*nlocal]
+ elif tflag == 2:
+ if numpyflag == 0:
+ print "Cannot return Numpy array w/out numpy package"
+ sys.exit()
+ # NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int
+ # not sure why, reported as bug between ctypes and Numpy here:
+ # https://stackoverflow.com/questions/4964101/pep-3118-
+ # warning-when-using-ctypes-array-as-numpy-array
+ # but why not same warning when just using unpack() ??
+ # in Python these lines give same warning:
+ # >>> import ctypes,numpy
+ # >>> a = (10 * ctypes.c_longlong)()
+ # >>> b = numpy.ctypeslib.as_array(a)
+ data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,))
+ elif tflag == 3:
+ data = cdata
+
+ return data
+
+ # extract a library value
+
+ def extract(self,flag):
+ return self.lib.cslib_extract(self.cs,flag)
diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c2d69eaf0d62863b1226f1d7119a627dd59c741a
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.cpp
@@ -0,0 +1,239 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+// C style library interface to CSlib class
+
+#include <mpi.h>
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cslib_wrap.h"
+#include "cslib.h"
+
+using namespace CSLIB_NS;
+
+// ----------------------------------------------------------------------
+
+void cslib_open(int csflag, const char *mode, const void *ptr,
+ const void *pcomm, void **csptr)
+{
+ CSlib *cs = new CSlib(csflag,mode,ptr,pcomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran(int csflag, const char *mode, const char *str,
+ const void *pcomm, void **csptr)
+{
+ MPI_Comm ccomm;
+ void *pccomm = NULL;
+
+ if (pcomm) {
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+ }
+
+ CSlib *cs = new CSlib(csflag,mode,str,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_open_fortran_mpi_one(int csflag, const char *mode,
+ const void *pboth, const void *pcomm,
+ void **csptr)
+{
+ MPI_Comm ccomm,cboth;
+ void *pccomm,*pcboth;
+
+ MPI_Fint *fcomm = (MPI_Fint *) pcomm;
+ ccomm = MPI_Comm_f2c(*fcomm);
+ pccomm = &ccomm;
+
+ MPI_Fint *fboth = (MPI_Fint *) pboth;
+ cboth = MPI_Comm_f2c(*fboth);
+ pcboth = &cboth;
+
+ CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm);
+ *csptr = (void *) cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_close(void *ptr)
+{
+ CSlib *cs = (CSlib *) ptr;
+ delete cs;
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_send(void *ptr, int msgID, int nfield)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->send(msgID,nfield);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int(void *ptr, int id, int value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_int64(void *ptr, int id, int64_t value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_int64(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_float(void *ptr, int id, float value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_float(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_double(void *ptr, int id, double value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_double(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_string(void *ptr, int id, char *value)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_string(id,value);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack(void *ptr, int id, int ftype, int flen, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack(id,ftype,flen,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_pack_parallel(void *ptr, int id, int ftype,
+ int nlocal, int *ids, int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->pack_parallel(id,ftype,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_recv(void *ptr, int *nfield_caller,
+ int **fieldID_caller, int **fieldtype_caller,
+ int **fieldlen_caller)
+{
+ CSlib *cs = (CSlib *) ptr;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ *nfield_caller = nfield;
+ *fieldID_caller = fieldID;
+ *fieldtype_caller = fieldtype;
+ *fieldlen_caller = fieldlen;
+
+ return msgID;
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_unpack_int(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int(id);
+}
+// ----------------------------------------------------------------------
+
+int64_t cslib_unpack_int64(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_int64(id);
+}
+
+// ----------------------------------------------------------------------
+
+float cslib_unpack_float(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_float(id);
+}
+
+// ----------------------------------------------------------------------
+
+double cslib_unpack_double(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_double(id);
+}
+
+// ----------------------------------------------------------------------
+
+char *cslib_unpack_string(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack_string(id);
+}
+
+// ----------------------------------------------------------------------
+
+void *cslib_unpack(void *ptr, int id)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->unpack(id);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_data(void *ptr, int id, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack(id,data);
+}
+
+// ----------------------------------------------------------------------
+
+void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids,
+ int nper, void *data)
+{
+ CSlib *cs = (CSlib *) ptr;
+ cs->unpack_parallel(id,nlocal,ids,nper,data);
+}
+
+// ----------------------------------------------------------------------
+
+int cslib_extract(void *ptr, int flag)
+{
+ CSlib *cs = (CSlib *) ptr;
+ return cs->extract(flag);
+}
diff --git a/lib/message/cslib/src/cslib_wrap.f90 b/lib/message/cslib/src/cslib_wrap.f90
new file mode 100644
index 0000000000000000000000000000000000000000..cd2e058b78c6d16efbae4c503145148e8acd88a5
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.f90
@@ -0,0 +1,147 @@
+! ISO_C_binding wrapper on CSlib C interface
+
+module cslib_wrap
+
+interface
+ subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*),str(*)
+ type(c_ptr), value :: pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran
+
+ subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c)
+ use iso_c_binding
+ integer(c_int), value :: csflag
+ character(c_char) :: mode(*)
+ type(c_ptr), value :: pboth,pcomm
+ type(c_ptr) :: ptr
+ end subroutine cslib_open_fortran_mpi_one
+
+ subroutine cslib_close(ptr) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ end subroutine cslib_close
+
+ subroutine cslib_send(ptr,msgID,nfield) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: msgID,nfield
+ end subroutine cslib_send
+
+ subroutine cslib_pack_int(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int), value :: value
+ end subroutine cslib_pack_int
+
+ subroutine cslib_pack_int64(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ integer(c_int64_t), value :: value
+ end subroutine cslib_pack_int64
+
+ subroutine cslib_pack_float(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_float), value :: value
+ end subroutine cslib_pack_float
+
+ subroutine cslib_pack_double(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ real(c_double), value :: value
+ end subroutine cslib_pack_double
+
+ subroutine cslib_pack_string(ptr,id,value) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ character(c_char) :: value(*)
+ end subroutine cslib_pack_string
+
+ subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,flen
+ type(c_ptr), value :: data
+ end subroutine cslib_pack
+
+ subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,ftype,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_pack_parallel
+
+ function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_recv
+ type(c_ptr), value :: ptr
+ integer(c_int) :: nfield
+ type(c_ptr) :: fieldID,fieldtype,fieldlen
+ end function cslib_recv
+
+ function cslib_unpack_int(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_unpack_int
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int
+
+ function cslib_unpack_int64(ptr,id) bind(c)
+ use iso_c_binding
+ integer(c_int64_t) :: cslib_unpack_int64
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_int64
+
+ function cslib_unpack_float(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_float) :: cslib_unpack_float
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_float
+
+ function cslib_unpack_double(ptr,id) bind(c)
+ use iso_c_binding
+ real(c_double) :: cslib_unpack_double
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_double
+
+ function cslib_unpack_string(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack_string
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack_string
+
+ function cslib_unpack(ptr,id) bind(c)
+ use iso_c_binding
+ type(c_ptr) :: cslib_unpack
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id
+ end function cslib_unpack
+
+ subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c)
+ use iso_c_binding
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: id,nlocal,nper
+ type(c_ptr), value :: ids,data
+ end subroutine cslib_unpack_parallel
+
+ function cslib_extract(ptr,flag) bind(c)
+ use iso_c_binding
+ integer(c_int) :: cslib_extract
+ type(c_ptr), value :: ptr
+ integer(c_int), value :: flag
+ end function cslib_extract
+end interface
+
+end module cslib_wrap
diff --git a/lib/message/cslib/src/cslib_wrap.h b/lib/message/cslib/src/cslib_wrap.h
new file mode 100644
index 0000000000000000000000000000000000000000..bf7df029c391095f82bdbdd9891b4350ffd18375
--- /dev/null
+++ b/lib/message/cslib/src/cslib_wrap.h
@@ -0,0 +1,54 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+/* C style library interface to CSlib class
+ ifdefs allow this file to be included in a C program
+*/
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void cslib_open(int, const char *, const void *, const void *, void **);
+void cslib_open_fortran(int, const char *, const char *, const void *, void **);
+void cslib_open_fortran_mpi_one(int, const char *, const void *,
+ const void *, void **);
+void cslib_close(void *);
+
+void cslib_send(void *, int, int);
+
+void cslib_pack_int(void *, int, int);
+void cslib_pack_int64(void *, int, int64_t);
+void cslib_pack_float(void *, int, float);
+void cslib_pack_double(void *, int, double);
+void cslib_pack_string(void *, int, char *);
+void cslib_pack(void *, int, int, int, void *);
+void cslib_pack_parallel(void *, int, int, int, int *, int, void *);
+
+int cslib_recv(void *, int *, int **, int **, int **);
+
+int cslib_unpack_int(void *, int);
+int64_t cslib_unpack_int64(void *, int);
+float cslib_unpack_float(void *, int);
+double cslib_unpack_double(void *, int);
+char *cslib_unpack_string(void *, int);
+void *cslib_unpack(void *, int);
+void cslib_unpack_data(void *, int, void *);
+void cslib_unpack_parallel(void *, int, int, int *, int, void *);
+
+int cslib_extract(void *, int);
+
+#ifdef __cplusplus
+}
+#endif
diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c67e4a5c8ccf869c249ea926f96cc968dd2c33e7
--- /dev/null
+++ b/lib/message/cslib/src/msg.cpp
@@ -0,0 +1,110 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "msg.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
+{
+ world = cworld;
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+Msg::Msg(int csflag, const void *ptr)
+{
+ world = 0;
+ me = 0;
+ nprocs = 1;
+
+ init(csflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::init(int csflag)
+{
+ client = server = 0;
+ if (csflag == 0) client = 1;
+ else if (csflag == 1) server = 1;
+
+ nsend = nrecv = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::allocate(int nheader, int &maxheader, int *&header,
+ int nbuf, int &maxbuf, char *&buf)
+{
+ if (nheader > maxheader) {
+ sfree(header);
+ maxheader = nheader;
+ header = (int *) smalloc(maxheader*sizeof(int));
+ }
+
+ if (nbuf > maxbuf) {
+ sfree(buf);
+ maxbuf = nbuf;
+ buf = (char *) smalloc(maxbuf*sizeof(char));
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *Msg::smalloc(int nbytes)
+{
+ if (nbytes == 0) return NULL;
+ void *ptr = (void *) malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"Failed to allocate %d bytes",nbytes);
+ }
+ return ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::sfree(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_all(const char *str)
+{
+ if (me == 0) printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Msg::error_one(const char *str)
+{
+ printf("CSlib ERROR: %s\n",str);
+ MPI_Abort(world,1);
+}
diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h
new file mode 100644
index 0000000000000000000000000000000000000000..f75942b027827e5f61a00837f95419e64bde1b94
--- /dev/null
+++ b/lib/message/cslib/src/msg.h
@@ -0,0 +1,52 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_H
+#define MSG_H
+
+#include <mpi.h>
+
+namespace CSLIB_NS {
+
+class Msg {
+ public:
+ int nsend,nrecv;
+ MPI_Comm world;
+
+ Msg(int, const void *, MPI_Comm);
+ Msg(int, const void *);
+ virtual ~Msg() {}
+ virtual void send(int, int *, int, char *) = 0;
+ virtual void recv(int &, int *&, int &, char *&) = 0;
+
+ protected:
+ int me,nprocs;
+ int client,server;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int lengths[2];
+
+ void init(int);
+ void allocate(int, int &, int *&, int, int &, char *&);
+ void *smalloc(int);
+ void sfree(void *);
+ void error_all(const char *);
+ void error_one(const char *);
+};
+
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d97e249fad7efdbc3228c6b463995facc315c7f3
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <unistd.h>
+
+#include "msg_file.h"
+
+using namespace CSLIB_NS;
+
+#define MAXLINE 256
+#define SLEEP 0.1 // delay in CPU secs to check for message file
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgFile::~MsgFile()
+{
+ delete [] fileroot;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::init(char *filename)
+{
+ int n = strlen(filename) + 1;
+ fileroot = new char[n];
+ strcpy(fileroot,filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::send(int nheader, int *header, int nbuf, char *buf)
+{
+ char filename[MAXLINE];
+
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server");
+
+ fp = fopen(filename,"wb");
+ if (!fp) error_one("send(): Could not open send message file");
+ fwrite(lengths,sizeof(int),2,fp);
+ fwrite(header,sizeof(int),nheader,fp);
+ fwrite(buf,1,nbuf,fp);
+ fclose(fp);
+ }
+
+ // create empty signal file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ fp = fopen(filename,"w");
+ fclose(fp);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ char filename[MAXLINE];
+
+ // wait until signal file exists to open message file
+
+ if (me == 0) {
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+
+ int delay = (int) (1000000 * SLEEP);
+ while (1) {
+ fp = fopen(filename,"r");
+ if (fp) break;
+ usleep(delay);
+ }
+ fclose(fp);
+
+ if (client) sprintf(filename,"%s.%s",fileroot,"server");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client");
+ fp = fopen(filename,"rb");
+ if (!fp) error_one("recv(): Could not open recv message file");
+ }
+
+ // read and broadcast data
+
+ if (me == 0) fread(lengths,sizeof(int),2,fp);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) fread(header,sizeof(int),nheader,fp);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) fread(buf,1,nbuf,fp);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+
+ // delete both message and signal file
+
+ if (me == 0) {
+ fclose(fp);
+ unlink(filename);
+ if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
+ else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
+ unlink(filename);
+ }
+}
diff --git a/lib/message/cslib/src/msg_file.h b/lib/message/cslib/src/msg_file.h
new file mode 100644
index 0000000000000000000000000000000000000000..d6bd802607aa18c1b34b7c92a2ea3f08e4180563
--- /dev/null
+++ b/lib/message/cslib/src/msg_file.h
@@ -0,0 +1,40 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_FILE_H
+#define MSG_FILE_H
+
+#include <stdio.h>
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgFile : public Msg {
+ public:
+ MsgFile(int, const void *, MPI_Comm);
+ MsgFile(int, const void *);
+ ~MsgFile();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ char *fileroot;
+ FILE *fp;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..db11735b277699dd08f30c7b8ec112050779fa19
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.cpp
@@ -0,0 +1,82 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_one.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ // NOTE: ideally would skip this call if mpi/two
+ init(ptr);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::init(const void *ptr)
+{
+ MPI_Comm *pbothcomm = (MPI_Comm *) ptr;
+ bothcomm = *pbothcomm;
+
+ if (client) {
+ MPI_Comm_size(world,&nprocs);
+ otherroot = nprocs;
+ } else if (server) {
+ otherroot = 0;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm);
+ MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ MPI_Status status;
+
+ if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_mpi_one.h b/lib/message/cslib/src/msg_mpi_one.h
new file mode 100644
index 0000000000000000000000000000000000000000..4b4140a3f70edaff50a1fe1aa6e0af2cfca2ed0a
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_one.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_ONE_H
+#define MSG_MPI_ONE_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgMPIOne : public Msg {
+ public:
+ MsgMPIOne(int, const void *, MPI_Comm);
+ virtual ~MsgMPIOne() {}
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ protected:
+ MPI_Comm bothcomm;
+ int otherroot;
+
+ void init(const void *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e9a9e87eeba99b802554383473ba806e179dab06
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.cpp
@@ -0,0 +1,81 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <unistd.h>
+
+#include "msg_mpi_two.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) :
+ MsgMPIOne(csflag, ptr, cworld)
+{
+ char *filename = (char *) ptr;
+ init(filename);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgMPITwo::~MsgMPITwo()
+{
+ // free the inter comm that spans both client and server
+
+ MPI_Comm_free(&bothcomm);
+ MPI_Close_port(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgMPITwo::init(char *filename)
+{
+ if (client) {
+ if (me == 0) {
+ FILE *fp = NULL;
+ while (!fp) {
+ fp = fopen(filename,"r");
+ if (!fp) sleep(1);
+ }
+ fgets(port,MPI_MAX_PORT_NAME,fp);
+ //printf("Client port: %s\n",port);
+ fclose(fp);
+ }
+
+ MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world);
+ MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("CLIENT comm connect\n");
+ if (me == 0) unlink(filename);
+
+ } else if (server) {
+ MPI_Open_port(MPI_INFO_NULL,port);
+
+ if (me == 0) {
+ //printf("Server name: %s\n",port);
+ FILE *fp = fopen(filename,"w");
+ fprintf(fp,"%s",port);
+ fclose(fp);
+ }
+
+ MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm);
+ //if (me == 0) printf("SERVER comm accept\n");
+ }
+
+ otherroot = 0;
+}
diff --git a/lib/message/cslib/src/msg_mpi_two.h b/lib/message/cslib/src/msg_mpi_two.h
new file mode 100644
index 0000000000000000000000000000000000000000..7b31db5a63a49ac4eba75fa37b172262c59a017a
--- /dev/null
+++ b/lib/message/cslib/src/msg_mpi_two.h
@@ -0,0 +1,35 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_MPI_TWO_H
+#define MSG_MPI_TWO_H
+
+#include "msg_mpi_one.h"
+
+namespace CSLIB_NS {
+
+class MsgMPITwo : public MsgMPIOne {
+ public:
+ MsgMPITwo(int, const void *, MPI_Comm);
+ ~MsgMPITwo();
+
+ private:
+ char port[MPI_MAX_PORT_NAME];
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c2d408f3a5d73a35330b951e4d150d5312dea727
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.cpp
@@ -0,0 +1,140 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <zmq.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+
+#include "msg_zmq.h"
+
+using namespace CSLIB_NS;
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) :
+ Msg(csflag, ptr, cworld)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr)
+{
+ char *port = (char *) ptr;
+ init(port);
+}
+
+/* ---------------------------------------------------------------------- */
+
+MsgZMQ::~MsgZMQ()
+{
+ if (me == 0) {
+ zmq_close(socket);
+ zmq_ctx_destroy(context);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void MsgZMQ::init(char *port)
+{
+#ifdef ZMQ_NO
+ error_all("constructor(): Library not built with ZMQ support");
+#endif
+
+ if (me == 0) {
+ int n = strlen(port) + 8;
+ char *socket_name = new char[n];
+ strcpy(socket_name,"tcp://");
+ strcat(socket_name,port);
+
+ if (client) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REQ);
+ zmq_connect(socket,socket_name);
+ } else if (server) {
+ context = zmq_ctx_new();
+ socket = zmq_socket(context,ZMQ_REP);
+ int rc = zmq_bind(socket,socket_name);
+ if (rc) error_one("constructor(): Server could not make socket connection");
+ }
+
+ delete [] socket_name;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ send below has a following ZMQ recv, except last one
+ if client calls send(), it will next call recv()
+ if server calls send(), it will next call recv() from its wait loop
+ in either case, recv() issues a ZMQ recv to match last ZMQ send here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf)
+{
+ lengths[0] = nheader;
+ lengths[1] = nbuf;
+
+ if (me == 0) {
+ zmq_send(socket,lengths,2*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) {
+ zmq_send(socket,header,nheader*sizeof(int),0);
+ zmq_recv(socket,NULL,0,0);
+ }
+
+ if (me == 0) zmq_send(socket,buf,nbuf,0);
+}
+
+/* ----------------------------------------------------------------------
+ client/server sockets (REQ/REP) must follow this protocol:
+ client sends request (REQ) which server receives
+ server sends response (REP) which client receives
+ every exchange is of this form, server cannot initiate a send
+ thus each ZMQ recv below has a following ZMQ send, except last one
+ if client calls recv(), it will next call send() to ping server again,
+ if server calls recv(), it will next call send() to respond to client
+ in either case, send() issues a ZMQ send to match last ZMQ recv here
+------------------------------------------------------------------------- */
+
+void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
+{
+ if (me == 0) {
+ zmq_recv(socket,lengths,2*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
+
+ int nheader = lengths[0];
+ int nbuf = lengths[1];
+ allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
+
+ if (me == 0) {
+ zmq_recv(socket,header,nheader*sizeof(int),0);
+ zmq_send(socket,NULL,0,0);
+ }
+ if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
+
+ if (me == 0) zmq_recv(socket,buf,nbuf,0);
+ if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
+}
diff --git a/lib/message/cslib/src/msg_zmq.h b/lib/message/cslib/src/msg_zmq.h
new file mode 100644
index 0000000000000000000000000000000000000000..c0621a26ff1356a6410c6f8267a5640f04522681
--- /dev/null
+++ b/lib/message/cslib/src/msg_zmq.h
@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+ CSlib - Client/server library for code coupling
+ http://cslib.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright 2018 National Technology & Engineering Solutions of
+ Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
+ NTESS, the U.S. Government retains certain rights in this software.
+ This software is distributed under the modified Berkeley Software
+ Distribution (BSD) License.
+
+ See the README file in the top-level CSlib directory.
+------------------------------------------------------------------------- */
+
+#ifndef MSG_ZMQ_H
+#define MSG_ZMQ_H
+
+#include "msg.h"
+
+namespace CSLIB_NS {
+
+class MsgZMQ : public Msg {
+ public:
+ MsgZMQ(int, const void *, MPI_Comm);
+ MsgZMQ(int, const void *);
+ ~MsgZMQ();
+ void send(int, int *, int, char *);
+ void recv(int &, int *&, int &, char *&);
+
+ private:
+ void *context,*socket;
+
+ void init(char *);
+};
+
+}
+
+#endif
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index a33848f1a1dac5c143c411414a8eba0c8a50c683..61e3c35293bb9eb146e4a4b05573f384373ce995 100644
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -62,7 +62,7 @@ void FixNVEAsphere::init()
/* ---------------------------------------------------------------------- */
-void FixNVEAsphere::initial_integrate(int vflag)
+void FixNVEAsphere::initial_integrate(int /*vflag*/)
{
double dtfm;
double inertia[3],omega[3];
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index d944b68f35a425cceae1f6faec6ed3b5e70a68ac..9cc430592a075bd7e61fbf7fe56f8c9882daf7f9 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -64,7 +64,7 @@ void FixNVEAsphereNoforce::init()
/* ---------------------------------------------------------------------- */
-void FixNVEAsphereNoforce::initial_integrate(int vflag)
+void FixNVEAsphereNoforce::initial_integrate(int /*vflag*/)
{
AtomVecEllipsoid::Bonus *bonus;
if (avec) bonus = avec->bonus;
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index c145e99fcb1a608e540941eb2b6402a58e6a5a33..51a502df89fffcf4dfacd4407e01934ad41a41ef 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -81,7 +81,7 @@ void FixNVELine::init()
/* ---------------------------------------------------------------------- */
-void FixNVELine::initial_integrate(int vflag)
+void FixNVELine::initial_integrate(int /*vflag*/)
{
double dtfm,dtirotate,length,theta;
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index d06063d905940276941a14f1d3f46e1f95a0ff5d..fb9bf64c58bf7cbbede432939718394e7cd73d17 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -75,7 +75,7 @@ void FixNVETri::init()
/* ---------------------------------------------------------------------- */
-void FixNVETri::initial_integrate(int vflag)
+void FixNVETri::initial_integrate(int /*vflag*/)
{
double dtfm;
double omega[3];
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index 684e5768dae00176fa05eaacf75cf43c1cb60468..10529ad3af8252c713c18bb9914f757aebb5e075 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -195,7 +195,7 @@ void BodyNparticle::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyNparticle::radius_body(int ninteger, int ndouble,
+double BodyNparticle::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -258,7 +258,7 @@ void BodyNparticle::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyNparticle::image(int ibonus, double flag1, double flag2,
+int BodyNparticle::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
double p[3][3];
diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp
index 1e232f0f3f59fbbdab6bf470920bcf2a70ff2036..00a09c912d8982e959de8c1ab46ff719fcfe39f6 100644
--- a/src/BODY/body_rounded_polygon.cpp
+++ b/src/BODY/body_rounded_polygon.cpp
@@ -323,7 +323,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyRoundedPolygon::radius_body(int ninteger, int ndouble,
+double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -392,7 +392,7 @@ void BodyRoundedPolygon::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyRoundedPolygon::image(int ibonus, double flag1, double flag2,
+int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
int j;
diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp
index 6a9b97ae2348ec344b75656afbb3d5261282e5b5..0e2ebbed8307e90341247be332e1d9a90f0219d6 100644
--- a/src/BODY/body_rounded_polyhedron.cpp
+++ b/src/BODY/body_rounded_polyhedron.cpp
@@ -96,7 +96,7 @@ int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus)
{
int nvertices = bonus->ivalue[0];
int nedges = bonus->ivalue[1];
- int nfaces = bonus->ivalue[2];
+ //int nfaces = bonus->ivalue[2];
if (nvertices == 1) return 0;
else if (nvertices == 2) return 1;
return nedges; //(nvertices+nfaces-2); // Euler's polyon formula: V-E+F=2
@@ -381,7 +381,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
called by Molecule class which needs single body size
------------------------------------------------------------------------- */
-double BodyRoundedPolyhedron::radius_body(int ninteger, int ndouble,
+double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble,
int *ifile, double *dfile)
{
int nsub = ifile[0];
@@ -460,10 +460,10 @@ void BodyRoundedPolyhedron::output(int ibonus, int m, double *values)
/* ---------------------------------------------------------------------- */
-int BodyRoundedPolyhedron::image(int ibonus, double flag1, double flag2,
+int BodyRoundedPolyhedron::image(int ibonus, double flag1, double /*flag2*/,
int *&ivec, double **&darray)
{
- int j, nelements;
+ int nelements;
double p[3][3];
double *x, rrad;
@@ -488,7 +488,7 @@ int BodyRoundedPolyhedron::image(int ibonus, double flag1, double flag2,
nelements = nvertices;
} else {
- int nfaces = bonus->ivalue[2];
+ //int nfaces = bonus->ivalue[2];
int nedges = bonus->ivalue[1]; //nvertices + nfaces - 2;
if (nvertices == 2) nedges = 1; // special case: rods
double* edge_ends = &bonus->dvalue[3*nvertices];
diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp
index 0606723cb77d558c8500c5469e16d64773f962fd..0c74facf34b83e5c152f8511073c7f56c95b5754 100644
--- a/src/BODY/fix_nve_body.cpp
+++ b/src/BODY/fix_nve_body.cpp
@@ -54,7 +54,7 @@ void FixNVEBody::init()
/* ---------------------------------------------------------------------- */
-void FixNVEBody::initial_integrate(int vflag)
+void FixNVEBody::initial_integrate(int /*vflag*/)
{
double dtfm;
double omega[3];
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 0e7aaea1e1a2a6c9ac0060c092eb703eaf90f2b6..3f8c08b6bdfae307512aae97d1b88be821a4b433 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -204,7 +204,7 @@ void FixWallBodyPolygon::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallBodyPolygon::post_force(int vflag)
+void FixWallBodyPolygon::post_force(int /*vflag*/)
{
double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
int i,ni,npi,ifirst,nei,iefirst,side;
@@ -310,9 +310,6 @@ void FixWallBodyPolygon::post_force(int vflag)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) continue;
- double r = sqrt(rsq);
- double rsqinv = 1.0 / rsq;
-
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
@@ -475,12 +472,11 @@ void FixWallBodyPolygon::body2space(int i)
int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
double** x, double** f, double** torque, int side,
- Contact* contact_list, int &num_contacts, double* facc)
+ Contact* contact_list, int &num_contacts, double* /*facc*/)
{
int ni, npi, ifirst, interact;
- double xpi[3], xpj[3], dist, eradi, rradi;
- double fx, fy, fz, rx, ry, rz;
- int nlocal = atom->nlocal;
+ double xpi[3], eradi, rradi;
+ double fx, fy, fz;
npi = dnum[i];
ifirst = dfirst[i];
@@ -499,9 +495,9 @@ int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
xpi[1] = x[i][1] + discrete[ifirst+ni][1];
xpi[2] = x[i][2] + discrete[ifirst+ni][2];
- int mode, contact, p2vertex;
- double d, R, hi[3], t, delx, dely, delz, fpair, shift;
- double xj[3], rij;
+ int mode, contact;
+ double d, R, hi[3], delx, dely, delz, fpair;
+ double rij;
// compute the distance from the vertex xpi to the wall
@@ -671,7 +667,7 @@ void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
double** torque, double* vwall, double* facc)
{
- int ibody,ibonus,ifirst, jefirst, ni;
+ int ibody,ibonus,ifirst, ni;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double fn[3],ft[3],vi[3];
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 17e9f0b8b5e05441dff0c93f333dde24793fd3e8..9504e256b497b45a9266a4680be2d5c8a4c7d9a4 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -211,9 +211,9 @@ void FixWallBodyPolyhedron::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallBodyPolyhedron::post_force(int vflag)
+void FixWallBodyPolyhedron::post_force(int /*vflag*/)
{
- double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
+ double vwall[3],dx,dy,dz,del1,del2,rsq,eradi,rradi,wall_pos;
int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side;
double facc[3];
@@ -325,9 +325,6 @@ void FixWallBodyPolyhedron::post_force(int vflag)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) continue;
- double r = sqrt(rsq);
- double rsqinv = 1.0 / rsq;
-
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
@@ -359,8 +356,7 @@ void FixWallBodyPolyhedron::post_force(int vflag)
edge[iefirst+ni][5] = 0;
}
- int interact, num_contacts, done;
- double delta_a, delta_ua, j_a;
+ int interact, num_contacts;
Contact contact_list[MAX_CONTACTS];
num_contacts = 0;
@@ -485,7 +481,7 @@ void FixWallBodyPolyhedron::body2space(int i)
---------------------------------------------------------------------- */
int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
- int side, double* vwall, double** x, double** v, double** f,
+ int /*side*/, double* vwall, double** x, double** v, double** f,
double** angmom, double** torque)
{
int mode;
@@ -545,12 +541,11 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
---------------------------------------------------------------------- */
int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
- int side, double* vwall, double** x, double** f, double** torque,
- Contact* contact_list, int &num_contacts, double* facc)
+ int side, double* vwall, double** x, double** /*f*/, double** /*torque*/,
+ Contact* /*contact_list*/, int &/*num_contacts*/, double* /*facc*/)
{
int ni, nei, mode, contact;
double rradi;
- int nlocal = atom->nlocal;
nei = ednum[i];
rradi = rounded_radius[i];
@@ -584,7 +579,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
double *xmi, double rounded_radius_i, double wall_pos,
- int side, double* vwall, int &contact)
+ int /*side*/, double* vwall, int &contact)
{
int mode,ifirst,iefirst,npi1,npi2;
double d1,d2,xpi1[3],xpi2[3],hi[3];
@@ -698,14 +693,14 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
------------------------------------------------------------------------- */
void FixWallBodyPolyhedron::contact_forces(int ibody,
- double j_a, double *xi, double *xj, double delx, double dely, double delz,
+ double j_a, double *xi, double * /*xj*/, double delx, double dely, double delz,
double fx, double fy, double fz, double** x, double** v, double** angmom,
double** f, double** torque, double* vwall)
{
- int ibonus,jbonus;
+ int ibonus;
double fxt,fyt,fzt,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
- double fn[3],ft[3],vi[3],vj[3];
+ double fn[3],ft[3],vi[3];
double *quat, *inertia;
AtomVecBody::Bonus *bonus;
@@ -787,7 +782,7 @@ void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
double** torque, double* vwall, double* facc)
{
- int ibody,ibonus,ifirst, jefirst, ni;
+ int ibody,ibonus,ifirst,ni;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double fn[3],ft[3],vi[3];
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 14ef70f476061f1240dad92b7e694e6aa1f5957c..6a176f1083542857951051d2cf6d456991663854 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -105,10 +105,9 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
int i,j,ii,jj,inum,jnum,itype,jtype;
int ni,nj,npi,npj,ifirst,jfirst;
int nei,nej,iefirst,jefirst;
- double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fx,fy,fz;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl;
double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij;
- double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3],facc[3];
- double *dxi,*dxj;
+ double xi[3],xj[3],facc[3];
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
@@ -598,7 +597,7 @@ void PairBodyRoundedPolygon::body2space(int i)
void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j,
double delx, double dely, double delz, double rsq,
- double k_n, double k_na, double** x, double** v,
+ double k_n, double k_na, double** /*x*/, double** v,
double** f, int evflag)
{
double eradi,eradj,rradi,rradj;
@@ -709,9 +708,8 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
int ni, npi, ifirst, nei, iefirst;
int nj, npj, jfirst, nej, jefirst;
double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj;
- double fx, fy, fz, rx, ry, rz, energy;
+ double fx, fy, fz, energy;
int interact;
- int nlocal = atom->nlocal;
npi = dnum[i];
ifirst = dfirst[i];
@@ -758,7 +756,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
int mode, contact, p2vertex;
double d, R, hi[3], t, delx, dely, delz, fpair, shift;
- double xj[3], rij;
+ double rij;
// loop through body j's edges
@@ -781,6 +779,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j,
if (mode == VERTEXI) p2vertex = edge[jefirst+nj][0];
else if (mode == VERTEXJ) p2vertex = edge[jefirst+nj][1];
+ // double xj[3];
// p2.body2space(p2vertex, xj);
xpj[0] = x[j][0] + discrete[jfirst+p2vertex][0];
xpj[1] = x[j][1] + discrete[jfirst+p2vertex][1];
@@ -1166,7 +1165,7 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody,
void PairBodyRoundedPolygon::contact_forces(Contact& contact, double j_a,
double** x, double** v, double** angmom, double** f,
- double** torque, double &evdwl, double* facc)
+ double** torque, double &/*evdwl*/, double* facc)
{
int ibody,jbody,ibonus,jbonus,ifirst,jefirst,ni,nj;
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp
index 051be762e5a432193326596e6acbc3ad7bb9e616..eea2aa37249e011bab1a5122282c4b3511f48f5d 100644
--- a/src/BODY/pair_body_rounded_polyhedron.cpp
+++ b/src/BODY/pair_body_rounded_polyhedron.cpp
@@ -603,7 +603,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
{
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
- double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy;
+ double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,energy;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
@@ -685,7 +685,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
{
int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
- double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -835,7 +835,7 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
{
int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp;
double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d;
- double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy;
+ double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
@@ -988,7 +988,7 @@ int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
- int ni,nei,nj,nej,contact,interact;
+ int ni,nei,nj,nej,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
@@ -1045,7 +1045,7 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
- int ni,nei,nj,nfj,contact,interact;
+ int ni,nei,nj,nfj,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
@@ -1118,7 +1118,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact;
double xi1[3],xi2[3],xpj1[3],xpj2[3];
double r,t1,t2,h1[3],h2[3];
- double contact_dist, shift;
+ double contact_dist;
double** x = atom->x;
double** v = atom->v;
@@ -1314,7 +1314,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
// determine the intersection of the edge to the face
- double hi1[3], hi2[3], d1, d2, contact_dist, shift;
+ double hi1[3], hi2[3], d1, d2, contact_dist;
int inside1 = 0;
int inside2 = 0;
@@ -2345,9 +2345,8 @@ void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
void PairBodyRoundedPolyhedron::sanity_check()
{
- double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b,u[3],v[3],n[3];
+ double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b;
double a[3],b[3],t_a,t_b;
- int inside_a, inside_b;
x1[0] = 0; x1[1] = 3; x1[2] = 0;
x2[0] = 3; x2[1] = 0; x2[2] = 0;
@@ -2364,9 +2363,11 @@ void PairBodyRoundedPolyhedron::sanity_check()
h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a, d_b);
*/
/*
+ int inside_a, inside_b;
int mode = edge_face_intersect(x1, x2, x3, a, b, h_a, h_b, d_a, d_b,
inside_a, inside_b);
+ double u[3],v[3],n[3];
MathExtra::sub3(x2, x1, u);
MathExtra::sub3(x3, x1, v);
MathExtra::cross3(u, v, n);
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index c3dc09715c9c341b57a73e274251cdc35bdeb0da..af20313e0ad1f6e6ffbe7f259ede42ce09abe0bb 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -209,7 +209,7 @@ void BondClass2::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondClass2::single(int type, double rsq, int i, int j, double &fforce)
+double BondClass2::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
{
double r = sqrt(rsq);
double dr = r - r0[type];
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index 3b3811584d07e4f71a53b986084cd735841decbd..77f594af9d33cbeb6f92c8d70a365c3837df432d 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -633,7 +633,7 @@ void ImproperClass2::read_restart(FILE *fp)
angle-angle interactions within improper
------------------------------------------------------------------------- */
-void ImproperClass2::angleangle(int eflag, int vflag)
+void ImproperClass2::angleangle(int eflag, int /*vflag*/)
{
int i1,i2,i3,i4,i,j,k,n,type;
double eimproper;
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index e255807ab6a5f217f076892d9a695d5d5d4cd787..6451921dc54ee6a348fe0e6de1d3fd9cec1b6e93 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -377,8 +377,8 @@ void PairLJClass2::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJClass2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index 4448d6e110ec8ca21840eab06258692e356ca650..c16dbf41af4e8c35082bb1d107c34ca744c88a24 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -469,8 +469,8 @@ void PairColloid::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairColloid::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double K[9],h[4],g[4];
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index f0f7ce8c143f259c298e053ae1b509f1531837ce..de53d918181b0542d6e044a611b81a9f6294f286 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -749,7 +749,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
int PairLubricate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
@@ -797,7 +797,7 @@ void PairLubricate::unpack_forward_comm(int n, int first, double *buf)
if type pair setting, return -2 if no type pairs are set
------------------------------------------------------------------------- */
-int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
+int PairLubricate::pre_adapt(char *name, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/)
{
if (strcmp(name,"mu") == 0) return 0;
return -1;
@@ -809,7 +809,7 @@ int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
if type pair setting, set I-J and J-I coeffs
------------------------------------------------------------------------- */
-void PairLubricate::adapt(int which, int ilo, int ihi, int jlo, int jhi,
+void PairLubricate::adapt(int /*which*/, int /*ilo*/, int /*ihi*/, int /*jlo*/, int /*jhi*/,
double value)
{
mu = value;
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 11fb2131577c6f32a20358fc9a769038d20e0075..35fe33c84eb7203f89804265c27f1784114735c7 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -2010,7 +2010,7 @@ void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
/* ---------------------------------------------------------------------- */
int PairLubricateU::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index 5965fd3aa86913824e3a21be449d607a89f87e83..d21bc43524307448f905b0de8c63a721a6fbea4d 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -160,9 +160,9 @@ double PairYukawaColloid::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-double PairYukawaColloid::single(int i, int j, int itype, int jtype,
+double PairYukawaColloid::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,rinv,screening,forceyukawa,phi;
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 0f581be01c4718b52e6fa9b686329c2c26fc34b4..73c1c9fc111a3239993ebe88d8154a8698ecdc16 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -83,7 +83,7 @@ void FixFreeze::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixFreeze::post_force(int vflag)
+void FixFreeze::post_force(int /*vflag*/)
{
double **f = atom->f;
double **torque = atom->torque;
@@ -110,7 +110,7 @@ void FixFreeze::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixFreeze::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFreeze::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 368ff99fb75929303f85b7a2bf8ffaaacc3a37ed..f0957423f94f6d9cb4db4400693619abb2a5bf9f 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -302,7 +302,7 @@ void FixWallGran::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallGran::post_force(int vflag)
+void FixWallGran::post_force(int /*vflag*/)
{
int i,j;
double dx,dy,dz,del1,del2,delxy,delr,rsq,rwall,meff;
@@ -446,7 +446,7 @@ void FixWallGran::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallGran::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallGran::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -1041,7 +1041,7 @@ void FixWallGran::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixWallGran::copy_arrays(int i, int j, int delflag)
+void FixWallGran::copy_arrays(int i, int j, int /*delflag*/)
{
if (history)
for (int m = 0; m < sheardim; m++)
@@ -1136,7 +1136,7 @@ int FixWallGran::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixWallGran::size_restart(int nlocal)
+int FixWallGran::size_restart(int /*nlocal*/)
{
if (!history) return 0;
return 1 + sheardim;
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index 12fa25714ccbbf8447cbda043ee8ba00d0d66c14..4a6be5f3c9950790c5f0a02644128f340268dec7 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -130,7 +130,7 @@ void FixWallGranRegion::init()
/* ---------------------------------------------------------------------- */
-void FixWallGranRegion::post_force(int vflag)
+void FixWallGranRegion::post_force(int /*vflag*/)
{
int i,m,nc,iwall;
double dx,dy,dz,rsq,meff;
@@ -347,7 +347,7 @@ void FixWallGranRegion::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixWallGranRegion::copy_arrays(int i, int j, int delflag)
+void FixWallGranRegion::copy_arrays(int i, int j, int /*delflag*/)
{
int m,n,iwall;
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index 9d4f5c1a9b8a703d4dd83600e84186a6f140f5fe..d1f3c7bbe1eb02e0a23a00071ca4728292f62ef0 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -306,9 +306,9 @@ void PairGranHertzHistory::settings(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
+double PairGranHertzHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum;
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index 4937c2fe8b1142816d20c03f8548b208b594a860..5244396ead10434b1d5b39fb9cfc29d4ca4a7210 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -219,8 +219,8 @@ void PairGranHooke::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum,r,rinv,rsqinv;
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index d70c7391e2ba896961640895ce98e07acc6a0cd5..c014510fca2d36d9575c32600f64c27f3a426747 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -587,9 +587,9 @@ void PairGranHookeHistory::reset_dt()
/* ---------------------------------------------------------------------- */
-double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
+double PairGranHookeHistory::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double radi,radj,radsum;
@@ -746,7 +746,7 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairGranHookeHistory::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index 4b10782ee646c23268fb5603cacb3f730336f1ba..8db5979b39378db0d66053651f5a08f8af875241 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -338,9 +338,9 @@ void PairCoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulLong::single(int i, int j, int itype, int jtype,
+double PairCoulLong::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp
index f5cd9a04452a2a6c16a03e15527c47c331d11913..ab59dfa4c1bb69f551b5aa0672dd20e485e913c0 100644
--- a/src/KSPACE/pair_coul_msm.cpp
+++ b/src/KSPACE/pair_coul_msm.cpp
@@ -169,9 +169,9 @@ void PairCoulMSM::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-double PairCoulMSM::single(int i, int j, int itype, int jtype,
+double PairCoulMSM::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,egamma,fgamma,prefactor;
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index aea57da326e7f75b15a23ad3945a552f3eb56be9..b8cd52c5fef758eb398b9204cd7befa7a2c5dd1c 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -8052,7 +8052,7 @@ void PPPMDisp::compute_rho_coeff(FFT_SCALAR **coeff , FFT_SCALAR **dcoeff,
extended to non-neutral systems (J. Chem. Phys. 131, 094107).
------------------------------------------------------------------------- */
-void PPPMDisp::slabcorr(int eflag)
+void PPPMDisp::slabcorr(int /*eflag*/)
{
// compute local contribution to global dipole moment
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index 81dd692f4f91a44cebfdf68ab2ca79d8d37f0973..26541f121e0f735e1b094d2e19edbdd5a68764b9 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -234,7 +234,7 @@ struct remap_plan_3d *remap_3d_create_plan(
int in_klo, int in_khi,
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
int out_klo, int out_khi,
- int nqty, int permute, int memory, int precision, int usecollective)
+ int nqty, int permute, int memory, int /*precision*/, int usecollective)
{
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index 18502dd0138d56fc6ebe73fa1f37461e5357c848..a89be57beda1419af68bad20e494bfa6d26a3bf9 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -189,7 +189,7 @@ void FixLatte::init()
/* ---------------------------------------------------------------------- */
-void FixLatte::init_list(int id, NeighList *ptr)
+void FixLatte::init_list(int /*id*/, NeighList * /*ptr*/)
{
// list = ptr;
}
@@ -223,13 +223,13 @@ void FixLatte::setup_pre_reverse(int eflag, int vflag)
integrate electronic degrees of freedom
------------------------------------------------------------------------- */
-void FixLatte::initial_integrate(int vflag) {}
+void FixLatte::initial_integrate(int /*vflag*/) {}
/* ----------------------------------------------------------------------
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixLatte::pre_reverse(int eflag, int vflag)
+void FixLatte::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index b8d9c7e6dfb7b0c739f5195e538f7c4c399625db..e46da9bfe7be379fe988b2494d455e53dc85984a 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -159,7 +159,7 @@ void FixQEQComb::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEQComb::post_force(int vflag)
+void FixQEQComb::post_force(int /*vflag*/)
{
int i,ii,iloop,loopmax,inum,*ilist;
double heatpq,qmass,dtq,dtq2;
@@ -276,7 +276,7 @@ void FixQEQComb::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEQComb::post_force_respa(int vflag, int ilevel, int iloop)
+void FixQEQComb::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -293,7 +293,7 @@ double FixQEQComb::memory_usage()
/* ---------------------------------------------------------------------- */
int FixQEQComb::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index d0b4d197583d260ccf42592dbb7b5921b0384d9d..831f1d0efae68ca51fa74d6f2251b3db2bf37c5e 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -424,7 +424,7 @@ void PairADP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairADP::settings(int narg, char **arg)
+void PairADP::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -521,7 +521,7 @@ void PairADP::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairADP::init_one(int i, int j)
+double PairADP::init_one(int /*i*/, int /*j*/)
{
// single global cutoff = max of cut from all files read in
// for funcfl could be multiple files
@@ -935,7 +935,7 @@ void PairADP::grab(FILE *fp, int n, double *list)
/* ---------------------------------------------------------------------- */
int PairADP::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index 3be27354c15c46929e4700e8f453f2f1cce45c5e..ac3ed36a83557e2b67d582859f0e219816765128 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -425,7 +425,7 @@ void PairAIREBO::REBO_neigh()
REBO forces and energy
------------------------------------------------------------------------- */
-void PairAIREBO::FREBO(int eflag, int vflag)
+void PairAIREBO::FREBO(int eflag, int /*vflag*/)
{
int i,j,k,m,ii,inum,itype,jtype;
tagint itag,jtag;
@@ -524,7 +524,7 @@ void PairAIREBO::FREBO(int eflag, int vflag)
find 3- and 4-step paths between atoms I,J via REBO neighbor lists
------------------------------------------------------------------------- */
-void PairAIREBO::FLJ(int eflag, int vflag)
+void PairAIREBO::FLJ(int eflag, int /*vflag*/)
{
int i,j,k,m,ii,jj,kk,mm,inum,jnum,itype,jtype,ktype,mtype;
int atomi,atomj,atomk,atomm;
@@ -893,7 +893,7 @@ void PairAIREBO::FLJ(int eflag, int vflag)
torsional forces and energy
------------------------------------------------------------------------- */
-void PairAIREBO::TORSION(int eflag, int vflag)
+void PairAIREBO::TORSION(int eflag, int /*vflag*/)
{
int i,j,k,l,ii,inum;
tagint itag,jtag;
@@ -2116,7 +2116,7 @@ but of the vector r_ij.
*/
-double PairAIREBO::bondorderLJ(int i, int j, double rij_mod[3], double rijmag_mod,
+double PairAIREBO::bondorderLJ(int i, int j, double /*rij_mod*/[3], double rijmag_mod,
double VA, double rij[3], double rijmag,
double **f, int vflag_atom)
{
diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a6e52faeba2428c41681d4ee060aa4dd0d4ea088
--- /dev/null
+++ b/src/MANYBODY/pair_atm.cpp
@@ -0,0 +1,374 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Sergey Lishchuk
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include "pair_atm.h"
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_atm_package[] =
+ "ATM package:\n\n"
+ "@Article{Lishchuk:2012:164501,\n"
+ " author = {S. V. Lishchuk},\n"
+ " title = {Role of three-body interactions in formation of bulk viscosity in liquid argon},\n"
+ " journal = {J.~Chem.~Phys.},\n"
+ " year = 2012,\n"
+ " volume = 136,\n"
+ " pages = {164501}\n"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_atm_package);
+
+ single_enable = 0;
+ restartinfo = 1;
+ one_coeff = 0;
+ manybody_flag = 1;
+}
+
+/* ----------------------------------------------------------------------
+ check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairATM::~PairATM()
+{
+ if (copymode) return;
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(nu);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ workhorse routine that computes pairwise interactions
+------------------------------------------------------------------------- */
+
+void PairATM::compute(int eflag, int vflag)
+{
+ int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
+ double xi,yi,zi,evdwl;
+ double rij2,rik2,rjk2;
+ double rij[3],rik[3],rjk[3],fj[3],fk[3];
+ double nu_local;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int *type = atom->type;
+
+ double cutoff_squared = cut_global*cut_global;
+ double triple = cut_triple*cut_triple*cut_triple;
+ double cutoff_triple_sixth = triple*triple;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // triple loop over local atoms and neighbors twice
+ // must compute each IJK triplet interaction exactly once
+ // by proc that owns the triplet atom with smallest x coord
+ // special logic to break ties if multiple atoms have same x or y coords
+ // inner two loops for jj=1,Jnum and kk=jj+1,Jnum insure
+ // the pair of other 2 non-minimum-x atoms is only considered once
+ // triplet geometry criteria for calculation:
+ // each pair distance <= cutoff
+ // produce of 3 pair distances <= cutoff_triple^3
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ xi = x[i][0];
+ yi = x[i][1];
+ zi = x[i][2];
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+ jnumm1 = jnum - 1;
+
+ for (jj = 0; jj < jnumm1; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ rij[0] = x[j][0] - xi;
+ if (rij[0] < 0.0) continue;
+ rij[1] = x[j][1] - yi;
+ if (rij[0] == 0.0 and rij[1] < 0.0) continue;
+ rij[2] = x[j][2] - zi;
+ if (rij[0] == 0.0 and rij[1] == 0.0 and rij[2] < 0.0) continue;
+ rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+ if (rij2 > cutoff_squared) continue;
+
+ for (kk = jj+1; kk < jnum; kk++) {
+ k = jlist[kk];
+ k &= NEIGHMASK;
+
+ rik[0] = x[k][0] - xi;
+ if (rik[0] < 0.0) continue;
+ rik[1] = x[k][1] - yi;
+ if (rik[0] == 0.0 and rik[1] < 0.0) continue;
+ rik[2] = x[k][2] - zi;
+ if (rik[0] == 0.0 and rik[1] == 0.0 and rik[2] < 0.0) continue;
+ rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
+ if (rik2 > cutoff_squared) continue;
+
+ rjk[0] = x[k][0] - x[j][0];
+ rjk[1] = x[k][1] - x[j][1];
+ rjk[2] = x[k][2] - x[j][2];
+ rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+ if (rjk2 > cutoff_squared) continue;
+
+ double r6 = rij2*rjk2*rik2;
+ if (r6 > cutoff_triple_sixth) continue;
+
+ nu_local = nu[type[i]][type[j]][type[k]];
+ if (nu_local == 0.0) continue;
+
+ interaction_ddd(nu_local,
+ r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+
+ f[i][0] -= fj[0] + fk[0];
+ f[i][1] -= fj[1] + fk[1];
+ f[i][2] -= fj[2] + fk[2];
+ f[j][0] += fj[0];
+ f[j][1] += fj[1];
+ f[j][2] += fj[2];
+ f[k][0] += fk[0];
+ f[k][1] += fk[1];
+ f[k][2] += fk[2];
+
+ if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,rij,rik);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairATM::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(nu,n+1,n+1,n+1,"pair:nu");
+
+ // initialize all nu values to 0.0
+
+ for (int i = 1; i <= n; i++)
+ for (int j = 1; j <= n; j++)
+ for (int k = 1; k <= n; k++)
+ nu[i][j][k] = 0.0;
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairATM::settings(int narg, char **arg)
+{
+ if (narg != 2) error->all(FLERR,"Illegal pair_style command");
+
+ cut_global = force->numeric(FLERR,arg[0]);
+ cut_triple = force->numeric(FLERR,arg[1]);
+}
+
+/* ----------------------------------------------------------------------
+ set coefficients for one I,J,K type triplet
+------------------------------------------------------------------------- */
+
+void PairATM::coeff(int narg, char **arg)
+{
+ if (narg != 4) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi,klo,khi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+ force->bounds(FLERR,arg[2],atom->ntypes,klo,khi);
+
+ double nu_one = force->numeric(FLERR,arg[3]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j<=jhi; j++) {
+ for (int k = MAX(klo,j); k<=khi; k++) {
+ nu[i][j][k] = nu_one;
+ count++;
+ }
+ setflag[i][j] = 1;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairATM::init_style()
+{
+ if (force->newton_pair == 0)
+ error->all(FLERR,"Pair style ATM requires newton pair on");
+
+ // need a full neighbor list
+
+ int irequest = neighbor->request(this,instance_me);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+}
+
+/* ----------------------------------------------------------------------
+ init for one i,j type pair and corresponding j,i
+ also for all k type permutations
+------------------------------------------------------------------------- */
+
+double PairATM::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ // set all 6 symmetric permutations of I,J,K types to same nu value
+
+ int ntypes = atom->ntypes;
+ for (int k = j; k <= ntypes; k++)
+ nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] =
+ nu[i][j][k];
+
+ return cut_global;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j,k;
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j])
+ for (k = j; k <= atom->ntypes; k++)
+ fwrite(&nu[i][j][k],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j,k;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++) {
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) for (k = j; k <= atom->ntypes; k++) {
+ if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
+ MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart_settings(FILE *fp)
+{
+ fwrite(&cut_global,sizeof(double),1,fp);
+ fwrite(&cut_triple,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart_settings(FILE *fp)
+{
+ int me = comm->me;
+ if (me == 0) {
+ fread(&cut_global,sizeof(double),1,fp);
+ fread(&cut_triple,sizeof(double),1,fp);
+ }
+ MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_triple,1,MPI_DOUBLE,0,world);
+}
+
+/* ----------------------------------------------------------------------
+ Axilrod-Teller-Muto (dipole-dipole-dipole) potential
+------------------------------------------------------------------------- */
+
+void PairATM::interaction_ddd(double nu, double r6,
+ double rij2, double rik2, double rjk2,
+ double *rij, double *rik, double *rjk,
+ double *fj, double *fk, int eflag, double &eng)
+{
+ double r5inv,rri,rrj,rrk,rrr;
+ r5inv = nu / (r6*r6*sqrt(r6));
+ rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
+ rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
+ rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
+ rrr = 5.0*rri*rrj*rrk;
+ for (int i = 0; i < 3; i++) {
+ fj[i] = rrj*(rrk - rri)*rik[i] -
+ (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] +
+ (rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i];
+ fj[i] *= 3.0*r5inv;
+ fk[i] = rrk*(rri + rrj)*rij[i] +
+ (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] +
+ (rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i];
+ fk[i] *= 3.0*r5inv;
+ }
+ if (eflag) eng = (r6 - 0.6*rrr)*r5inv;
+}
diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h
new file mode 100644
index 0000000000000000000000000000000000000000..70883a81c76fa62fd05ae6aa4d1d1df9572da845
--- /dev/null
+++ b/src/MANYBODY/pair_atm.h
@@ -0,0 +1,77 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(atm,PairATM)
+
+#else
+
+#ifndef LMP_PAIR_ATM_H
+#define LMP_PAIR_ATM_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairATM : public Pair {
+ public:
+ PairATM(class LAMMPS *);
+ virtual ~PairATM();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ virtual void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+
+ protected:
+ double cut_global,cut_triple;
+ double ***nu;
+
+ void allocate();
+ void interaction_ddd(double, double, double, double, double, double *,
+ double *, double *, double *, double *, int, double &);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal pair_style command
+
+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: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style ATM requires newton pair on
+
+See the newton command. This is a restriction to use the ATM
+potential.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index de686d4bcf5e68ebf9dedaf9aacc72dd3a3e8c65..e7b0d27b6e1e7c503ead43c500b258fc220e21de 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -432,7 +432,7 @@ void PairComb::allocate()
global settings
------------------------------------------------------------------------- */
-void PairComb::settings(int narg, char **arg)
+void PairComb::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -1542,7 +1542,7 @@ void PairComb::potal_calc(double &calc1, double &calc2, double &calc3)
void PairComb::tri_point(double rsq, int &mr1, int &mr2,
int &mr3, double &sr1, double &sr2,
- double &sr3, int &itype)
+ double &sr3, int &/*itype*/)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
@@ -1572,7 +1572,7 @@ void PairComb::tri_point(double rsq, int &mr1, int &mr2,
void PairComb::direct(int inty, int mr1, int mr2, int mr3, double rsq,
double sr1, double sr2, double sr3,
double iq, double jq,
- double potal, double fac11, double fac11e,
+ double /*potal*/, double fac11, double fac11e,
double &pot_tmp, double &pot_d)
{
double r,erfcc,fafbn1,potij,sme2,esucon;
@@ -2002,7 +2002,7 @@ void PairComb::Over_cor(Param *param, double rsq1, int NCoi,
/* ---------------------------------------------------------------------- */
int PairComb::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index b4f9c02206f926d39307b19317bd7e00b9cd16eb..72360be5f0a93a42e7113b2f6e7931c464c122b1 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -1569,7 +1569,7 @@ void PairComb3::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
- double &fforce,int eflag, double &eng, double iq, double jq)
+ double &fforce,int /*eflag*/, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,Di,Dj;
double caj,vrcs,fvrcs;
@@ -1614,7 +1614,7 @@ void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
- double rsqik, double *delrij, double *delrik, int i, double xcn)
+ double rsqik, double *delrij, double *delrik, int /*i*/, double xcn)
{
double rij,rik,costheta,arg,ex_delr,rlm3;
@@ -1661,7 +1661,7 @@ void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
/* ---------------------------------------------------------------------- */
double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
- double *delrij, double *delrik , double &zet_add)
+ double *delrij, double *delrik , double &/*zet_add*/)
{
double comtt;
double pplp0 = paramj->p6p0;
@@ -2109,7 +2109,7 @@ void PairComb3::coord(Param *param, double r, int i,
void PairComb3::cntri_int(int tri_flag, double xval, double yval,
double zval, int ixmin, int iymin, int izmin, double &vval,
- double &dvalx, double &dvaly, double &dvalz, Param *param)
+ double &dvalx, double &dvaly, double &dvalz, Param * /*param*/)
{
double x;
vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0;
@@ -2254,7 +2254,7 @@ void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1,
double prefac_ij2, double prefac_ij3, double prefac_ij4,
double prefac_ij5, double rsqij, double rsqik, double *delrij,
- double *delrik, double *fi, double *fj,double *fk, int i, double xcn)
+ double *delrik, double *fi, double *fj,double *fk, int /*i*/, double xcn)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
@@ -2867,7 +2867,7 @@ void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
/* ---------------------------------------------------------------------- */
-double PairComb3::rad_init(double rsq2,Param *param,int i,
+double PairComb3::rad_init(double rsq2,Param *param,int /*i*/,
double &radtot, double cnconj)
{
double r, fc1k, radcut;
@@ -2882,7 +2882,7 @@ double PairComb3::rad_init(double rsq2,Param *param,int i,
/* ---------------------------------------------------------------------- */
void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn)
{
int ixmin, iymin, izmin;
int radindx;
@@ -3061,7 +3061,7 @@ double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
/* ---------------------------------------------------------------------- */
void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
- double kconjug, double lconjug, int i, int j, double xcn, double ycn)
+ double kconjug, double lconjug, int /*i*/, int /*j*/, double xcn, double ycn)
{
int ixmin, iymin, izmin;
double vtor, dtorx, dtory, dtorz;
@@ -3589,7 +3589,7 @@ void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3,
void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
double iq, double jq, double &fqij, double &fqji,
- int i, int j, int nj)
+ int i, int /*j*/, int nj)
{
double r, tmp_fc;
double Di, Dj, dDi, dDj, Bsi, Bsj, dBsi, dBsj;
@@ -3863,7 +3863,7 @@ double PairComb3::switching_d(double rr)
/* ---------------------------------------------------------------------- */
int PairComb3::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 9e70b19eea753ee8174808c5e063390123f6ba47..87bcebb111cde8366fdc6ec1e6fcdd4de679790d 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -347,7 +347,7 @@ void PairEAM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEAM::settings(int narg, char **arg)
+void PairEAM::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -795,7 +795,7 @@ void PairEAM::grab(FILE *fptr, int n, double *list)
/* ---------------------------------------------------------------------- */
double PairEAM::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int m;
@@ -829,7 +829,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
int PairEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp
index 66ebad6244a9d16b939bfb61c63862742e709cc8..5b8b241b4537647b0dcdf4c59eab38ec65e4c5ef 100644
--- a/src/MANYBODY/pair_eam_cd.cpp
+++ b/src/MANYBODY/pair_eam_cd.cpp
@@ -539,7 +539,7 @@ void PairEAMCD::read_h_coeff(char *filename)
/* ---------------------------------------------------------------------- */
int PairEAMCD::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index b810d444fc6483cde6a87733b9376557efce7739..6703e159e66aa0d8691c9a2782984961c328936d 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -342,7 +342,7 @@ void PairEIM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEIM::settings(int narg, char **arg)
+void PairEIM::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -850,7 +850,7 @@ void PairEIM::array2spline()
/* ---------------------------------------------------------------------- */
void PairEIM::interpolate(int n, double delta, double *f,
- double **spline, double origin)
+ double **spline, double /*origin*/)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
@@ -1087,7 +1087,7 @@ double PairEIM::funccoul(int i, int j, double r)
/* ---------------------------------------------------------------------- */
int PairEIM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index 35f092b580e4693e45db8bbda6b0a12d20a094ac..0aff4970bb9fdae1050e4b3f980223f479f7ebfd 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -257,7 +257,7 @@ void PairGW::allocate()
global settings
------------------------------------------------------------------------- */
-void PairGW::settings(int narg, char **arg)
+void PairGW::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index d334defcc607447a357b6a2da1d215d6dcd6cba5..57373c4f854b341756f770af51c6e16424abef3e 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -121,7 +121,7 @@ void PairLCBOP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairLCBOP::settings(int narg, char **arg) {
+void PairLCBOP::settings(int narg, char **/*arg*/) {
if( narg != 0 ) error->all(FLERR,"Illegal pair_style command");
}
@@ -353,7 +353,7 @@ void PairLCBOP::SR_neigh()
Short range forces and energy
------------------------------------------------------------------------- */
-void PairLCBOP::FSR(int eflag, int vflag)
+void PairLCBOP::FSR(int eflag, int /*vflag*/)
{
int i,j,jj,ii,inum;
tagint itag,jtag;
@@ -449,7 +449,7 @@ void PairLCBOP::FSR(int eflag, int vflag)
compute long range forces and energy
------------------------------------------------------------------------- */
-void PairLCBOP::FLR(int eflag, int vflag)
+void PairLCBOP::FLR(int eflag, int /*vflag*/)
{
int i,j,jj,ii;
tagint itag,jtag;
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index 36be9c2b90758b075a7566f6c469d038049c2f5d..01718d14cdbef43be9dc1f8d7bd969e9ebdd93aa 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -174,7 +174,7 @@ void PairNb3bHarmonic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairNb3bHarmonic::settings(int narg, char **arg)
+void PairNb3bHarmonic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -454,7 +454,7 @@ void PairNb3bHarmonic::setup_params()
/* ---------------------------------------------------------------------- */
-void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik,
+void PairNb3bHarmonic::threebody(Param * /*paramij*/, Param * /*paramik*/,
Param *paramijk,
double rsq1, double rsq2,
double *delr1, double *delr2,
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index 2afb08b7a1e6e56059a44c3e862d047bb95566be..ce9af66d306d677e63d3dea23e46ccb18261b745 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -450,7 +450,7 @@ void PairPolymorphic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPolymorphic::settings(int narg, char **arg)
+void PairPolymorphic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_rebo.cpp b/src/MANYBODY/pair_rebo.cpp
index 37948f3038757ae1d22504a794fb9dc614b567e5..1f31c0b0cd67478b38c7f5d0ff67a0eb93b3e045 100644
--- a/src/MANYBODY/pair_rebo.cpp
+++ b/src/MANYBODY/pair_rebo.cpp
@@ -24,7 +24,7 @@ PairREBO::PairREBO(LAMMPS *lmp) : PairAIREBO(lmp) {}
global settings
------------------------------------------------------------------------- */
-void PairREBO::settings(int narg, char **arg)
+void PairREBO::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index 6fbc00204c3ba8e046262799357281d8730e4d22..da470d568aa6e16b0467382c73f5683224caff40 100644
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -239,7 +239,7 @@ void PairSW::allocate()
global settings
------------------------------------------------------------------------- */
-void PairSW::settings(int narg, char **arg)
+void PairSW::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 507b07e29a21fc1031b1c25269f35da942d19715..45068e5c2e59068996965ac3aac5409a33729e36 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -280,7 +280,7 @@ void PairTersoff::allocate()
global settings
------------------------------------------------------------------------- */
-void PairTersoff::settings(int narg, char **arg)
+void PairTersoff::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index 8506c9a69fd79f35f362f5f24f65854cf34e5537..54b184ea398c9b85c1c2e294c8c87424d29f25a6 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -245,7 +245,7 @@ void PairVashishta::allocate()
global settings
------------------------------------------------------------------------- */
-void PairVashishta::settings(int narg, char **arg)
+void PairVashishta::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 4d9377022b265fe1488bf241e4ac69f3c1185252..3e981c56097a511afd335b00acfc3c4ed45d3974 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -695,7 +695,7 @@ void FixAtomSwap::update_swap_atoms_list()
/* ---------------------------------------------------------------------- */
-int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixAtomSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 9a5b59b60188b89d2cf671a1a3fbf1db1e265daa..a1c9bb3ab00a61fae6cf9c3ba9c680633673508b 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -693,7 +693,7 @@ int FixBondBreak::dedup(int nstart, int nstop, tagint *copy)
/* ---------------------------------------------------------------------- */
-void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
+void FixBondBreak::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -701,7 +701,7 @@ void FixBondBreak::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondBreak::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 8e9db6a18b130819adbbf280fdbdae9ce2c9fea4..e1dd18cb5bebe868d21991498b304ce9a0246d80 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -258,14 +258,14 @@ void FixBondCreate::init()
/* ---------------------------------------------------------------------- */
-void FixBondCreate::init_list(int id, NeighList *ptr)
+void FixBondCreate::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
-void FixBondCreate::setup(int vflag)
+void FixBondCreate::setup(int /*vflag*/)
{
int i,j,m;
@@ -1206,7 +1206,7 @@ int FixBondCreate::dedup(int nstart, int nstop, tagint *copy)
/* ---------------------------------------------------------------------- */
-void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
+void FixBondCreate::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -1214,7 +1214,7 @@ void FixBondCreate::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondCreate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
@@ -1347,7 +1347,7 @@ void FixBondCreate::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixBondCreate::copy_arrays(int i, int j, int delflag)
+void FixBondCreate::copy_arrays(int i, int j, int /*delflag*/)
{
bondcount[j] = bondcount[i];
}
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index d6df4d9a960343520e610280e5941600584b6050..9a726679077c22846740281bf2af1f2272bfb795 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -182,7 +182,7 @@ void FixBondSwap::init()
/* ---------------------------------------------------------------------- */
-void FixBondSwap::init_list(int id, NeighList *ptr)
+void FixBondSwap::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index b8217103535a2e08826fffa134c831e3856bdffe..46c5e592ae9e54b8e8dce22f4e70060c638295e8 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -158,7 +158,7 @@ void FixTFMC::init()
/* ---------------------------------------------------------------------- */
-void FixTFMC::initial_integrate(int vflag)
+void FixTFMC::initial_integrate(int /*vflag*/)
{
double boltz = force->boltz;
double **x = atom->x;
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index 02f9754c2a2fdd1a78565931d607010ca66e1a49..c71eaa2295bd0460c16edb27aee9d5ff915ae955 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -65,7 +65,7 @@ PairDSMC::~PairDSMC()
/* ---------------------------------------------------------------------- */
-void PairDSMC::compute(int eflag, int vflag)
+void PairDSMC::compute(int /*eflag*/, int /*vflag*/)
{
double **x = atom->x;
double *mass = atom->mass;
@@ -405,7 +405,7 @@ void PairDSMC::read_restart_settings(FILE *fp)
the next nrezero timesteps
-------------------------------------------------------------------------*/
-void PairDSMC::recompute_V_sigma_max(int icell)
+void PairDSMC::recompute_V_sigma_max(int /*icell*/)
{
int i,j,k;
double Vsigma_max = 0;
@@ -459,7 +459,7 @@ double PairDSMC::V_sigma(int i, int j)
generate new velocities for collided particles
-------------------------------------------------------------------------*/
-void PairDSMC::scatter_random(int i, int j, int icell)
+void PairDSMC::scatter_random(int i, int j, int /*icell*/)
{
double mag_delv,cos_phi,cos_squared,r,theta;
double delv[3],vcm[3];
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index 687055aa6a6735fceb1749c4124ae73797dc8d9f..5aa13ab02e1aa7ea0a7eb511a141ec455d5eb4ca 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -325,7 +325,7 @@ void PairMEAM::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAM::settings(int narg, char **arg)
+void PairMEAM::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -448,7 +448,7 @@ void PairMEAM::init_list(int id, NeighList *ptr)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAM::init_one(int i, int j)
+double PairMEAM::init_one(int /*i*/, int /*j*/)
{
return cutmax;
}
@@ -734,7 +734,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAM::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
diff --git a/src/MESSAGE/Install.sh b/src/MESSAGE/Install.sh
new file mode 100644
index 0000000000000000000000000000000000000000..853dbddcddab6a5eceaea467276834139a53ce12
--- /dev/null
+++ b/src/MESSAGE/Install.sh
@@ -0,0 +1,67 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# arg1 = file, arg2 = file it depends on
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+action () {
+ if (test $mode = 0) then
+ rm -f ../$1
+ elif (! cmp -s $1 ../$1) then
+ if (test -z "$2" || test -e ../$2) then
+ cp $1 ..
+ if (test $mode = 2) then
+ echo " updating src/$1"
+ fi
+ fi
+ elif (test -n "$2") then
+ if (test ! -e ../$2) then
+ rm -f ../$1
+ fi
+ fi
+}
+
+# all package files with no dependencies
+
+for file in *.cpp *.h; do
+ test -f ${file} && action $file
+done
+
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package
+ sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ # multiline form needed for BSD sed on Macs
+ sed -i -e '4 i \
+include ..\/..\/lib\/message\/Makefile.lammps
+' ../Makefile.package.settings
+ fi
+
+elif (test $1 = 0) then
+
+ if (test -e ../Makefile.package) then
+ sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
+ fi
+
+ if (test -e ../Makefile.package.settings) then
+ sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
+ fi
+
+fi
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..aca5cd41f9184c947e102c6dc21b33d9e5e2d135
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -0,0 +1,325 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstdio>
+#include <cstring>
+#include "fix_client_md.h"
+#include "update.h"
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+using namespace FixConst;
+
+enum{OTHER,REAL,METAL};
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ if (lmp->clientserver != 1)
+ error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
+ if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");
+
+ if (sizeof(tagint) != 4)
+ error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
+
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else units = OTHER;
+
+ scalar_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ virial_flag = 1;
+ thermo_virial = 1;
+
+ inv_nprocs = 1.0 / comm->nprocs;
+ if (domain->dimension == 2)
+ box[0][2] = box[1][2] = box[2][0] = box[2][1] = box[2][2] = 0.0;
+
+ maxatom = 0;
+ xpbc = NULL;
+
+ // unit conversion factors for REAL
+ // otherwise not needed
+ // message received in METAL units, convert to local REAL units
+
+ fconvert = econvert = pconvert = 1.0;
+ if (units == REAL) {
+ fconvert = econvert = 23.06035; // eV -> Kcal/mole
+ pconvert = 0.986923; // bars -> atmospheres
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixClientMD::~FixClientMD()
+{
+ memory->destroy(xpbc);
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // all-done message to server
+
+ cs->send(-1,0);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ // clean-up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixClientMD::setmask()
+{
+ int mask = 0;
+ mask |= POST_FORCE;
+ mask |= MIN_POST_FORCE;
+ mask |= THERMO_ENERGY;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::init()
+{
+ if (3*atom->natoms > INT_MAX)
+ error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::setup(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // SETUP send at beginning of each run
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
+ // optional fields: others in enum above
+
+ int nfields = 8;
+ if (units == OTHER) nfields++;
+ if (atom->q_flag) nfields++;
+
+ cs->send(SETUP,nfields);
+
+ cs->pack_int(DIM,domain->dimension);
+ cs->pack(PERIODICITY,1,3,domain->periodicity);
+
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
+
+ cs->pack_int(NATOMS,atom->natoms);
+ cs->pack_int(NTYPES,atom->ntypes);
+
+ cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (units == OTHER) cs->pack_string(UNITS,update->unit_style);
+
+ if (atom->q_flag)
+ cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
+
+ // receive initial forces, energy, virial
+
+ receive_fev(vflag);
+
+ if (server_error) {
+ char str[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_setup(int vflag)
+{
+ setup(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::post_force(int vflag)
+{
+ int i,j,m;
+
+ // energy and virial setup
+
+ if (vflag) v_setup(vflag);
+ else evflag = 0;
+
+ // STEP send every step
+ // required fields: COORDS
+ // optional fields: ORIGIN, BOX
+
+ // send coords
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfields = 1;
+ if (domain->box_change) nfields += 2;
+
+ cs->send(STEP,nfields);
+
+ pack_coords();
+ cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
+
+ if (domain->box_change) {
+ pack_box();
+ cs->pack(ORIGIN,4,3,domain->boxlo);
+ cs->pack(BOX,4,9,&box[0][0]);
+ }
+
+ // receive forces, energy, virial
+
+ receive_fev(vflag);
+
+ if (server_error) {
+ char str[64];
+ sprintf(str,"Fix client/md received server error %d\n",server_error);
+ error->all(FLERR,str);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixClientMD::min_post_force(int vflag)
+{
+ post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+ potential energy from server
+------------------------------------------------------------------------- */
+
+double FixClientMD::compute_scalar()
+{
+ return eng;
+}
+
+/* ----------------------------------------------------------------------
+ pack local coords into xpbc, enforcing PBC
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_coords()
+{
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+
+ if (nlocal > maxatom) {
+ memory->destroy(xpbc);
+ maxatom = atom->nmax;
+ memory->create(xpbc,3*maxatom,"message:xpbc");
+ }
+
+ memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
+
+ int j = 0;
+ for (int i = 0; i < nlocal; i++) {
+ domain->remap(&xpbc[j]);
+ j += 3;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack box info into box = 3 edge vectors of simulation box
+------------------------------------------------------------------------- */
+
+void FixClientMD::pack_box()
+{
+ double *boxlo = domain->boxlo;
+ double *boxhi = domain->boxhi;
+
+ box[0][0] = boxhi[0] - boxlo[0];
+ box[0][1] = 0.0;
+ box[0][2] = 0.0;
+ box[1][0] = domain->xy;
+ box[1][1] = boxhi[1] - boxlo[1];
+ box[1][2] = 0.0;
+ box[2][0] = domain->xz;
+ box[2][1] = domain->yz;
+ box[2][2] = boxhi[2] - boxlo[2];
+}
+
+/* ----------------------------------------------------------------------
+ receive message from server
+ required fields: FORCES, ENERGY, PRESSURE
+ optional field: ERROR
+------------------------------------------------------------------------- */
+
+void FixClientMD::receive_fev(int vflag)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+ double *forces = (double *) cs->unpack(FORCES);
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ bigint natoms = atom->natoms;
+ int m;
+
+ int j = 0;
+ for (tagint id = 1; id <= natoms; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ f[m][0] += fconvert * forces[j++];
+ f[m][1] += fconvert * forces[j++];
+ f[m][2] += fconvert * forces[j++];
+ }
+ }
+
+ eng = econvert * cs->unpack_double(ENERGY);
+
+ if (vflag) {
+ double *v = (double *) cs->unpack(PRESSURE);
+
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = inv_nprocs * pconvert * volume / nktv2p;
+
+ for (int i = 0; i < 6; i++)
+ virial[i] = factor * v[i];
+ }
+
+ // error return
+
+ server_error = 0;
+ if (nfield == 4) server_error = cs->unpack_int(ERROR);
+}
diff --git a/src/MESSAGE/fix_client_md.h b/src/MESSAGE/fix_client_md.h
new file mode 100644
index 0000000000000000000000000000000000000000..1c874c7278e6b7474e52d1929b4767e9afea2606
--- /dev/null
+++ b/src/MESSAGE/fix_client_md.h
@@ -0,0 +1,65 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(client/md,FixClientMD)
+
+#else
+
+#ifndef LMP_FIX_CLIENT_MD_H
+#define LMP_FIX_CLIENT_MD_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixClientMD : public Fix {
+ public:
+ FixClientMD(class LAMMPS *, int, char **);
+ ~FixClientMD();
+ int setmask();
+ void init();
+ void setup(int);
+ void min_setup(int);
+ void post_force(int);
+ void min_post_force(int);
+ double compute_scalar();
+
+ private:
+ int maxatom,units,server_error;
+ double eng;
+ double inv_nprocs;
+ double fconvert,econvert,pconvert;
+ double box[3][3];
+ double *xpbc;
+
+ void pack_coords();
+ void pack_box();
+ void receive_fev(int);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+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.
+
+*/
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..329ce1fbd9e46fec5e0fd5665659f794431d0065
--- /dev/null
+++ b/src/MESSAGE/message.cpp
@@ -0,0 +1,90 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include "message.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+// customize by adding a new server protocol enum
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Message::command(int narg, char **arg)
+{
+ if (narg < 3) error->all(FLERR,"Illegal message command");
+
+ int clientserver;
+ if (strcmp(arg[0],"client") == 0) clientserver = 1;
+ else if (strcmp(arg[0],"server") == 0) clientserver = 2;
+ else error->all(FLERR,"Illegal message command");
+ lmp->clientserver = clientserver;
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[1],"md") == 0) protocol = MD;
+ else if (strcmp(arg[1],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ // instantiate CSlib with chosen communication mode
+
+ if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 ||
+ strcmp(arg[2],"mpi/two") == 0) {
+ if (narg != 4) error->all(FLERR,"Illegal message command");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world);
+
+ } else if (strcmp(arg[2],"mpi/one") == 0) {
+ if (narg != 3) error->all(FLERR,"Illegal message command");
+ if (!lmp->cscomm)
+ error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used");
+ lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world);
+
+ } else error->all(FLERR,"Illegal message command");
+
+ // perform initial handshake between client and server
+ // other code being coupled to must perform similar operation
+ // client sends protocol with msgID = 0
+ // server matches it and replies
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ if (clientserver == 1) {
+ cs->send(0,1);
+ cs->pack_string(1,arg[1]);
+
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+
+ } else {
+ int nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+ int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
+ char *pstr = cs->unpack_string(1);
+ if (strcmp(pstr,arg[1]) != 0)
+ error->one(FLERR,"Mismatch in client/server protocol");
+
+ cs->send(0,0);
+ }
+}
diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h
new file mode 100644
index 0000000000000000000000000000000000000000..c384a5a7b7f4c5a8206a6f6d004f576e6157e946
--- /dev/null
+++ b/src/MESSAGE/message.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(message,Message)
+
+#else
+
+#ifndef LMP_MESSAGE_H
+#define LMP_MESSAGE_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Message : protected Pointers {
+ public:
+ Message(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server.cpp b/src/MESSAGE/server.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f587fb76dfd6e488a56483edee9db6d56d74ff0e
--- /dev/null
+++ b/src/MESSAGE/server.cpp
@@ -0,0 +1,50 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include "server.h"
+#include "error.h"
+
+// customize by adding a new server protocol include and enum
+
+#include "server_md.h"
+#include "server_mc.h"
+
+using namespace LAMMPS_NS;
+
+enum{MD,MC};
+
+/* ---------------------------------------------------------------------- */
+
+void Server::command(int narg, char **arg)
+{
+ if (narg != 1) error->all(FLERR,"Illegal server command");
+
+ if (lmp->clientserver != 2)
+ error->all(FLERR,"Message command not used to setup LAMMPS as a server");
+
+ // customize by adding a new server protocol
+
+ int protocol;
+ if (strcmp(arg[0],"md") == 0) protocol = MD;
+ else if (strcmp(arg[0],"mc") == 0) protocol = MC;
+ else error->all(FLERR,"Unknown message protocol");
+
+ if (protocol == MD) {
+ ServerMD *server = new ServerMD(lmp);
+ server->loop();
+ } else if (protocol == MC) {
+ ServerMC *server = new ServerMC(lmp);
+ server->loop();
+ }
+}
diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h
new file mode 100644
index 0000000000000000000000000000000000000000..579f6ab6f12603ae516d39ec4b88f62fe58b341f
--- /dev/null
+++ b/src/MESSAGE/server.h
@@ -0,0 +1,40 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMMAND_CLASS
+
+CommandStyle(server,Server)
+
+#else
+
+#ifndef LMP_SERVER_H
+#define LMP_SERVER_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Server : protected Pointers {
+ public:
+ Server(class LAMMPS *lmp) : Pointers(lmp) {};
+ void command(int, char **);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..8a7344e86b6930483c5079e413372b578dff994c
--- /dev/null
+++ b/src/MESSAGE/server_mc.cpp
@@ -0,0 +1,148 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "server_mc.h"
+#include "atom.h"
+#include "update.h"
+#include "integrate.h"
+#include "input.h"
+#include "output.h"
+#include "thermo.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
+
+/* ---------------------------------------------------------------------- */
+
+ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMC::loop()
+{
+ int i,j,m;
+ double xold[3],xnew[3];
+ tagint atomid;
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // require atom map
+
+ if (!atom->map_style) error->all(FLERR,"Server mode requires atom map");
+
+ // initialize LAMMPS for dynamics
+
+ input->one("run 0");
+
+ //update->whichflag = 1;
+ //lmp->init();
+
+ // loop on messages
+ // receive a message, process it, send return message if necessary
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ if (msgID == NATOMS) {
+
+ cs->send(msgID,1);
+ cs->pack_int(1,atom->natoms);
+
+ } else if (msgID == EINIT) {
+
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,2);
+ cs->pack_double(1,dval);
+ double *coords = NULL;
+ if (atom->nlocal) coords = &atom->x[0][0];
+ cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords);
+
+ } else if (msgID == DISPLACE) {
+
+ atomid = cs->unpack_int(1);
+ double *xnew = (double *) cs->unpack(2);
+ double **x = atom->x;
+
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ xold[0] = x[m][0];
+ xold[1] = x[m][1];
+ xold[2] = x[m][2];
+ x[m][0] = xnew[0];
+ x[m][1] = xnew[1];
+ x[m][2] = xnew[2];
+ }
+
+ input->one("run 0");
+ double dval;
+ output->thermo->evaluate_keyword((char *) "pe",&dval);
+
+ cs->send(msgID,1);
+ cs->pack_double(1,dval);
+
+ } else if (msgID == ACCEPT) {
+
+ int accept = cs->unpack_int(1);
+ double **x = atom->x;
+
+ if (!accept) {
+ m = atom->map(atomid);
+ if (m >= 0 && m < atom->nlocal) {
+ x[m][0] = xold[0];
+ x[m][1] = xold[1];
+ x[m][2] = xold[2];
+ }
+ }
+
+ cs->send(msgID,0);
+
+ } else if (msgID == RUN) {
+
+ int nsteps = cs->unpack_int(1);
+
+ //input->one("run 100");
+
+ update->nsteps = nsteps;
+ update->firststep = update->ntimestep;
+ update->laststep = update->ntimestep + nsteps;
+
+ update->integrate->setup(1);
+ update->integrate->run(nsteps);
+
+ cs->send(msgID,0);
+
+ } else error->all(FLERR,"Server received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
diff --git a/src/MESSAGE/server_mc.h b/src/MESSAGE/server_mc.h
new file mode 100644
index 0000000000000000000000000000000000000000..d0fb48942929934bdf57580070c00e61118ec959
--- /dev/null
+++ b/src/MESSAGE/server_mc.h
@@ -0,0 +1,29 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MC_H
+#define LMP_SERVER_MC_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMC : protected Pointers {
+ public:
+ ServerMC(class LAMMPS *);
+ void loop();
+};
+
+}
+
+#endif
diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..aa771b7d4654b05469dd62b5d42e486532455323
--- /dev/null
+++ b/src/MESSAGE/server_md.cpp
@@ -0,0 +1,389 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cstring>
+#include "server_md.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "update.h"
+#include "integrate.h"
+#include "kspace.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "comm.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+// CSlib interface
+
+#include "cslib.h"
+
+using namespace LAMMPS_NS;
+using namespace CSLIB_NS;
+
+enum{OTHER,REAL,METAL};
+enum{SETUP=1,STEP};
+enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
+enum{FORCES=1,ENERGY,PRESSURE,ERROR};
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
+{
+ if (domain->box_exist == 0)
+ error->all(FLERR,"Server command before simulation box is defined");
+
+ if (!atom->map_style) error->all(FLERR,"Server md requires atom map");
+ if (atom->tag_enable == 0) error->all(FLERR,"Server md requires atom IDs");
+ if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
+
+ if (strcmp(update->unit_style,"real") == 0) units = REAL;
+ else if (strcmp(update->unit_style,"metal") == 0) units = METAL;
+ else units = OTHER;
+
+ // unit conversion factors for REAL
+ // otherwise not needed
+ // local computation in REAL units, send message in METAL units
+
+ fconvert = econvert = pconvert = 1.0;
+ if (units == REAL) {
+ fconvert = econvert = 1.0 / 23.06035; // Kcal/mole -> eV
+ pconvert = 1.0 / 0.986923; // atmospheres -> bars
+ }
+
+ fcopy = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ServerMD::~ServerMD()
+{
+ memory->destroy(fcopy);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ServerMD::loop()
+{
+ int i,j,m;
+
+ // cs = instance of CSlib
+
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ // counters
+
+ int forcecalls = 0;
+ int neighcalls = 0;
+
+ // loop on messages
+ // receive a message, process it, send return message
+
+ int msgID,nfield;
+ int *fieldID,*fieldtype,*fieldlen;
+
+ while (1) {
+ msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
+ if (msgID < 0) break;
+
+ // SETUP receive at beginning of each run
+ // required fields: DIM, PERIODICTY, ORIGIN, BOX,
+ // NATOMS, NTYPES, TYPES, COORDS
+ // optional fields: others in enum above
+
+ if (msgID == SETUP) {
+
+ int dim = 0;
+ int *periodicity = NULL;
+ int natoms = -1;
+ int ntypes = -1;
+ double *origin = NULL;
+ double *box = NULL;
+ int *types = NULL;
+ double *coords = NULL;
+ char *unit_style = NULL;
+ double *charge = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == DIM) {
+ dim = cs->unpack_int(DIM);
+ if (dim != domain->dimension)
+ error->all(FLERR,"Server md dimension mis-match with client");
+ } else if (fieldID[ifield] == PERIODICITY) {
+ periodicity = (int *) cs->unpack(PERIODICITY);
+ if (periodicity[0] != domain->periodicity[0] ||
+ periodicity[1] != domain->periodicity[1] ||
+ periodicity[2] != domain->periodicity[2])
+ error->all(FLERR,"Server md periodicity mis-match with client");
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
+ } else if (fieldID[ifield] == NATOMS) {
+ natoms = cs->unpack_int(NATOMS);
+ if (3*natoms > INT_MAX)
+ error->all(FLERR,"Server md max atoms is 1/3 of 2^31");
+ } else if (fieldID[ifield] == NTYPES) {
+ ntypes = cs->unpack_int(NTYPES);
+ if (ntypes != atom->ntypes)
+ error->all(FLERR,"Server md ntypes mis-match with client");
+ } else if (fieldID[ifield] == TYPES) {
+ types = (int *) cs->unpack(TYPES);
+ } else if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+
+ } else if (fieldID[ifield] == UNITS) {
+ unit_style = (char *) cs->unpack(UNITS);
+ } else if (fieldID[ifield] == CHARGE) {
+ charge = (double *) cs->unpack(CHARGE);
+ } else error->all(FLERR,"Server md setup field unknown");
+ }
+
+ if (dim == 0 || !periodicity || !origin || !box ||
+ natoms < 0 || ntypes < 0 || !types || !coords)
+ error->all(FLERR,"Required server md setup field not received");
+
+ if (unit_style && strcmp(unit_style,update->unit_style) != 0)
+ error->all(FLERR,"Server md does not match client units");
+
+ if (charge && atom->q_flag == 0)
+ error->all(FLERR,"Server md does not define atom attribute q");
+
+ // reset box, global and local
+ // reset proc decomposition
+
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
+
+ box_change(origin,box);
+
+ domain->set_initial_box();
+ domain->set_global_box();
+ comm->set_proc_grid();
+ domain->set_local_box();
+
+ // clear all atoms
+
+ atom->nlocal = 0;
+ atom->nghost = 0;
+
+ // add atoms that are in my sub-box
+
+ int nlocal = 0;
+ for (int i = 0; i < natoms; i++) {
+ if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue;
+ atom->avec->create_atom(types[i],&coords[3*i]);
+ atom->tag[nlocal] = i+1;
+ if (charge) atom->q[nlocal] = charge[i];
+ nlocal++;
+ }
+
+ int ntotal;
+ MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
+ if (ntotal != natoms)
+ error->all(FLERR,"Server md atom count does not match client");
+
+ atom->map_init();
+ atom->map_set();
+ atom->natoms = natoms;
+
+ // allocate fcopy if needed
+
+ if (units == REAL) {
+ memory->destroy(fcopy);
+ memory->create(fcopy,atom->nlocal,3,"server/md:fcopy");
+ }
+
+ // perform system setup() for dynamics
+ // also OK for minimization, since client runs minimizer
+ // return forces, energy, virial to client
+
+ update->whichflag = 1;
+ lmp->init();
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ forcecalls++;
+
+ send_fev(msgID);
+
+ // STEP receive at each timestep of run or minimization
+ // required fields: COORDS
+ // optional fields: ORIGIN, BOX
+
+ } else if (msgID == STEP) {
+
+ double *coords = NULL;
+ double *origin = NULL;
+ double *box = NULL;
+
+ for (int ifield = 0; ifield < nfield; ifield++) {
+ if (fieldID[ifield] == COORDS) {
+ coords = (double *) cs->unpack(COORDS);
+ } else if (fieldID[ifield] == ORIGIN) {
+ origin = (double *) cs->unpack(ORIGIN);
+ } else if (fieldID[ifield] == BOX) {
+ box = (double *) cs->unpack(BOX);
+ } else error->all(FLERR,"Server md step field unknown");
+ }
+
+ if (!coords)
+ error->all(FLERR,"Required server md step field not received");
+
+ // change box size/shape, only if origin and box received
+ // reset global/local box like FixDeform at end_of_step()
+
+ if (origin && box) {
+ if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) &&
+ domain->triclinic == 0)
+ error->all(FLERR,"Server md is not initialized for a triclinic box");
+ box_change(origin,box);
+ domain->set_global_box();
+ domain->set_local_box();
+ }
+
+ // assign received coords to owned atoms
+ // closest_image() insures xyz matches current server PBC
+
+ double **x = atom->x;
+ int nlocal = atom->nlocal;
+ int nall = atom->natoms;
+
+ j = 0;
+ for (tagint id = 1; id <= nall; id++) {
+ m = atom->map(id);
+ if (m < 0 || m >= nlocal) j += 3;
+ else {
+ domain->closest_image(x[m],&coords[j],x[m]);
+ j += 3;
+ }
+ }
+
+ // if no need to reneighbor:
+ // ghost comm
+ // setup_minimal(0) which just computes forces
+ // else:
+ // setup_minimal(1) for pbc, reset_box, reneigh, forces
+
+ int nflag = neighbor->decide();
+ if (nflag == 0) {
+ comm->forward_comm();
+ update->integrate->setup_minimal(0);
+ } else {
+ update->integrate->setup_minimal(1);
+ neighcalls++;
+ }
+
+ forcecalls++;
+
+ send_fev(msgID);
+
+ } else error->all(FLERR,"Server MD received unrecognized message");
+ }
+
+ // final reply to client
+
+ cs->send(0,0);
+
+ // stats
+
+ if (comm->me == 0) {
+ if (screen) {
+ fprintf(screen,"Server MD calls = %d\n",forcecalls);
+ fprintf(screen,"Server MD reneighborings = %d\n",neighcalls);
+ }
+ if (logfile) {
+ fprintf(logfile,"Server MD calls = %d\n",forcecalls);
+ fprintf(logfile,"Server MD reneighborings %d\n",neighcalls);
+ }
+ }
+
+ // clean up
+
+ delete cs;
+ lmp->cslib = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ box change due to received message
+------------------------------------------------------------------------- */
+
+void ServerMD::box_change(double *origin, double *box)
+{
+ domain->boxlo[0] = origin[0];
+ domain->boxlo[1] = origin[1];
+ domain->boxlo[2] = origin[2];
+
+ domain->boxhi[0] = origin[0] + box[0];
+ domain->boxhi[1] = origin[1] + box[4];
+ domain->boxhi[2] = origin[2] + box[8];
+
+ domain->xy = box[3];
+ domain->xz = box[6];
+ domain->yz = box[7];
+}
+
+/* ----------------------------------------------------------------------
+ return message with forces, energy, pressure tensor
+ pressure tensor should be just pair and KSpace contributions
+ required fields: FORCES, ENERGY, PRESSURE
+ optional field: ERROR (not ever sending)
+------------------------------------------------------------------------- */
+
+void ServerMD::send_fev(int msgID)
+{
+ CSlib *cs = (CSlib *) lmp->cslib;
+
+ cs->send(msgID,3);
+
+ double *forces = NULL;
+ if (atom->nlocal) {
+ if (units != REAL) forces = &atom->f[0][0];
+ else {
+ double **f = atom->f;
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ fcopy[i][0] = fconvert*f[i][0];
+ fcopy[i][1] = fconvert*f[i][1];
+ fcopy[i][2] = fconvert*f[i][2];
+ }
+ forces = &fcopy[0][0];
+ }
+ }
+ cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces);
+
+ double eng = force->pair->eng_vdwl + force->pair->eng_coul;
+ double engall;
+ MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
+ engall *= econvert;
+ cs->pack_double(ENERGY,engall);
+
+ double v[6],vall[6];
+ for (int i = 0; i < 6; i++)
+ v[i] = force->pair->virial[i];
+ MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
+
+ if (force->kspace)
+ for (int i = 0; i < 6; i++)
+ vall[i] += force->kspace->virial[i];
+
+ double nktv2p = force->nktv2p;
+ double volume = domain->xprd * domain->yprd * domain->zprd;
+ double factor = pconvert / volume * nktv2p;
+ for (int i = 0; i < 6; i++) vall[i] *= factor;
+
+ cs->pack(PRESSURE,4,6,vall);
+}
diff --git a/src/MESSAGE/server_md.h b/src/MESSAGE/server_md.h
new file mode 100644
index 0000000000000000000000000000000000000000..289d70bdd8a087f7f252ec9ac7e8f78155c2f4e7
--- /dev/null
+++ b/src/MESSAGE/server_md.h
@@ -0,0 +1,38 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_SERVER_MD_H
+#define LMP_SERVER_MD_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class ServerMD : protected Pointers {
+ public:
+ ServerMD(class LAMMPS *);
+ ~ServerMD();
+ void loop();
+
+ private:
+ int units;
+ double fconvert,econvert,pconvert;
+ double **fcopy;
+
+ void box_change(double *, double *);
+ void send_fev(int);
+};
+
+}
+
+#endif
diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp
index 1fa141e2bf3c9ea821436fc46a105dbbf034dd6b..004c8ad7bc4ac254c884a44f32cdef7aa03c010a 100644
--- a/src/MISC/fix_efield.cpp
+++ b/src/MISC/fix_efield.cpp
@@ -412,7 +412,7 @@ void FixEfield::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEfield::post_force_respa(int vflag, int ilevel, int iloop)
+void FixEfield::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 370730133ee1cc77eaa9dde98bb91ebb5e8bc01c..2bf02889a522a3639b7fd79bbe2c2661b169aea3 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -217,7 +217,7 @@ void FixGLD::init()
First half of a timestep (V^{n} -> V^{n+1/2}; X^{n} -> X^{n+1})
------------------------------------------------------------------------- */
-void FixGLD::initial_integrate(int vflag)
+void FixGLD::initial_integrate(int /*vflag*/)
{
double dtfm;
double ftm2v = force->ftm2v;
@@ -444,7 +444,7 @@ void FixGLD::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixGLD::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
@@ -458,7 +458,7 @@ void FixGLD::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixGLD::final_integrate_respa(int ilevel, int iloop)
+void FixGLD::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * (force->ftm2v);
final_integrate();
@@ -507,7 +507,7 @@ void FixGLD::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixGLD::copy_arrays(int i, int j, int delflag)
+void FixGLD::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < 3*prony_terms; k++) {
s_gld[j][k] = s_gld[i][k];
@@ -588,7 +588,7 @@ void FixGLD::unpack_restart(int nlocal, int nth)
fixes on a given processor.
------------------------------------------------------------------------- */
-int FixGLD::size_restart(int nlocal)
+int FixGLD::size_restart(int /*nlocal*/)
{
return 3*prony_terms+1;
}
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index c5ba6514a90c566688e530f85d65415039586b22..c61457793324f7ea14afd629a0044d7bfb251052 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -230,7 +230,7 @@ void FixOrientBCC::init()
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::init_list(int id, NeighList *ptr)
+void FixOrientBCC::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -250,7 +250,7 @@ void FixOrientBCC::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::post_force(int vflag)
+void FixOrientBCC::post_force(int /*vflag*/)
{
int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
tagint id_self;
@@ -471,7 +471,7 @@ void FixOrientBCC::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientBCC::post_force_respa(int vflag, int ilevel, int iloop)
+void FixOrientBCC::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -488,7 +488,7 @@ double FixOrientBCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientBCC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index 5786571a89e9a9ccb8445ee2bc4c5582af8c22f6..5b394adde70fdbe0dc3a18e9ff2439c9a71ecbec 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -228,7 +228,7 @@ void FixOrientFCC::init()
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::init_list(int id, NeighList *ptr)
+void FixOrientFCC::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -248,7 +248,7 @@ void FixOrientFCC::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::post_force(int vflag)
+void FixOrientFCC::post_force(int /*vflag*/)
{
int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort;
tagint id_self;
@@ -469,7 +469,7 @@ void FixOrientFCC::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixOrientFCC::post_force_respa(int vflag, int ilevel, int iloop)
+void FixOrientFCC::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -486,7 +486,7 @@ double FixOrientFCC::compute_scalar()
/* ---------------------------------------------------------------------- */
int FixOrientFCC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,num;
tagint id;
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index 7ffd979e5089ca391990427693276bc30c74b5a4..c8f33c73b7e28a45584648ccc6e4a43d3fc2e88f 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -235,7 +235,7 @@ void FixTTM::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force(int vflag)
+void FixTTM::post_force(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
@@ -287,7 +287,7 @@ void FixTTM::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_setup(int vflag)
+void FixTTM::post_force_setup(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -306,14 +306,14 @@ void FixTTM::post_force_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTTM::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
-void FixTTM::post_force_respa_setup(int vflag, int ilevel, int iloop)
+void FixTTM::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
@@ -685,7 +685,7 @@ int FixTTM::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTTM::size_restart(int nlocal)
+int FixTTM::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index a778d7a5b6c839f4bce0dcf1f08af09be831e56e..ce077a7a045f6de8d31eb51d720638357018286d 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -401,8 +401,8 @@ void PairNMCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairNMCut::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairNMCut::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r,forcenm,phinm;
diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp
index 3987aa02fc2e0252cdd1eff3ceaf0b2113cd72c1..0f4d73cdd9a3c35329c2cedd650747cad165bed0 100644
--- a/src/MISC/xdr_compat.cpp
+++ b/src/MISC/xdr_compat.cpp
@@ -650,7 +650,7 @@ xdrstdio_setpos (XDR *xdrs, unsigned int pos)
}
static xdr_int32_t *
-xdrstdio_inline (XDR *xdrs, int len)
+xdrstdio_inline (XDR * /*xdrs*/, int /*len*/)
{
/*
* Must do some work to implement this: must insure
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index e3472dfd7a6b3050a0ab2690764efb8ffaece032..7fb7ce4c277f3d54f4f9aec22f0a7b8f160816f2 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -172,7 +172,7 @@ void AngleCosine::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double AngleCosine::equilibrium_angle(int i)
+double AngleCosine::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index 4e620b436e4f0a3a505d683e792e1ea8fc5cc3a0..e8dd970b3b30ec92df5b6219e3d350a3a7f4dba7 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -222,7 +222,7 @@ void AngleCosinePeriodic::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
-double AngleCosinePeriodic::equilibrium_angle(int i)
+double AngleCosinePeriodic::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index b6da72bfaf6b6968609ed1670a14149b66cd5be3..671290b0add318040bcb94fd8026c3294f28aede 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -242,7 +242,7 @@ void BondFENE::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondFENE::single(int type, double rsq, int i, int j,
+double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r0sq = r0[type] * r0[type];
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index 26b699d7bfdcca6cdd8d1ecb2d87e0d610c4ac38..3e191683fb8354240ad588fb4b6a764162918a0d 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -253,7 +253,7 @@ void BondFENEExpand::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondFENEExpand::single(int type, double rsq, int i, int j,
+double BondFENEExpand::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp
index 8e989259afa750eabdf5f44ac2ef91ab8f943b58..279f4fb2d40c0a714416014b94c3bae2c1da9629 100644
--- a/src/MOLECULE/bond_gromos.cpp
+++ b/src/MOLECULE/bond_gromos.cpp
@@ -190,7 +190,7 @@ void BondGromos::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondGromos::single(int type, double rsq, int i, int j,
+double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double dr = rsq - r0[type]*r0[type];
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index e7f510d2de9c59607351eba0b80ac51ce19a7831..f795610b37efb435f728e1be8a6df6ac7ff32a33 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -190,7 +190,7 @@ void BondHarmonic::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonic::single(int type, double rsq, int i, int j,
+double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 35be50e8df9b6eebd071933953b1298c9d6e8ad3..06af28f2b0c1f780b86288c502ffcabd1457c03b 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -196,7 +196,7 @@ void BondMorse::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondMorse::single(int type, double rsq, int i, int j,
+double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index 3926c3494b3666e0a30af5b5c51bd00bc92476ca..645b08177919a444f512d32eb090358fcc609f03 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -191,7 +191,7 @@ void BondNonlinear::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondNonlinear::single(int type, double rsq, int i, int j,
+double BondNonlinear::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index f581c7f33155e6d0059d0925e6be5524680e2574..f200030d6cccae7df156da3389d8f14715059a3a 100644
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -251,7 +251,7 @@ void BondQuartic::init_style()
return an equilbrium bond length
------------------------------------------------------------------------- */
-double BondQuartic::equilibrium_distance(int i)
+double BondQuartic::equilibrium_distance(int /*i*/)
{
return 0.97;
}
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index 7515f713df7db4d3e07fe0019f4fec10e93303a0..a5c579042b018d32e062393bc8a2738566fcd7d2 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -244,7 +244,7 @@ void BondTable::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondTable::single(int type, double rsq, int i, int j,
+double BondTable::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index 5ef2e662abfb6cc618cb8c377fef940385410b38..b527eef020ef2fb592b1681662ec4af25d03fe78 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -295,7 +295,7 @@ void FixCMAP::pre_neighbor()
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixCMAP::pre_reverse(int eflag, int vflag)
+void FixCMAP::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
@@ -604,7 +604,7 @@ void FixCMAP::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixCMAP::post_force_respa(int vflag, int ilevel, int iloop)
+void FixCMAP::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -1163,7 +1163,7 @@ void FixCMAP::read_data_section(char *keyword, int n, char *buf,
/* ---------------------------------------------------------------------- */
-bigint FixCMAP::read_data_skip_lines(char *keyword)
+bigint FixCMAP::read_data_skip_lines(char * /*keyword*/)
{
return ncmap;
}
@@ -1173,7 +1173,7 @@ bigint FixCMAP::read_data_skip_lines(char *keyword)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_header(FILE *fp, int mth)
+void FixCMAP::write_data_header(FILE *fp, int /*mth*/)
{
fprintf(fp,BIGINT_FORMAT " cmap crossterms\n",ncmap);
}
@@ -1186,7 +1186,7 @@ void FixCMAP::write_data_header(FILE *fp, int mth)
ny = columns = type + 5 atom IDs
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
+void FixCMAP::write_data_section_size(int /*mth*/, int &nx, int &ny)
{
int i,m;
@@ -1206,7 +1206,7 @@ void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
buf allocated by caller as owned crossterms by 6
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_pack(int mth, double **buf)
+void FixCMAP::write_data_section_pack(int /*mth*/, double **buf)
{
int i,m;
@@ -1237,7 +1237,7 @@ void FixCMAP::write_data_section_pack(int mth, double **buf)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
+void FixCMAP::write_data_section_keyword(int /*mth*/, FILE *fp)
{
fprintf(fp,"\nCMAP\n\n");
}
@@ -1249,7 +1249,7 @@ void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
only called by proc 0
------------------------------------------------------------------------- */
-void FixCMAP::write_data_section(int mth, FILE *fp,
+void FixCMAP::write_data_section(int /*mth*/, FILE *fp,
int n, double **buf, int index)
{
for (int i = 0; i < n; i++)
@@ -1383,7 +1383,7 @@ void FixCMAP::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixCMAP::copy_arrays(int i, int j, int delflag)
+void FixCMAP::copy_arrays(int i, int j, int /*delflag*/)
{
num_crossterm[j] = num_crossterm[i];
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index 26ff499dec6cd0dd2b6b8bb6ad15c95fb97032ca..c0c885d4d4ccd3cb144cc7d6958c384f5cc58d2b 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -468,7 +468,7 @@ double PairHbondDreidingLJ::init_one(int i, int j)
double PairHbondDreidingLJ::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int k,kk,ktype,knum,m;
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 749053164cf5746602ac31e933ac533659e51609..f464d2c621f38183ce57eb72e14525b8a23c7e9e 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -371,7 +371,7 @@ void PairHbondDreidingMorse::init_style()
double PairHbondDreidingMorse::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
int k,kk,ktype,knum,m;
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index e9f52b87246c3ef076818253b160893d019c44b6..79dd79b18013094187985c8a72d66f6e72fa1eaf 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -443,7 +443,7 @@ void PairTIP4PCut::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairTIP4PCut::init_one(int i, int j)
+double PairTIP4PCut::init_one(int /*i*/, int /*j*/)
{
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe078a51e70ca617375e0b90b44a3257..b9cabfd67bbd533db4a8427880c89a3f05d90932 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -53,7 +53,7 @@ endif
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
- granular kim kokkos kspace latte manybody mc meam misc \
+ granular kim kokkos kspace latte manybody mc meam message misc \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap spin srd voronoi
@@ -65,14 +65,14 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
-PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
+PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-qmmm user-quip user-smd user-vtk
PACKSYS = compress mpiio python user-lb
-PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
+PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
user-h5md user-molfile user-netcdf user-qmmm user-quip \
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 42d86e14b2b4eec17c78d95457c48647af0f7b86..66137e6a01445c5168f4a6a6cb3484f989954157 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -140,7 +140,7 @@ void FixPeriNeigh::init()
/* ---------------------------------------------------------------------- */
-void FixPeriNeigh::init_list(int id, NeighList *ptr)
+void FixPeriNeigh::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -159,7 +159,7 @@ void FixPeriNeigh::min_setup(int vflag)
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
-void FixPeriNeigh::setup(int vflag)
+void FixPeriNeigh::setup(int /*vflag*/)
{
int i,j,ii,jj,itype,jtype,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -441,7 +441,7 @@ void FixPeriNeigh::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
+void FixPeriNeigh::copy_arrays(int i, int j, int /*delflag*/)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
@@ -514,7 +514,7 @@ int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index 9950c36f41446ca28adbeb0162dd188adf0eb6e6..76267426c64f6627b723d8268693f65267e60cbb 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -434,7 +434,7 @@ void PairPeriEPS::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriEPS::settings(int narg, char **arg)
+void PairPeriEPS::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -799,7 +799,7 @@ double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
---------------------------------------------------------------------- */
int PairPeriEPS::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 4c48223b0749e9ebc7b4cbe4e4d1345854da21b9..383b91c6f554e62ae1e8c00497bcc69350f29830 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -364,7 +364,7 @@ void PairPeriLPS::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriLPS::settings(int narg, char **arg)
+void PairPeriLPS::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -631,7 +631,7 @@ void PairPeriLPS::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriLPS::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 81461f0b83f0c7c12df432046036a6003199397f..772e47f2d64b60839af00f6d5a98f9e104bdf958 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -297,7 +297,7 @@ void PairPeriPMB::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriPMB::settings(int narg, char **arg)
+void PairPeriPMB::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -441,7 +441,7 @@ void PairPeriPMB::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairPeriPMB::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double delx0,dely0,delz0,rsq0;
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index a9f620ef4b7bcbc4b92b7881a6ebaf8e8ea0e8fc..7590077f0e3f55c89057f70b746cbcec989838dc 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -411,7 +411,7 @@ void PairPeriVES::allocate()
global settings
------------------------------------------------------------------------- */
-void PairPeriVES::settings(int narg, char **arg)
+void PairPeriVES::settings(int narg, char **/*arg*/)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
@@ -697,7 +697,7 @@ void PairPeriVES::compute_dilatation()
---------------------------------------------------------------------- */
int PairPeriVES::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 8acf4498f5c6f67db6a1640d4872ff34efe2b746..0fe041209f083d46ce6f674c088c3c71673b0d2b 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -274,7 +274,7 @@ void FixQEq::reallocate_matrix()
/* ---------------------------------------------------------------------- */
-void FixQEq::init_list(int id, NeighList *ptr)
+void FixQEq::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -329,7 +329,7 @@ void FixQEq::init_storage()
/* ---------------------------------------------------------------------- */
-void FixQEq::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixQEq::pre_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) pre_force(vflag);
}
@@ -471,7 +471,7 @@ void FixQEq::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEq::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m;
@@ -552,7 +552,7 @@ void FixQEq::grow_arrays(int nmax)
copy values within fictitious charge arrays
------------------------------------------------------------------------- */
-void FixQEq::copy_arrays(int i, int j, int delflag)
+void FixQEq::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index aeb8dd2c59043d1c1852e8cd678074d19e51785c..f496c7e6c0c28c58b2466f17bbb15a07b1dc9d4a 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -88,7 +88,7 @@ void FixQEqDynamic::init()
/* ---------------------------------------------------------------------- */
-void FixQEqDynamic::pre_force(int vflag)
+void FixQEqDynamic::pre_force(int /*vflag*/)
{
int i,ii,iloop,inum,*ilist;
double qmass,dtq2;
@@ -247,7 +247,7 @@ double FixQEqDynamic::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m=0;
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index db63bec2063f98de16b963be899e72b920d06023..83c9907f1b6e29c2cd3530a14d10720a682d3fe2 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -104,7 +104,7 @@ void FixQEqFire::init()
/* ---------------------------------------------------------------------- */
-void FixQEqFire::pre_force(int vflag)
+void FixQEqFire::pre_force(int /*vflag*/)
{
int inum, *ilist;
int i,ii,iloop;
@@ -311,7 +311,7 @@ double FixQEqFire::compute_eneg()
/* ---------------------------------------------------------------------- */
int FixQEqFire::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m = 0;
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index bf7130c1d6704b334f05c227245082e61f107fd9..db2d800c06b40f5a6405f6fcc376562fe60259de 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -67,7 +67,7 @@ void FixQEqPoint::init()
/* ---------------------------------------------------------------------- */
-void FixQEqPoint::pre_force(int vflag)
+void FixQEqPoint::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index 70898fd96c68908ca4c74203a72c577883710ff0..88cd1ab3ad22509109df62714846fa2614c68b4e 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -111,7 +111,7 @@ void FixQEqShielded::init_shielding()
/* ---------------------------------------------------------------------- */
-void FixQEqShielded::pre_force(int vflag)
+void FixQEqShielded::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 4ddcf06357b3e5c42e010a47c16f1fd8177a0a16..81fdc73241d4f171f155692952d2fd57bbb9f71f 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -107,7 +107,7 @@ void FixQEqSlater::extract_streitz()
/* ---------------------------------------------------------------------- */
-void FixQEqSlater::pre_force(int vflag)
+void FixQEqSlater::pre_force(int /*vflag*/)
{
if (update->ntimestep % nevery) return;
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index 3b9b49ac57a24977766a144388a99b52cf3d8103..8fc5de6b1600edf0fec80b3b71b3b83f0408461a 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -241,7 +241,7 @@ void FixEvent::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixEvent::copy_arrays(int i, int j, int delflag)
+void FixEvent::copy_arrays(int i, int j, int /*delflag*/)
{
xevent[j][0] = xevent[i][0];
xevent[j][1] = xevent[i][1];
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index e5d24da392649fe1f8cecbd9bc20fea0e17194b9..dc86c709564822e20929e5fcd0c3315ce37a7dcb 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -270,7 +270,7 @@ void FixNEB::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixNEB::min_post_force(int vflag)
+void FixNEB::min_post_force(int /*vflag*/)
{
double vprev,vnext;
double delxp,delyp,delzp,delxn,delyn,delzn;
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 7ade8d6848f176e64456dd875c53768a69fe2fab..403f3091c62d6a1941519f93b984cfe6637b8c76 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -185,7 +185,7 @@ void FixRattle::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRattle::post_force_respa(int vflag, int ilevel, int iloop)
+void FixRattle::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// remember vflag for the coordinate correction in this->final_integrate
@@ -625,7 +625,7 @@ void FixRattle::update_v_half_nocons()
/* ---------------------------------------------------------------------- */
-void FixRattle::update_v_half_nocons_respa(int ilevel)
+void FixRattle::update_v_half_nocons_respa(int /*ilevel*/)
{
// carry out unconstrained velocity update
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 7104d3084994d2c7d9c4b4ff5d89d8aa387d6c00..c15a909adae028a4cbc9c6c2416958768876659e 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -1030,7 +1030,6 @@ void FixRigid::enforce2d()
void FixRigid::compute_forces_and_torques()
{
int i,ibody;
- double dtfm;
// sum over atoms to get force and torque on rigid body
@@ -1096,7 +1095,7 @@ void FixRigid::compute_forces_and_torques()
/* ---------------------------------------------------------------------- */
-void FixRigid::post_force(int vflag)
+void FixRigid::post_force(int /*vflag*/)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
@@ -1141,7 +1140,7 @@ void FixRigid::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRigid::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -1153,7 +1152,7 @@ void FixRigid::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixRigid::final_integrate_respa(int ilevel, int iloop)
+void FixRigid::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
@@ -2478,7 +2477,7 @@ void FixRigid::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixRigid::copy_arrays(int i, int j, int delflag)
+void FixRigid::copy_arrays(int i, int j, int /*delflag*/)
{
body[j] = body[i];
xcmimage[j] = xcmimage[i];
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 96c44d15b5b0e1861803203e4d20e0d0e052e891..4dceb1b8b4c214aab95999db1ff901df53341062 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -591,9 +591,9 @@ void FixRigidNH::initial_integrate(int vflag)
void FixRigidNH::final_integrate()
{
- int i,ibody;
+ int ibody;
double tmp,scale_t[3],scale_r;
- double dtfm,xy,xz,yz;
+ double dtfm;
double mbody[3],tbody[3],fquat[4];
double dtf2 = dtf * 2.0;
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 135a1fb4bdb0e8ee37b8e958bb31e5b6117a1a33..5016d3f1685eed9d809172de4d24344a056c5f75 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -618,7 +618,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
void FixRigidNHSmall::final_integrate()
{
- int i,ibody;
+ int ibody;
double tmp,scale_t[3],scale_r;
double dtfm;
double mbody[3],tbody[3],fquat[4];
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index c1de89efc70da5221fd8c0ee6c75a0ec5312d450..d5d3d36083d6047ef2f2c744ad4e7557ea582571 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -867,7 +867,7 @@ void FixRigidSmall::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::post_force(int vflag)
+void FixRigidSmall::post_force(int /*vflag*/)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
@@ -1004,7 +1004,7 @@ void FixRigidSmall::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -1016,7 +1016,7 @@ void FixRigidSmall::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::final_integrate_respa(int ilevel, int iloop)
+void FixRigidSmall::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
@@ -2999,7 +2999,7 @@ int FixRigidSmall::unpack_exchange(int nlocal, double *buf)
------------------------------------------------------------------------- */
int FixRigidSmall::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j;
double *xcm,*vcm,*quat,*omega,*ex_space,*ey_space,*ez_space,*conjqm;
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 0beef3bfa24cec383ba2a5d29304aff1bb596366..e0d1bf132b49f6c14029bc052e23fc4cb6d0fa9e 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -2451,7 +2451,7 @@ void FixShake::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixShake::copy_arrays(int i, int j, int delflag)
+void FixShake::copy_arrays(int i, int j, int /*delflag*/)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
@@ -2528,7 +2528,7 @@ void FixShake::update_arrays(int i, int atom_offset)
------------------------------------------------------------------------- */
void FixShake::set_molecule(int nlocalprev, tagint tagprev, int imol,
- double *xgeom, double *vcm, double *quat)
+ double * /*xgeom*/, double * /*vcm*/, double * /*quat*/)
{
int m,flag;
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index d898d2a790d62a03c8451eaf9c564fe52334f3f1..2e515839c5ecb5d5100697e436eb17e493a7950a 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -231,7 +231,7 @@ int FixAppendAtoms::setmask()
/* ---------------------------------------------------------------------- */
-void FixAppendAtoms::initial_integrate(int vflag)
+void FixAppendAtoms::initial_integrate(int /*vflag*/)
{
if (update->ntimestep % freq == 0) next_reneighbor = update->ntimestep;
}
@@ -331,7 +331,7 @@ int FixAppendAtoms::get_spatial()
/* ---------------------------------------------------------------------- */
-void FixAppendAtoms::post_force(int vflag)
+void FixAppendAtoms::post_force(int /*vflag*/)
{
double **f = atom->f;
double **v = atom->v;
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index a7890c3afa4ab8825c585c06faae9cd4ef5135de..c800e8a85da63b21eb245158986010e222dd442e 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -357,7 +357,7 @@ void FixMSST::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixMSST::setup(int vflag)
+void FixMSST::setup(int /*vflag*/)
{
lagrangian_position = 0.0;
@@ -442,7 +442,7 @@ void FixMSST::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixMSST::initial_integrate(int vflag)
+void FixMSST::initial_integrate(int /*vflag*/)
{
int i,k;
double p_msst; // MSST driving pressure
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 7146b46c1e12f4a021a71b9d4c1f0dd963975cd3..eb89e19517d5b02ed2db08dbb4824c52615cf037 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -171,7 +171,7 @@ int FixWallPiston::setmask()
/* ---------------------------------------------------------------------- */
-void FixWallPiston::initial_integrate(int vflag)
+void FixWallPiston::initial_integrate(int /*vflag*/)
{
next_reneighbor = update->ntimestep;
}
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 0d8b0bae14c3f82ccac058b88c9e37757c8f1e12..a2c1f55788e64b57e14b671cbf7e88767af47a57 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -184,7 +184,7 @@ void ComputeSNAAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNAAtom::init_list(int id, NeighList *ptr)
+void ComputeSNAAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index b0fef8e1e3fe5203f8c8d978b0f356671acbd97b..800d1942e3f9da7a18f30d0c3e9b4241b39e3534 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -186,7 +186,7 @@ void ComputeSNADAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNADAtom::init_list(int id, NeighList *ptr)
+void ComputeSNADAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index cf66b1c136ae8cbe32f1014005c49ce32f8d9d77..2b823f7b8b5804071a50723d2296d2e15c7d55b0 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -181,7 +181,7 @@ void ComputeSNAVAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeSNAVAtom::init_list(int id, NeighList *ptr)
+void ComputeSNAVAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 2eb9fb804f7420aab541b5995b81e39a2ca83766..7d39786ef98723991b5e35a28c3e219daeb2d8db 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -45,7 +45,6 @@ class ComputeSNAVAtom : public Compute {
double *radelem;
double *wjelem;
class SNA** snaptr;
- double cutmax;
int quadraticflag;
};
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 31505730433a4b00b2956c10afb5a272e94a0f55..7ed1bc1e23e25aa12db502152fd5d37b9fac9494 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -1231,7 +1231,7 @@ void SNA::compute_uarray(double x, double y, double z,
}
void SNA::compute_uarray_omp(double x, double y, double z,
- double z0, double r, int sub_threads)
+ double z0, double r, int /*sub_threads*/)
{
double r0inv;
double a_r, b_r, a_i, b_i;
diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp
index 6460a6185fb72d0635b623dbd7e8a2e7a2d27ba6..24c4480e049e9ac9fe0de19f7095776d4c04fc42 100644
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@@ -943,7 +943,7 @@ bigint AtomVecSpin::memory_usage()
return bytes;
}
-void AtomVecSpin::force_clear(int n, size_t nbytes)
+void AtomVecSpin::force_clear(int /*n*/, size_t nbytes)
{
memset(&atom->f[0][0],0,3*nbytes);
memset(&atom->fm[0][0],0,3*nbytes);
diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h
index 59f0ce2876d3e718d08c88bece84475a74dc04ef..b57876b7a0b93c84424c0234f578e6b89270deb7 100644
--- a/src/SPIN/compute_spin.h
+++ b/src/SPIN/compute_spin.h
@@ -33,7 +33,6 @@ class ComputeSpin : public Compute {
private:
double kb,hbar;
- int usecenter;
void allocate();
};
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index cb344654826883c41b7d6fcf8802d5ebacdccd0d..55b4d8dfec51f091bec6139a86815c251006535a 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -192,7 +192,7 @@ void FixLangevinSpin::add_temperature(double fmi[3])
/* ---------------------------------------------------------------------- */
-void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp
index b75f03212a143e0e5ebab08afd6d026834a6f210..898eb953960590f3840b82c22c7133b11e5541ed 100644
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@@ -258,7 +258,7 @@ void FixNVESpin::init()
/* ---------------------------------------------------------------------- */
-void FixNVESpin::initial_integrate(int vflag)
+void FixNVESpin::initial_integrate(int /*vflag*/)
{
double dtfm;
diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp
index b908478952941416546c4b083833f59dd9729a1c..d3edb3ae8a4eaaa56faf63ef8f418858239c49e3 100644
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@@ -169,7 +169,7 @@ void FixPrecessionSpin::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPrecessionSpin::post_force(int vflag)
+void FixPrecessionSpin::post_force(int /*vflag*/)
{
// update mag field with time (potential improvement)
@@ -245,7 +245,7 @@ void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3])
/* ---------------------------------------------------------------------- */
-void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index 398206b26ee3233b42707585d4bb2dd7dac0c4c6..929b79bef3feccd319649caf54cbb014c2084899 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -63,7 +63,7 @@ PairSpin::~PairSpin() {}
global settings
------------------------------------------------------------------------- */
-void PairSpin::settings(int narg, char **arg)
+void PairSpin::settings(int narg, char **/*arg*/)
{
if (narg < 1 || narg > 2)
error->all(FLERR,"Incorrect number of args in pair_style pair/spin command");
diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp
index 08e2c63e7f6ba147c6062da17f92a68b2a5d090a..6f8114042e83370ad8fe66dddee1f82c74226fc0 100644
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@@ -414,7 +414,7 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double
compute the mechanical force due to the dmi interaction between atom i and atom j
------------------------------------------------------------------------- */
-void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double eij[3],
+void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3],
double fi[3], double spi[3], double spj[3])
{
int *type = atom->type;
diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp
index 6bc1f71947333ac405e29d6342696165b47379ab..570c995754bad829711c8f5caf747273c0ab4ba6 100644
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@@ -380,7 +380,7 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3])
/* ---------------------------------------------------------------------- */
-void PairSpinMagelec::compute_magelec(int i, int j, double rsq, double eij[3], double fmi[3], double spj[3])
+void PairSpinMagelec::compute_magelec(int i, int j, double /*rsq*/, double eij[3], double fmi[3], double spj[3])
{
int *type = atom->type;
int itype, jtype;
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 564c1e98d7362a5947bc281a8b766ad5b6f4e479..186f51e06a5ba44bb668157d9ae9a4a668d72511 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -440,7 +440,7 @@ void FixSRD::init()
/* ---------------------------------------------------------------------- */
-void FixSRD::setup(int vflag)
+void FixSRD::setup(int /*vflag*/)
{
setup_bounds();
@@ -703,7 +703,7 @@ void FixSRD::pre_neighbor()
when collision occurs, change x,v of SRD, force,torque of BIG particle
------------------------------------------------------------------------- */
-void FixSRD::post_force(int vflag)
+void FixSRD::post_force(int /*vflag*/)
{
int i,m,ix,iy,iz;
@@ -2168,8 +2168,8 @@ void FixSRD::collision_ellipsoid_inexact(double *xs, double *xb,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_line_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
+double FixSRD::collision_line_exact(double * /*xs*/, double * /*xb*/,
+ double * /*vs*/, double * /*vb*/, Big * /*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
@@ -2197,8 +2197,8 @@ double FixSRD::collision_line_exact(double *xs, double *xb,
norm = surface normal of collision pt at time of collision
------------------------------------------------------------------------- */
-double FixSRD::collision_tri_exact(double *xs, double *xb,
- double *vs, double *vb, Big *big,
+double FixSRD::collision_tri_exact(double * /*xs*/, double * /*xb*/,
+ double * /*vs*/, double * /*vb*/, Big * /*big*/,
double dt_step,
double *xscoll, double *xbcoll,
double *norm)
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index 7fb8a27110ba2528bf81e53f4e6e9c78de23ee54..03fc94ae58b6a3cdf64e34cf306a7c8b28eafed5 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -625,11 +625,9 @@ void FixBocs::init()
// NJD MRD 2 functions
int FixBocs::read_F_table( char *filename, int p_basis_type )
{
- char separator = ',';
FILE *fpi;
int N_columns = 2, n_entries = 0, i;
float f1, f2;
- double n1, n2;
int test_sscanf;
double **data = (double **) calloc(N_columns,sizeof(double *));
char * line = (char *) calloc(200,sizeof(char));
@@ -790,7 +788,7 @@ void FixBocs::build_cubic_splines( double **data )
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixBocs::setup(int vflag)
+void FixBocs::setup(int /*vflag*/)
{
// tdof needed by compute_temp_target()
@@ -875,7 +873,7 @@ void FixBocs::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixBocs::initial_integrate(int vflag)
+void FixBocs::initial_integrate(int /*vflag*/)
{
// update eta_press_dot
@@ -970,7 +968,7 @@ void FixBocs::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixBocs::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
// set timesteps by level
@@ -1039,7 +1037,7 @@ void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixBocs::final_integrate_respa(int ilevel, int iloop)
+void FixBocs::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index 47d8d8f60b3854632e13bdf7358200f596fef98c..34a25a9b5a56b78b9ed50bb98a417d971594021c 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -56,7 +56,7 @@ BondOxdnaFene::~BondOxdnaFene()
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
void BondOxdnaFene::compute_interaction_sites(double e1[3],
- double e2[3], double r[3])
+ double /*e2*/[3], double r[3])
{
double d_cs=-0.4;
@@ -316,7 +316,7 @@ void BondOxdnaFene::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondOxdnaFene::single(int type, double rsq, int i, int j,
+double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp
index 63f38a4e12af727939cb5848153315f44f43b662..72b33887936daf62d25f9ad2f5d479db3f4800f8 100644
--- a/src/USER-CGDNA/fix_nve_dot.cpp
+++ b/src/USER-CGDNA/fix_nve_dot.cpp
@@ -62,7 +62,7 @@ void FixNVEDot::init()
/* ---------------------------------------------------------------------- */
-void FixNVEDot::initial_integrate(int vflag)
+void FixNVEDot::initial_integrate(int /*vflag*/)
{
double *shape,*quat;
double fquat[4],conjqm[4],inertia[3];
diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
index 90f7b1caebbc56e5849e47b72895128b22afcbbb..c73801c97aeb2962377b59f6d562430c2c850b46 100644
--- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
+++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
@@ -127,7 +127,7 @@ void FixNVEDotcLangevin::compute_target()
/* ---------------------------------------------------------------------- */
-void FixNVEDotcLangevin::initial_integrate(int vflag)
+void FixNVEDotcLangevin::initial_integrate(int /*vflag*/)
{
double *shape,*quat;
double fquat[4],conjqm[4],inertia[3];
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 151e7526924f508677c0c4648203b1091db9a4a0..d31890ea52b9dbfad89e5aec7088fb1826752369 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -542,7 +542,7 @@ void PairOxdna2Coaxstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdna2Coaxstk::settings(int narg, char **arg)
+void PairOxdna2Coaxstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 974ade89c1230b3e6fff154855cdf8c7d13513f3..da6e1f8bbd95be3d169f58ef1d9041cb5e01c013 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -264,7 +264,7 @@ void PairOxdna2Dh::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdna2Dh::settings(int narg, char **arg)
+void PairOxdna2Dh::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 0eb75fbb43b39b6bf29c460e2ebc0680d1cb66cb..ca03bcb35c2158ab341da19c67f74b4271ee766e 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -666,7 +666,7 @@ void PairOxdnaCoaxstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaCoaxstk::settings(int narg, char **arg)
+void PairOxdnaCoaxstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index e2b8334078cc4c0fae3dc34dcceb6bdefc662657..719a63b5f417eb20c6502d43ea26d436a3916c6e 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -92,7 +92,7 @@ PairOxdnaExcv::~PairOxdnaExcv()
compute vector COM-excluded volume interaction sites in oxDNA
------------------------------------------------------------------------- */
void PairOxdnaExcv::compute_interaction_sites(double e1[3],
- double e2[3], double rs[3], double rb[3])
+ double /*e2*/[3], double rs[3], double rb[3])
{
double d_cs=-0.4, d_cb=+0.4;
@@ -441,7 +441,7 @@ void PairOxdnaExcv::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaExcv::settings(int narg, char **arg)
+void PairOxdnaExcv::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index ce1bfe036a3842ae07ceb2baf3b42eef63bd3c7b..cb9f61bd7e78d7eb3a229c4c876b575ea44f3ff9 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -601,7 +601,7 @@ void PairOxdnaHbond::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaHbond::settings(int narg, char **arg)
+void PairOxdnaHbond::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index 8c4498e627cfecb185289cf1834e74fab1f484a8..f713e4d27ca7c2dcc682908b7813dd4b0253b123 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -647,7 +647,7 @@ void PairOxdnaStk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaStk::settings(int narg, char **arg)
+void PairOxdnaStk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index e5b9de81c09c4450584434a8dfa006c826675c0a..c4c23bf2c9ab89ec78d6516e9f25adcbd3fcd2c8 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -611,7 +611,7 @@ void PairOxdnaXstk::allocate()
global settings
------------------------------------------------------------------------- */
-void PairOxdnaXstk::settings(int narg, char **arg)
+void PairOxdnaXstk::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h
index c1f2cf215a68966884b90778bcd09319fe5e935b..51dcb4c2b7c8fa906af144ca2c222169b8dcefb9 100644
--- a/src/USER-CGSDK/lj_sdk_common.h
+++ b/src/USER-CGSDK/lj_sdk_common.h
@@ -27,6 +27,7 @@ namespace LJSDKParms {
// LJ type flags. list of supported LJ exponent combinations
enum {LJ_NOT_SET=0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES};
+#if defined(LMP_NEED_SDK_FIND_LJ_TYPE)
static int find_lj_type(const char *label,
const char * const * const list) {
for (int i=0; i < NUM_LJ_TYPES; ++i)
@@ -34,6 +35,7 @@ namespace LJSDKParms {
return LJ_NOT_SET;
}
+#endif
static const char * const lj_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6"};
static const double lj_prefact[] = {0.0, 6.75, 2.59807621135332, 4.0};
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index cbcba7f6b260dc777bd40433aaa5610d33be0800..3404beb58a95528cd3def330ff78e88910be99fb 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -33,6 +33,7 @@
#include "memory.h"
#include "error.h"
+#define LMP_NEED_SDK_FIND_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index 1d93363e207f185d7460b3f038fb1042a82eb2b4..c51235518b38ccbe5057ecc4d838aa6827c842f6 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -34,6 +34,7 @@
#include "memory.h"
#include "error.h"
+#define LMP_NEED_SDK_FIND_LJ_TYPE 1
#include "lj_sdk_common.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index 45bfeca48bd2269d0579672994fca283d8495ae1..ad9c76ac6ba12a13ce5cdf462c021f7e3ccb68f9 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -325,7 +325,7 @@ void FixSAEDVTK::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixSAEDVTK::setup(int vflag)
+void FixSAEDVTK::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp
index d89ea7759a8fbae547aeb4d724b3b8c82ca73472..5759a164f5cbec2bef1102c1380e3c01c222f9af 100644
--- a/src/USER-DPD/fix_dpd_energy.cpp
+++ b/src/USER-DPD/fix_dpd_energy.cpp
@@ -57,7 +57,7 @@ int FixDPDenergy::setmask()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixDPDenergy::initial_integrate(int vflag)
+void FixDPDenergy::initial_integrate(int /*vflag*/)
{
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index 73144c0a0f9423196b106ba67ebd917f56bf8c77..181c7dccfa3f706a930ce8134615982f6e4baa08 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -178,7 +178,7 @@ int FixEOStableRX::setmask()
/* ---------------------------------------------------------------------- */
-void FixEOStableRX::setup(int vflag)
+void FixEOStableRX::setup(int /*vflag*/)
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
@@ -803,7 +803,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
/* ---------------------------------------------------------------------- */
-int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixEOStableRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double *uChem = atom->uChem;
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index be78989bb5a81de1f686b10afd59d9989a9375dd..1a9c43704d6e508bf9e17375ac87072e1d05693a 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -668,7 +668,7 @@ void FixRX::init_list(int, class NeighList* ptr)
/* ---------------------------------------------------------------------- */
-void FixRX::setup_pre_force(int vflag)
+void FixRX::setup_pre_force(int /*vflag*/)
{
int nlocal = atom->nlocal;
int nghost = atom->nghost;
@@ -727,9 +727,9 @@ void FixRX::setup_pre_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRX::pre_force(int vflag)
+void FixRX::pre_force(int /*vflag*/)
{
- TimerType timer_start = getTimeStamp();
+ //TimerType timer_start = getTimeStamp();
int nlocal = atom->nlocal;
int nghost = atom->nghost;
@@ -808,7 +808,7 @@ void FixRX::pre_force(int vflag)
comm->forward_comm_fix(this);
if(localTempFlag) delete [] dpdThetaLocal;
- TimerType timer_stop = getTimeStamp();
+ //TimerType timer_stop = getTimeStamp();
double time_ODE = getElapsedTime(timer_localTemperature, timer_ODE);
@@ -1191,7 +1191,7 @@ void FixRX::rkf45_step (const int neq, const double h, double y[], double y_out[
return;
}
-int FixRX::rkf45_h0 (const int neq, const double t, const double t_stop,
+int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/,
const double hmin, const double hmax,
double& h0, double y[], double rwk[], void* v_params)
{
@@ -1668,7 +1668,7 @@ int FixRX::rhs(double t, const double *y, double *dydt, void *params)
/* ---------------------------------------------------------------------- */
-int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params)
+int FixRX::rhs_dense(double /*t*/, const double *y, double *dydt, void *params)
{
UserRHSData *userData = (UserRHSData *) params;
@@ -1702,7 +1702,7 @@ int FixRX::rhs_dense(double t, const double *y, double *dydt, void *params)
/* ---------------------------------------------------------------------- */
-int FixRX::rhs_sparse(double t, const double *y, double *dydt, void *v_params) const
+int FixRX::rhs_sparse(double /*t*/, const double *y, double *dydt, void *v_params) const
{
UserRHSData *userData = (UserRHSData *) v_params;
@@ -1885,7 +1885,7 @@ void FixRX::computeLocalTemperature()
/* ---------------------------------------------------------------------- */
-int FixRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double tmp;
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index 7fe865c8e6a9bce50d863c5f5cb14d8b119c1fef..4e133480ad4d97cbd830cd962bcb971c2ac9df9d 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -145,14 +145,14 @@ void FixShardlow::init()
/* ---------------------------------------------------------------------- */
-void FixShardlow::init_list(int id, NeighList *ptr)
+void FixShardlow::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
-void FixShardlow::setup(int vflag)
+void FixShardlow::setup(int /*vflag*/)
{
bool fixShardlow = false;
@@ -527,7 +527,7 @@ while (ct-- > 0) {
rand_state[id] = RNGstate;
}
-void FixShardlow::initial_integrate(int vflag)
+void FixShardlow::initial_integrate(int /*vflag*/)
{
int ii;
@@ -646,7 +646,7 @@ fprintf(stdout, "\n%6d %6d,%6d %6d: "
/* ---------------------------------------------------------------------- */
-int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int ii,jj,m;
double **v = atom->v;
diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp
index aeade16e7cb0525a5e1ce75dba723832646b7ad4..12e6d9f257c84eac8fa61bf637851ef704e2fb95 100644
--- a/src/USER-DPD/pair_dpd_fdt.cpp
+++ b/src/USER-DPD/pair_dpd_fdt.cpp
@@ -433,8 +433,8 @@ void PairDPDfdt::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPDfdt::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPDfdt::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wr,wd,phi;
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 05dc52eac787b974cf628bf9fd22b984763fab57..42c23e3ad234a682e1b513f778bb209f0e6aa066 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -534,8 +534,8 @@ void PairDPDfdtEnergy::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPDfdtEnergy::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPDfdtEnergy::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wr,wd,phi;
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index 3d204a849e3bfe1d70497f0c2c2340f48b3dab47..f911d8299e8c872f8dcb05d1ab8a52a36e473fd1 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -781,7 +781,7 @@ void PairMultiLucy::computeLocalDensity()
}
/* ---------------------------------------------------------------------- */
-int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairMultiLucy::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 0070ca82d9c5eed5f07fa16defbf4b0da7944829..13c838fe0168a481fee18e2b01dee6e1383be682 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -1019,7 +1019,7 @@ void PairMultiLucyRX::getMixingWeights(int id, double &mixWtSite1old, double &mi
/* ---------------------------------------------------------------------- */
-int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double *rho = atom->rho;
diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp
index 221944edc5170612b0ae7a246f3dd7bc61e6a26d..1e7bc440d11107bbbdf224668e10b3be85727e14 100644
--- a/src/USER-DPD/pair_table_rx.cpp
+++ b/src/USER-DPD/pair_table_rx.cpp
@@ -439,7 +439,7 @@ void PairTableRX::coeff(int narg, char **arg)
/* ---------------------------------------------------------------------- */
double PairTableRX::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
int itable;
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index 19fd775715822d040edf8b3bf4621902fbafb71d..7800efe7ff74aa5174a041853557f7b2ce5dbf32 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -235,7 +235,7 @@ void FixDrude::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixDrude::copy_arrays(int i, int j, int delflag)
+void FixDrude::copy_arrays(int i, int j, int /*delflag*/)
{
drudeid[j] = drudeid[i];
}
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index 235c5d224ba8e1914e201b95055cf072d3c9b64b..b9d1139f83df65d20644bc9356733c0c2e48701c 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -157,7 +157,7 @@ void FixLangevinDrude::init()
/* ---------------------------------------------------------------------- */
-void FixLangevinDrude::setup(int vflag)
+void FixLangevinDrude::setup(int /*vflag*/)
{
if (!strstr(update->integrate_style,"verlet"))
error->all(FLERR,"RESPA style not compatible with fix langevin/drude");
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 8c20ee8c4208e7cd59377d184b99662444bf35bd..6901ad1f2d6e64ae3686c4eb381730f099d6347d 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -363,7 +363,7 @@ void PairThole::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairThole::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,rinv,r,phicoul;
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index d3856e431d0d427e1f90c3435f99e63c37097c60..23abb4f99da6280caefdb0f40f8b441228124ddd 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -290,7 +290,7 @@ void ComputeTempDeformEff::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempDeformEff::restore_bias(int i, double *v)
+void ComputeTempDeformEff::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index 4548914ce13f5a349c0a6b00db726e5160c6cef3..659bdfca5e3a06bc189b69ed521a0c824a578cda 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -263,7 +263,7 @@ void ComputeTempRegionEff::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRegionEff::restore_bias(int i, double *v)
+void ComputeTempRegionEff::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index 2d0eef8e8573293af0ae480abb86898273d92a4a..d362113997fde58d193cb318968f86da02950410 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -63,7 +63,7 @@ FixLangevinEff::~FixLangevinEff()
/* ---------------------------------------------------------------------- */
-void FixLangevinEff::post_force(int vflag)
+void FixLangevinEff::post_force(int /*vflag*/)
{
if (tallyflag) post_force_tally();
else post_force_no_tally();
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index 584714a44e7413e0eed09fedb95994a853b37811..699dd9f9497e1433e9b22202fd5b714df87ff174 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -68,7 +68,7 @@ void FixNVEEff::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVEEff::initial_integrate(int vflag)
+void FixNVEEff::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -145,7 +145,7 @@ void FixNVEEff::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -159,7 +159,7 @@ void FixNVEEff::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVEEff::final_integrate_respa(int ilevel, int iloop)
+void FixNVEEff::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index 0379c0264b5570f18ab1f8d401078c1abe700de9..b4e9011e332b3d586dd249dabc705c133cddd7d9 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -1009,7 +1009,7 @@ void PairEffCut::read_restart_settings(FILE *fp)
these arrays are stored locally by pair style
------------------------------------------------------------------------- */
-void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
+void PairEffCut::min_xf_pointers(int /*ignore*/, double **xextra, double **fextra)
{
// grow arrays if necessary
// need to be atom->nmax in length
@@ -1031,7 +1031,7 @@ void PairEffCut::min_xf_pointers(int ignore, double **xextra, double **fextra)
calculate and store in min_eradius and min_erforce
------------------------------------------------------------------------- */
-void PairEffCut::min_xf_get(int ignore)
+void PairEffCut::min_xf_get(int /*ignore*/)
{
double *eradius = atom->eradius;
double *erforce = atom->erforce;
@@ -1050,7 +1050,7 @@ void PairEffCut::min_xf_get(int ignore)
propagate the change back to eradius
------------------------------------------------------------------------- */
-void PairEffCut::min_x_set(int ignore)
+void PairEffCut::min_x_set(int /*ignore*/)
{
double *eradius = atom->eradius;
int *spin = atom->spin;
diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp
index 3b8c9d4201f592343dff8d9e43c6a6b7ae9f1407..7304bc4ef6f36496200c950f9541407838b315d3 100644
--- a/src/USER-FEP/fix_adapt_fep.cpp
+++ b/src/USER-FEP/fix_adapt_fep.cpp
@@ -387,7 +387,7 @@ void FixAdaptFEP::init()
/* ---------------------------------------------------------------------- */
-void FixAdaptFEP::setup_pre_force(int vflag)
+void FixAdaptFEP::setup_pre_force(int /*vflag*/)
{
change_settings();
}
@@ -402,7 +402,7 @@ void FixAdaptFEP::setup_pre_force_respa(int vflag, int ilevel)
/* ---------------------------------------------------------------------- */
-void FixAdaptFEP::pre_force(int vflag)
+void FixAdaptFEP::pre_force(int /*vflag*/)
{
if (nevery == 0) return;
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index 5bcb5a752256a07ac83d4d74c2d044681b891b40..529ffe6b0983f9dc160aa336b80310c41471907c 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -347,7 +347,7 @@ void PairCoulCutSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulCutSoft::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double forcecoul,phicoul;
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index 94bb3659fa3beea5a4025ace13b876ad6405375b..e45dbe72d6c38b6e6dd84053cad4f2e5ffda1d7c 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -348,7 +348,7 @@ void PairCoulLongSoft::read_restart_settings(FILE *fp)
double PairCoulLongSoft::single(int i, int j, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r,grij,expm2,t,erfc,prefactor;
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 4aaa5c292531f7cc0aee51712576de220fe56909..a33445f6f8d7cc28e1863205b37f17c737a3729d 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -735,8 +735,8 @@ void PairLJCutSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJCutSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double forcelj,philj;
diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp
index 7a897e1870ed96a0aad08671b5d031e7764557d7..965d5708633d0d410d02c77bbad664a7310ca6b4 100644
--- a/src/USER-FEP/pair_morse_soft.cpp
+++ b/src/USER-FEP/pair_morse_soft.cpp
@@ -360,8 +360,8 @@ void PairMorseSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorseSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorseSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r, dr, dexp, dexp2, dexp3, phi;
diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp
index 672b70b6f68785256c67b694b58b8d8e741dce87..f2542fc0c7f43dd3d7bb1717f20f44ffbce6b9de 100644
--- a/src/USER-INTEL/angle_charmm_intel.cpp
+++ b/src/USER-INTEL/angle_charmm_intel.cpp
@@ -332,7 +332,7 @@ void AngleCharmmIntel::init_style()
template <class flt_t, class acc_t>
void AngleCharmmIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp
index 74639f3aebddd8c705f622c2165edcf033617ea0..5777dad9479957be52f9496435a6fdf845d828ff 100644
--- a/src/USER-INTEL/angle_harmonic_intel.cpp
+++ b/src/USER-INTEL/angle_harmonic_intel.cpp
@@ -314,7 +314,7 @@ void AngleHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void AngleHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nangletypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp
index 2d70049a89b705918589f6402e987f6eb3edff34..9d54269c0563cb4134fdd278eb123ebc66ace8b4 100644
--- a/src/USER-INTEL/bond_fene_intel.cpp
+++ b/src/USER-INTEL/bond_fene_intel.cpp
@@ -291,7 +291,7 @@ void BondFENEIntel::init_style()
template <class flt_t, class acc_t>
void BondFENEIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp
index ed9cab082ed5553c9afd38ddf12f2aabf98861fe..65894efa056cba90a4da72dbfbe6ee3c4157577c 100644
--- a/src/USER-INTEL/bond_harmonic_intel.cpp
+++ b/src/USER-INTEL/bond_harmonic_intel.cpp
@@ -262,7 +262,7 @@ void BondHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void BondHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nbondtypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index 6ad25f1ce49228f5f719cc21277b01a9bcfd26d8..6ccc165c612fd01bc66b8fec7541adc3ffbae2f5 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -401,7 +401,7 @@ void DihedralFourierIntel::init_style()
template <class flt_t, class acc_t>
void DihedralFourierIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1, setflag, nterms, memory);
diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp
index b2bf54102c4b8cfb05d8cfbe949d4cca4261ead9..ae5eb914e74d0af7ce5b727ed83761fea9d4d7b9 100644
--- a/src/USER-INTEL/dihedral_harmonic_intel.cpp
+++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp
@@ -396,7 +396,7 @@ void DihedralHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void DihedralHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index 832ce7ed50e482c787bd4e14e22d225b7b3be721..ef95cc75bb1bf998418152d47e994edbeb35f976 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -416,7 +416,7 @@ void DihedralOPLSIntel::init_style()
template <class flt_t, class acc_t>
void DihedralOPLSIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->ndihedraltypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index 7a206f472a92eed49e814e9029d69a936b196daa..3a67b606323978a043482a01cb60b5b1fb61ce5a 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -349,7 +349,7 @@ void FixIntel::init()
/* ---------------------------------------------------------------------- */
-void FixIntel::setup(int vflag)
+void FixIntel::setup(int /*vflag*/)
{
if (neighbor->style != Neighbor::BIN)
error->all(FLERR,
@@ -539,7 +539,7 @@ void FixIntel::check_neighbor_intel()
/* ---------------------------------------------------------------------- */
-void FixIntel::pre_reverse(int eflag, int vflag)
+void FixIntel::pre_reverse(int /*eflag*/, int /*vflag*/)
{
if (_force_array_m != 0) {
if (_need_reduce) {
@@ -652,7 +652,7 @@ template <class ft, class acc_t>
void FixIntel::add_results(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
const int eatom, const int vatom,
- const int offload) {
+ const int /*offload*/) {
start_watch(TIME_PACK);
int f_length;
#ifdef _LMP_INTEL_OFFLOAD
@@ -719,16 +719,18 @@ void FixIntel::add_results(const ft * _noalias const f_in,
template <class ft, class acc_t>
void FixIntel::add_oresults(const ft * _noalias const f_in,
const acc_t * _noalias const ev_global,
- const int eatom, const int vatom,
+ const int eatom, const int /*vatom*/,
const int out_offset, const int nall) {
lmp_ft * _noalias const f = (lmp_ft *) lmp->atom->f[0] + out_offset;
if (atom->torque) {
if (f_in[1].w)
+ {
if (f_in[1].w == 1)
error->all(FLERR,"Bad matrix inversion in mldivide3");
else
error->all(FLERR,
"Sphere particles not yet supported for gayberne/intel");
+ }
}
int packthreads;
diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h
index 79fb23ab3d98cfb7cdbf62a3d1cf35fa58415b8c..e6e09be503dc0d69840e251c0abc20a103890a04 100644
--- a/src/USER-INTEL/fix_intel.h
+++ b/src/USER-INTEL/fix_intel.h
@@ -74,7 +74,7 @@ class FixIntel : public Fix {
inline int nbor_pack_width() const { return _nbor_pack_width; }
inline void nbor_pack_width(const int w) { _nbor_pack_width = w; }
inline int three_body_neighbor() { return _three_body_neighbor; }
- inline void three_body_neighbor(const int i) { _three_body_neighbor = 1; }
+ inline void three_body_neighbor(const int /*i*/) { _three_body_neighbor = 1; }
inline int need_zero(const int tid) {
if (_need_reduce == 0 && tid > 0) return 1;
@@ -159,8 +159,8 @@ class FixIntel : public Fix {
inline int host_start_neighbor() { return 0; }
inline int host_start_pair() { return 0; }
inline void zero_timers() {}
- inline void start_watch(const int which) {}
- inline double stop_watch(const int which) { return 0.0; }
+ inline void start_watch(const int /*which*/) {}
+ inline double stop_watch(const int /*which*/) { return 0.0; }
double * off_watch_pair() { return NULL; }
double * off_watch_neighbor() { return NULL; }
inline void balance_stamp() {}
@@ -238,7 +238,7 @@ class FixIntel : public Fix {
/* ---------------------------------------------------------------------- */
-void FixIntel::get_buffern(const int offload, int &nlocal, int &nall,
+void FixIntel::get_buffern(const int /*offload*/, int &nlocal, int &nall,
int &minlocal) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers) {
@@ -273,7 +273,7 @@ void FixIntel::get_buffern(const int offload, int &nlocal, int &nall,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<double,double>::vec3_acc_t *f_in,
- double *ev_in, const int offload,
+ double *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
@@ -301,7 +301,7 @@ void FixIntel::add_result_array(IntelBuffers<double,double>::vec3_acc_t *f_in,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<float,double>::vec3_acc_t *f_in,
- double *ev_in, const int offload,
+ double *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
@@ -329,7 +329,7 @@ void FixIntel::add_result_array(IntelBuffers<float,double>::vec3_acc_t *f_in,
/* ---------------------------------------------------------------------- */
void FixIntel::add_result_array(IntelBuffers<float,float>::vec3_acc_t *f_in,
- float *ev_in, const int offload,
+ float *ev_in, const int /*offload*/,
const int eatom, const int vatom,
const int rflag) {
#ifdef _LMP_INTEL_OFFLOAD
diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp
index 44253e8bb0b9c3b5750c6e0a46e2f3c3cf25a7ab..bf4764f10460405807b03db0bf5de9d5f5facbf2 100644
--- a/src/USER-INTEL/fix_nh_intel.cpp
+++ b/src/USER-INTEL/fix_nh_intel.cpp
@@ -464,7 +464,6 @@ void FixNHIntel::nve_x()
{
double * _noalias const x = atom->x[0];
double * _noalias const v = atom->v[0];
- const double * _noalias const f = atom->f[0];
// x update by full step only for atoms in group
diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp
index 17bbcff77140de04b60b4cfdf8f79867d11f87d8..7eeb8a163557ef9c8521bffea5090a5ff4879601 100644
--- a/src/USER-INTEL/fix_nve_asphere_intel.cpp
+++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp
@@ -79,12 +79,8 @@ void FixNVEAsphereIntel::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixNVEAsphereIntel::initial_integrate(int vflag)
+void FixNVEAsphereIntel::initial_integrate(int /*vflag*/)
{
- double dtfm;
- double inertia[3],omega[3];
- double *shape,*quat;
-
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double * _noalias const x = atom->x[0];
@@ -94,7 +90,6 @@ void FixNVEAsphereIntel::initial_integrate(int vflag)
double **angmom = atom->angmom;
double **torque = atom->torque;
- double *rmass = atom->rmass;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
@@ -143,8 +138,6 @@ void FixNVEAsphereIntel::final_integrate()
{
if (neighbor->ago == 0) reset_dt();
- double dtfm;
-
double * _noalias const v = atom->v[0];
const double * _noalias const f = atom->f[0];
double * _noalias const angmom = atom->angmom[0];
diff --git a/src/USER-INTEL/fix_nve_intel.cpp b/src/USER-INTEL/fix_nve_intel.cpp
index c0f6da06ae9d6f53ed5a875fdb17137f73551665..7dee31d2f447520a2f46dd8ac07ee7d3c33ec0e3 100644
--- a/src/USER-INTEL/fix_nve_intel.cpp
+++ b/src/USER-INTEL/fix_nve_intel.cpp
@@ -56,7 +56,7 @@ void FixNVEIntel::setup(int vflag)
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVEIntel::initial_integrate(int vflag)
+void FixNVEIntel::initial_integrate(int /*vflag*/)
{
// update v and x of atoms in group
diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp
index e0ef2162d1e72ce865cf080e5de9192c51247d6c..c20c004657b1b53ce16c55dd6a41a87f37d708f4 100644
--- a/src/USER-INTEL/improper_cvff_intel.cpp
+++ b/src/USER-INTEL/improper_cvff_intel.cpp
@@ -428,7 +428,7 @@ void ImproperCvffIntel::init_style()
template <class flt_t, class acc_t>
void ImproperCvffIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp
index 60cbe163586da454d9dd7d70710ad6551f0c89ff..167095150e8c8cb05af7fc4982980432eb0745a6 100644
--- a/src/USER-INTEL/improper_harmonic_intel.cpp
+++ b/src/USER-INTEL/improper_harmonic_intel.cpp
@@ -384,7 +384,7 @@ void ImproperHarmonicIntel::init_style()
template <class flt_t, class acc_t>
void ImproperHarmonicIntel::pack_force_const(ForceConst<flt_t> &fc,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
const int bp1 = atom->nimpropertypes + 1;
fc.set_ntypes(bp1,memory);
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 0f32cb48b201ca71c7181d512f241c0634db89ad..05176e1fd1e1bf4bc629dc6d8b40275b4bed81bb 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -109,7 +109,7 @@ void IntelBuffers<flt_t, acc_t>::free_buffers()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow(const int nall, const int nlocal,
const int nthreads,
- const int offload_end)
+ const int /*offload_end*/)
{
free_buffers();
_buf_size = static_cast<double>(nall) * 1.1 + 1;
@@ -200,7 +200,7 @@ void IntelBuffers<flt_t, acc_t>::free_nmax()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int offload_end)
+void IntelBuffers<flt_t, acc_t>::_grow_nmax(const int /*offload_end*/)
{
#ifdef _LMP_INTEL_OFFLOAD
free_nmax();
@@ -264,7 +264,7 @@ void IntelBuffers<flt_t, acc_t>::free_list_local()
template <class flt_t, class acc_t>
void IntelBuffers<flt_t, acc_t>::_grow_list_local(NeighList *list,
- const int offload_end)
+ const int /*offload_end*/)
{
free_list_local();
int size = list->get_maxlocal();
@@ -310,10 +310,10 @@ void IntelBuffers<flt_t, acc_t>::free_nbor_list()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList *list,
+void IntelBuffers<flt_t, acc_t>::_grow_nbor_list(NeighList * /*list*/,
const int nlocal,
const int nthreads,
- const int offload_end,
+ const int /*offload_end*/,
const int pack_width)
{
free_nbor_list();
@@ -382,7 +382,7 @@ void IntelBuffers<flt_t, acc_t>::free_ccache()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::grow_ccache(const int off_flag,
+void IntelBuffers<flt_t, acc_t>::grow_ccache(const int /*off_flag*/,
const int nthreads,
const int width)
{
@@ -481,7 +481,7 @@ void IntelBuffers<flt_t, acc_t>::free_ncache()
/* ---------------------------------------------------------------------- */
template <class flt_t, class acc_t>
-void IntelBuffers<flt_t, acc_t>::grow_ncache(const int off_flag,
+void IntelBuffers<flt_t, acc_t>::grow_ncache(const int /*off_flag*/,
const int nthreads)
{
const int nsize = get_max_nbors() * 3;
diff --git a/src/USER-INTEL/intel_buffers.h b/src/USER-INTEL/intel_buffers.h
index 8040715b2e197bea1a1d2eb4dea03b5ce4b6e15b..e8225a4a30f42f9d9012452fbf9bdfbebdce5195 100644
--- a/src/USER-INTEL/intel_buffers.h
+++ b/src/USER-INTEL/intel_buffers.h
@@ -135,24 +135,24 @@ class IntelBuffers {
void set_ntypes(const int ntypes, const int use_ghost_cut = 0);
- inline int * firstneigh(const NeighList *list) { return _list_alloc; }
- inline int * cnumneigh(const NeighList *list) { return _cnumneigh; }
+ inline int * firstneigh(const NeighList * /*list*/) { return _list_alloc; }
+ inline int * cnumneigh(const NeighList * /*list*/) { return _cnumneigh; }
inline int * get_atombin() { return _atombin; }
inline int * get_binpacked() { return _binpacked; }
- inline atom_t * get_x(const int offload = 1) {
+ inline atom_t * get_x(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_x;
#endif
return _x;
}
- inline flt_t * get_q(const int offload = 1) {
+ inline flt_t * get_q(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_q;
#endif
return _q;
}
- inline quat_t * get_quat(const int offload = 1) {
+ inline quat_t * get_quat(const int /*offload*/ = 1) {
#ifdef _LMP_INTEL_OFFLOAD
if (_separate_buffers && offload == 0) return _host_quat;
#endif
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index 4a86d8db290d096dff9ae1e16809176a6ce18930..b20f9c8ad13d37d79844250552f972240deb9dc1 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -2057,8 +2057,8 @@ public:
}
VEC_INLINE static ivec set(
- int i15, int i14, int i13, int i12, int i11, int i10, int i9, int i8,
- int i7, int i6, int i5, int i4, int i3, int i2, int i1, int i0
+ int /*i15*/, int /*i14*/, int /*i13*/, int /*i12*/, int /*i11*/, int /*i10*/, int /*i9*/, int /*i8*/,
+ int /*i7*/, int /*i6*/, int /*i5*/, int /*i4*/, int /*i3*/, int /*i2*/, int /*i1*/, int i0
) {
return i0;
}
@@ -2243,7 +2243,7 @@ public:
FVEC_BINOP(*, mul)
FVEC_BINOP(/, div)
- VEC_INLINE static void gather_prefetch0(const ivec &idx, const void * mem) {}
+ VEC_INLINE static void gather_prefetch0(const ivec & /*idx*/, const void * /*mem*/) {}
};
class avec {
diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp
index e071b141fe077895a19801b4c9260f2555a88213..789fa35b429448a5e50651b206d5baea7364dd63 100644
--- a/src/USER-INTEL/nbin_intel.cpp
+++ b/src/USER-INTEL/nbin_intel.cpp
@@ -192,15 +192,10 @@ void NBinIntel::bin_atoms(IntelBuffers<flt_t,acc_t> * buffers) {
// ---------- Bin Atoms -------------
_fix->start_watch(TIME_HOST_NEIGHBOR);
- const ATOM_T * _noalias const x = buffers->get_x();
+ //const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const atombin = this->_atombin;
int * _noalias const binpacked = this->_binpacked;
-
- const double sboxlo0 = bboxlo[0] + mbinxlo/bininvx;
- const double sboxlo1 = bboxlo[1] + mbinylo/bininvy;
- const double sboxlo2 = bboxlo[2] + mbinzlo/bininvz;
-
int i, ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
index ae961e84b59f0c52038f1f14e38123ace6877d27..74a04f0e7de9dd97197049c7ac9227d2b8ee2516 100644
--- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
+++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp
@@ -106,7 +106,7 @@ void NPairFullBinGhostIntel::fbi(NeighList * list,
/* ---------------------------------------------------------------------- */
template<class flt_t, class acc_t, int need_ic>
-void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
+void NPairFullBinGhostIntel::fbi(const int /*offload*/, NeighList * list,
IntelBuffers<flt_t,acc_t> * buffers,
const int pstart, const int pend) {
if (pend-pstart == 0) return;
@@ -115,7 +115,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
int nall_t = nall;
const int aend = nall;
- const int pack_width = _fix->nbor_pack_width();
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const firstneigh = buffers->firstneigh(list);
const int e_nall = nall_t;
@@ -155,9 +154,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
tagint * const molecule = atom->molecule;
#endif
- int *molindex = atom->molindex;
- int *molatom = atom->molatom;
- Molecule **onemols = atom->avec->onemols;
int moltemplate;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
@@ -167,8 +163,8 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
int tnum;
int *overflow;
- double *timer_compute;
#ifdef _LMP_INTEL_OFFLOAD
+ double *timer_compute;
if (offload) {
timer_compute = _fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
@@ -311,7 +307,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list,
int * _noalias const ttag = ncachetag + toffs;
// loop over all atoms in other bins in stencil, store every pair
- int istart, icount, ncount, oldbin = -9999999, lane, max_chunk;
+ int ncount, oldbin = -9999999;
for (int i = ifrom; i < ito; i++) {
const flt_t xtmp = x[i].x;
const flt_t ytmp = x[i].y;
diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp
index 355c8db199b9bd010abb81868ce22bd2cc34d8a9..6d4529752ab38dd490680069d627c97a0de22446 100644
--- a/src/USER-INTEL/npair_intel.cpp
+++ b/src/USER-INTEL/npair_intel.cpp
@@ -54,10 +54,10 @@ NPairIntel::~NPairIntel() {
template <class flt_t, class acc_t, int offload_noghost, int need_ic,
int FULL, int TRI, int THREE>
-void NPairIntel::bin_newton(const int offload, NeighList *list,
+void NPairIntel::bin_newton(const int /*offload*/, NeighList *list,
IntelBuffers<flt_t,acc_t> *buffers,
const int astart, const int aend,
- const int offload_end) {
+ const int /*offload_end*/) {
if (aend-astart == 0) return;
@@ -109,8 +109,8 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
int tnum;
int *overflow;
- double *timer_compute;
#ifdef _LMP_INTEL_OFFLOAD
+ double *timer_compute;
if (offload) {
timer_compute = _fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
@@ -265,8 +265,9 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
int * _noalias itjtype;
// loop over all atoms in other bins in stencil, store every pair
- int istart, icount, ncount, oldbin = -9999999, lane, max_chunk;
+ int istart, icount, ncount, oldbin = -9999999;
#ifdef LMP_INTEL_3BODY_FAST
+ int lane, max_chunk;
if (THREE) {
lane = 0;
max_chunk = 0;
@@ -579,7 +580,6 @@ void NPairIntel::bin_newton(const int offload, NeighList *list,
int ns;
if (THREE) {
- int alln = n;
ns = n - pack_offset;
atombin[i] = ns;
ns += n2 - pack_offset - maxnbors;
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index 07f33f7ebe10bdfb1fac0511b768a9eba1fa3148..601144a3c03ae6a14f8cb2cb697cf19d7cdb020e 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -2200,7 +2200,7 @@ typedef typename intr_types<flt_t, acc_t>::bvec bvec;
VEC_INLINE inline
static void aut_loadatoms_vec(
AtomAIREBOT<flt_t> * atoms, ivec j_vec,
- fvec *x, fvec * y, fvec * z, bvec * type_mask, int * map, ivec map_i,
+ fvec *x, fvec * y, fvec * z, bvec * type_mask, int * /*map*/, ivec map_i,
ivec c_1
) {
const ivec c_4 = ivec::set1(4);
@@ -2413,7 +2413,7 @@ static fvec aut_eval_poly_lin_pd_2(int n, flt_t * vals, ivec idx, fvec x,
}
static fvec aut_mask_gSpline_pd_2(KernelArgsAIREBOT<flt_t,acc_t> * ka,
- bvec active_mask, int itype, fvec cosjik,
+ bvec /*active_mask*/, int itype, fvec cosjik,
fvec Nij, fvec *dgdc, fvec *dgdN) {
int i;
flt_t * gDom = NULL;
@@ -2835,7 +2835,7 @@ static void aut_frebo_data_writeback(
static void aut_frebo_N_spline_force(
KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
struct aut_frebo_data * _noalias data, int itype, int jtype, ivec vi,
- ivec vj, fvec VA, fvec dN, fvec dNconj, fvec Nconj) {
+ ivec /*vj*/, fvec VA, fvec dN, fvec dNconj, fvec Nconj) {
ivec c_i1 = ivec::set1(1);
fvec c_2 = fvec::set1(2);
fvec c_TOL = fvec::set1(TOL);
@@ -2999,8 +2999,8 @@ static fvec aut_frebo_sum_omega(
KernelArgsAIREBOT<flt_t,acc_t> * _noalias ka,
struct aut_frebo_data * _noalias i_data,
struct aut_frebo_data * _noalias j_data,
- int itype, int jtype,
- ivec vi, ivec vj,
+ int /*itype*/, int /*jtype*/,
+ ivec /*vi*/, ivec /*vj*/,
fvec r23x, fvec r23y, fvec r23z, fvec r23mag,
fvec VA, fvec fij[3]
) {
@@ -3284,7 +3284,7 @@ static void aut_torsion_vec(
KernelArgsAIREBOT<flt_t,acc_t> * ka,
struct aut_frebo_data * i_data,
struct aut_frebo_data * j_data,
- ivec i, ivec j, fvec wij, fvec dwij
+ ivec /*i*/, ivec /*j*/, fvec wij, fvec dwij
) {
AtomAIREBOT<flt_t> * x = ka->x;
int * map = ka->map;
@@ -4134,7 +4134,7 @@ exceed_limits:
/*
* Attempt to look up an element in the hash-map.
*/
-static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * ka,
+static fvec aut_airebo_lj_tap_test_path(KernelArgsAIREBOT<flt_t,acc_t> * /*ka*/,
struct aut_airebo_lj_test_path_result_data * test_path_result,
bvec need_search, ivec i_bc, ivec j,
LennardJonesPathAIREBOT<flt_t> path[fvec::VL]
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index 201277e68dc7dc4fbcbe4b637716c1347615888a..ce9ede69d680684a6af9a896187d24fb425ed52b 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -784,7 +784,7 @@ void PairEAMIntel::ForceConst<flt_t>::set_ntypes(const int ntypes,
/* ---------------------------------------------------------------------- */
int PairEAMIntel::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
if (fix->precision() == FixIntel::PREC_MODE_DOUBLE)
return pack_forward_comm(n, list, buf, fp);
diff --git a/src/USER-INTEL/pair_rebo_intel.cpp b/src/USER-INTEL/pair_rebo_intel.cpp
index bc7197000bf3e8f94ee067c57f6f1310e2e440a8..3decc0154bdb0a0423baa348ed5e4f05a95106ab 100644
--- a/src/USER-INTEL/pair_rebo_intel.cpp
+++ b/src/USER-INTEL/pair_rebo_intel.cpp
@@ -28,7 +28,7 @@ PairREBOIntel::PairREBOIntel(LAMMPS *lmp) : PairAIREBOIntel(lmp) {}
global settings
------------------------------------------------------------------------- */
-void PairREBOIntel::settings(int narg, char **arg)
+void PairREBOIntel::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp
index d1d52270be27c3f8b393fc0da5cc1f3773fca4a8..aff8ba88a74971f7ee1e4e7f824334af0f056330 100644
--- a/src/USER-INTEL/pair_sw_intel.cpp
+++ b/src/USER-INTEL/pair_sw_intel.cpp
@@ -173,7 +173,7 @@ template <int SPQ,int ONETYPE,int EFLAG,class flt_t,class acc_t>
void PairSWIntel::eval(const int offload, const int vflag,
IntelBuffers<flt_t,acc_t> *buffers,
const ForceConst<flt_t> &fc, const int astart,
- const int aend, const int pad_width)
+ const int aend, const int /*pad_width*/)
{
const int inum = aend - astart;
if (inum == 0) return;
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index 0a41e5d8a5341c635853a2125ea2603ba6a9e64e..3b05658278fddc5548e6c8158fa1e446e3cc3331 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -723,7 +723,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
double sft, int** p2g, int nup, int nlow,
int nxlo, int nylo, int nzlo,
int nxhi, int nyhi, int nzhi,
- IntelBuffers<flt_t,acc_t> *buffers)
+ IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
int nlocal = atom->nlocal;
int nthr = comm->nthreads;
@@ -790,7 +790,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -940,7 +940,7 @@ void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -1091,7 +1091,7 @@ void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
@@ -1225,7 +1225,7 @@ void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
FFT_SCALAR * _noalias global_density = &(density_brick_none[0][nzlo_out_6][nylo_out_6][nxlo_out_6]);
@@ -1373,7 +1373,7 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1520,7 +1520,7 @@ void PPPMDispIntel::fieldforce_c_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1725,7 +1725,7 @@ void PPPMDispIntel::fieldforce_c_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -1869,7 +1869,7 @@ void PPPMDispIntel::fieldforce_g_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2069,7 +2069,7 @@ void PPPMDispIntel::fieldforce_g_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2282,7 +2282,7 @@ void PPPMDispIntel::fieldforce_a_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2594,7 +2594,7 @@ void PPPMDispIntel::fieldforce_a_ad(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
@@ -2755,7 +2755,7 @@ void PPPMDispIntel::fieldforce_none_ik(IntelBuffers<flt_t,acc_t> *buffers)
------------------------------------------------------------------------- */
template<class flt_t, class acc_t, int use_table>
-void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> *buffers)
+void PPPMDispIntel::fieldforce_none_ad(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// loop over my charges, interpolate electric field from nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index 46a55e558afbad5e408be10b24077430b53b65cc..e5540e637751bc758a347bcf00ee71aaf1c91e86 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -255,7 +255,7 @@ void PPPMIntel::compute_first(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
-void PPPMIntel::compute_second(int eflag, int vflag)
+void PPPMIntel::compute_second(int /*eflag*/, int /*vflag*/)
{
int i,j;
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 7a0bd0572ed63f1df5cd51eb8bead57d5ec05349..fecd6f2b25419088badbd29f29f4f557bb46aaf8 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -646,7 +646,7 @@ void FixLbFluid::init(void)
}
-void FixLbFluid::setup(int vflag)
+void FixLbFluid::setup(int /*vflag*/)
{
//--------------------------------------------------------------------------
// Need to calculate the force on the fluid for a restart run.
@@ -655,7 +655,7 @@ void FixLbFluid::setup(int vflag)
calc_fluidforce();
}
-void FixLbFluid::initial_integrate(int vflag)
+void FixLbFluid::initial_integrate(int /*vflag*/)
{
//--------------------------------------------------------------------------
// Print a header labelling any output printed to the screen.
@@ -711,7 +711,7 @@ void FixLbFluid::initial_integrate(int vflag)
streamout();
}
-void FixLbFluid::post_force(int vflag)
+void FixLbFluid::post_force(int /*vflag*/)
{
if(fixviscouslb==1)
calc_fluidforce();
@@ -741,7 +741,7 @@ void FixLbFluid::grow_arrays(int nmax)
//==========================================================================
// copy values within local atom-based array
//==========================================================================
-void FixLbFluid::copy_arrays(int i, int j, int delflag)
+void FixLbFluid::copy_arrays(int i, int j, int /*delflag*/)
{
hydroF[j][0] = hydroF[i][0];
hydroF[j][1] = hydroF[i][1];
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index 9fd0dab51de39ec708cad06ac94202321d3bb59c..c5c12d6c119e0cd62e8e06ccc4b2efe6c4e4510c 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -118,7 +118,7 @@ void FixLbPC::init()
}
/* ---------------------------------------------------------------------- */
-void FixLbPC::initial_integrate(int vflag) {
+void FixLbPC::initial_integrate(int /*vflag*/) {
double dtfm;
@@ -285,7 +285,7 @@ void FixLbPC::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixLbPC::copy_arrays(int i, int j, int delflag)
+void FixLbPC::copy_arrays(int i, int j, int /*delflag*/)
{
force_old[j][0] = force_old[i][0];
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index dddd060fa4cd416bb3e97a77bfffedcb0a05da03..260153972758a193889eafa8a646da9dc14b1d03 100644
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -1454,7 +1454,7 @@ void FixLbRigidPCSphere::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixLbRigidPCSphere::copy_arrays(int i, int j, int delflag)
+void FixLbRigidPCSphere::copy_arrays(int i, int j, int /*delflag*/)
{
body[j] = body[i];
up[j][0] = up[i][0];
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index 8ee4d8419e73e5a377fa65b2c8e40b13baef6b5a..afe23477be49fee5025294712ea6ee226c61f40b 100644
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -109,7 +109,7 @@ void FixLbViscous::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLbViscous::post_force(int vflag)
+void FixLbViscous::post_force(int /*vflag*/)
{
// apply drag force to atoms in group
// direction is opposed to velocity vector
@@ -132,7 +132,7 @@ void FixLbViscous::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLbViscous::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLbViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index 04172d5c92da874322344e33fcd0aa4189f184cd..4e717ce55653b799e094e92e490f233e8e8a9ab8 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -149,7 +149,7 @@ void FixManifoldForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixManifoldForce::post_force(int vflag)
+void FixManifoldForce::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -177,7 +177,7 @@ void FixManifoldForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixManifoldForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixManifoldForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 4dcc3f9704aa3543aeaa62ed7a9202135218c801..3c6c70f6dfe3ed2bc33750d60c40d626e0cd9bfc 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -307,7 +307,7 @@ void FixNVEManifoldRattle::update_var_params()
/* -----------------------------------------------------------------------------
---------------------------------------------------------------------------*/
-int FixNVEManifoldRattle::dof(int igroup)
+int FixNVEManifoldRattle::dof(int /*igroup*/)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -348,7 +348,7 @@ double FixNVEManifoldRattle::memory_usage()
/* -----------------------------------------------------------------------------
---------------------------------------------------------------------------*/
-void FixNVEManifoldRattle::initial_integrate(int vflag)
+void FixNVEManifoldRattle::initial_integrate(int /*vflag*/)
{
update_var_params();
nve_x_rattle(igroup, groupbit);
diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
index 973a5bcf43875d12af45655be1ff97f54c17e139..2a204d2048b79ddc2306ddd43b11c41438e207fb 100644
--- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
@@ -229,7 +229,7 @@ void FixNVTManifoldRattle::init()
-void FixNVTManifoldRattle::setup(int vflag)
+void FixNVTManifoldRattle::setup(int /*vflag*/)
{
compute_temp_target();
@@ -371,7 +371,7 @@ void FixNVTManifoldRattle::nh_v_temp()
// Most of this logic is based on fix_nh:
-void FixNVTManifoldRattle::initial_integrate(int vflag)
+void FixNVTManifoldRattle::initial_integrate(int /*vflag*/)
{
update_var_params();
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index 6eb09010efbb3022bed71c282744db7792140ba8..b0727c346d5efb70272b3493d8ef5ea746108aa3 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -61,7 +61,7 @@ namespace user_manifold {
virtual const char *id() = 0;
- virtual void set_atom_id( tagint a_id ){}
+ virtual void set_atom_id( tagint /*a_id*/ ){}
virtual int nparams() = 0;
// double *get_params(){ return params; };
diff --git a/src/USER-MANIFOLD/manifold_cylinder.cpp b/src/USER-MANIFOLD/manifold_cylinder.cpp
index c13581c640587c4fdb53c5334a3a844d1f5466e8..28062d7a27533ff7835e52622f918971c00bfcb4 100644
--- a/src/USER-MANIFOLD/manifold_cylinder.cpp
+++ b/src/USER-MANIFOLD/manifold_cylinder.cpp
@@ -5,8 +5,8 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int argc,
- char **argv ) : manifold(lmp)
+manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int /*argc*/,
+ char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
index 21d4087d7c240722162b0eb556aa0b873c1a8896..4df4c833d3fb9c798d7c625e8854f61858d95f36 100644
--- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
+++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
@@ -8,8 +8,8 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int argc,
- char **argv ) : manifold(lmp)
+manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int /*argc*/,
+ char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp
index fa7edc6e4afa4fa345c283187d073365a05dedb7..c40a5fff9f1538d391819262aa736f8a3a693ef3 100644
--- a/src/USER-MANIFOLD/manifold_dumbbell.cpp
+++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp
@@ -6,7 +6,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp)
+manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_ellipsoid.cpp b/src/USER-MANIFOLD/manifold_ellipsoid.cpp
index f590123dc3b8aa9385ed78994cf1b9fc841541e9..d5e7bb146ec82301e868b11a20518b4964047318 100644
--- a/src/USER-MANIFOLD/manifold_ellipsoid.cpp
+++ b/src/USER-MANIFOLD/manifold_ellipsoid.cpp
@@ -4,7 +4,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int narg, char **argv ) : manifold(lmp)
+manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int /*narg*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
index a9ee35bbfc5f23628c2943e70ea8043777028af1..b95162740bdd2deef1f8d47330689bae188ec9c4 100644
--- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
@@ -25,7 +25,6 @@ public:
cubic_hermite( double x0, double x1, double y0, double y1,
double yp0, double yp1, LAMMPS_NS::Error *err ) :
- x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1),
a( 2*x0 + 2 - 2*x1 ),
b( -3*x0 - 3 + 3*x1 ),
c( 1.0 ),
@@ -34,6 +33,7 @@ public:
u( -3*y0 + 3*y1 - 2*yp0 - yp1 ),
v( yp0 ),
w( y0 ),
+ x0(x0), x1(x1), y0(y0), y1(y1), yp0(yp0), yp1(yp1),
err(err)
{
test();
@@ -133,7 +133,7 @@ public:
// Manifold itself:
manifold_gaussian_bump::manifold_gaussian_bump(class LAMMPS* lmp,
- int narg, char **arg)
+ int /*narg*/, char **/*arg*/)
: manifold(lmp), lut_z(NULL), lut_zp(NULL) {}
diff --git a/src/USER-MANIFOLD/manifold_plane.cpp b/src/USER-MANIFOLD/manifold_plane.cpp
index d33617fbfba8d580b0457d46e6a5737ea04ff851..6c3f17393aed528231f8ea649bfaf5157cd3726a 100644
--- a/src/USER-MANIFOLD/manifold_plane.cpp
+++ b/src/USER-MANIFOLD/manifold_plane.cpp
@@ -4,7 +4,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_plane::manifold_plane( LAMMPS *lmp, int argc, char **argv ) :
+manifold_plane::manifold_plane( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) :
manifold(lmp)
{}
@@ -16,7 +16,7 @@ double manifold_plane::g( const double *x )
}
-void manifold_plane::n( const double *x, double *n )
+void manifold_plane::n( const double * /*x*/, double *n )
{
n[0] = params[0];
n[1] = params[1];
diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
index ccf0a794dadc28900dcee2a01cee1a6343d39b68..983702b6f3c60d57e2d12452ff2e605fb69cd1e7 100644
--- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
+++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
@@ -5,7 +5,7 @@
using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int argc, char **argv ) :
+manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) :
manifold(lmp)
{}
diff --git a/src/USER-MANIFOLD/manifold_sphere.h b/src/USER-MANIFOLD/manifold_sphere.h
index 5d4ae55fdace151347cb7039131d776abb0f9fb7..d9cd46c9c3f5be09dc716222098a78dd9872964d 100644
--- a/src/USER-MANIFOLD/manifold_sphere.h
+++ b/src/USER-MANIFOLD/manifold_sphere.h
@@ -40,7 +40,7 @@ namespace user_manifold {
nn[2] = 2*x[2];
}
- virtual void H( double *x, double h[3][3] )
+ virtual void H( double * /*x*/, double h[3][3] )
{
h[0][1] = h[0][2] = h[1][0] = h[1][2] = h[2][0] = h[2][1] = 0.0;
h[0][0] = h[1][1] = h[2][2] = 2.0;
diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp
index 308190c5288ea41ad9ceb689b9df1f849ffb8c08..0ca4c6700205399a0485ac65c2da5570f797f6d3 100644
--- a/src/USER-MANIFOLD/manifold_spine.cpp
+++ b/src/USER-MANIFOLD/manifold_spine.cpp
@@ -8,7 +8,7 @@ using namespace user_manifold;
-manifold_spine::manifold_spine( LAMMPS *lmp, int argc, char **argv )
+manifold_spine::manifold_spine( LAMMPS *lmp, int /*argc*/, char **/*argv*/ )
: manifold(lmp)
{
power = 4;
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp
index b7eb155ba27b5b40c4f4d1dafc87942839b887d4..93cf60ad0392f8e53a412b4dec57e982b956b1ec 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp
@@ -12,7 +12,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int narg, char ** arg)
+manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int /*narg*/, char ** /*arg*/)
: manifold(lmp)
{
// You can NOT depend on proper construction of the domains in
@@ -117,7 +117,7 @@ void manifold_thylakoid::n( const double *x, double *n )
}
}
-thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int *err_flag, std::size_t *idx )
+thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_flag*/, std::size_t *idx )
{
for( std::size_t i = 0; i < parts.size(); ++i ){
diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp
index 44a17725b5e2230e4cbc2e2fb5809ef693d99c0a..0b4ca24370ce11d9701013b21159ced669e09d24 100644
--- a/src/USER-MANIFOLD/manifold_torus.cpp
+++ b/src/USER-MANIFOLD/manifold_torus.cpp
@@ -6,7 +6,7 @@ using namespace LAMMPS_NS;
using namespace user_manifold;
-manifold_torus::manifold_torus( LAMMPS *lmp, int argc, char **argv ) : manifold(lmp)
+manifold_torus::manifold_torus( LAMMPS *lmp, int /*argc*/, char **/*argv*/ ) : manifold(lmp)
{}
diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp
index de188e497db05954deaa0e84ec9d9670c2a19b7e..2be215c282efd21397621c2cfe671d3f77737f27 100644
--- a/src/USER-MEAMC/meam_dens_final.cpp
+++ b/src/USER-MEAMC/meam_dens_final.cpp
@@ -5,7 +5,7 @@ using namespace LAMMPS_NS;
void
MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global, int eflag_atom, double* eng_vdwl,
- double* eatom, int ntype, int* type, int* fmap, int& errorflag)
+ double* eatom, int /*ntype*/, int* type, int* fmap, int& errorflag)
{
int i, elti;
int m;
diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp
index e1a7509ab30db041337bddc0d7bb2f6ea763f81e..4bbaa4259697f2f7728fe74ed6bddf00c63158a4 100644
--- a/src/USER-MEAMC/meam_dens_init.cpp
+++ b/src/USER-MEAMC/meam_dens_init.cpp
@@ -93,7 +93,7 @@ MEAM::meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,
void
MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double** x, int numneigh,
- int* firstneigh, int numneigh_full, int* firstneigh_full, int ntype, int* type, int* fmap)
+ int* firstneigh, int numneigh_full, int* firstneigh_full, int /*ntype*/, int* type, int* fmap)
{
int jn, j, kn, k;
int elti, eltj, eltk;
@@ -256,7 +256,7 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, double**
// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
void
-MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+MEAM::calc_rho1(int i, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
double* scrfcn, double* fcpair)
{
int jn, j, m, n, p, elti, eltj;
diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp
index 85314dd8a2f0ef5bcf319936183ff0f1e70dd280..06fbb57adb11a778d088c1fc166ffe231ff23ade 100644
--- a/src/USER-MEAMC/meam_force.cpp
+++ b/src/USER-MEAMC/meam_force.cpp
@@ -7,7 +7,7 @@ using namespace LAMMPS_NS;
void
MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl,
- double* eatom, int ntype, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
+ double* eatom, int /*ntype*/, int* type, int* fmap, double** x, int numneigh, int* firstneigh,
int numneigh_full, int* firstneigh_full, int fnoffset, double** f, double** vatom)
{
int j, jn, k, kn, kk, m, n, p, q;
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 7f8ad3d81f5f09fbff2224c28ee866ddf234686f..503ee6549647f8c654b6a3b3c6a1ecb6815cc058 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -3,7 +3,7 @@
using namespace LAMMPS_NS;
void
-MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt, double* alpha,
+MEAM::meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* /*atwt*/, double* alpha,
double* b0, double* b1, double* b2, double* b3, double* alat, double* esub,
double* asub, double* t0, double* t1, double* t2, double* t3, double* rozero,
int* ibar)
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 027e4c27a79ca000dd10a3b6383a97152f0a1bd1..eca1040c9c990aa392db7f0e3a9dccac6cad1fbc 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -195,7 +195,7 @@ void PairMEAMC::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMC::settings(int narg, char **arg)
+void PairMEAMC::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -312,7 +312,7 @@ void PairMEAMC::init_list(int id, NeighList *ptr)
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMC::init_one(int i, int j)
+double PairMEAMC::init_one(int /*i*/, int /*j*/)
{
return cutmax;
}
@@ -598,7 +598,7 @@ void PairMEAMC::read_files(char *globalfile, char *userfile)
/* ---------------------------------------------------------------------- */
int PairMEAMC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index 8b03e051814ffe6f636f01d7c8e92f4b83950464..24bef2b1f72fdfe4c1f06b21175b5d9b90ef6eff 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -87,7 +87,7 @@ void FixEDPDSource::init()
/* ---------------------------------------------------------------------- */
-void FixEDPDSource::post_force(int vflag)
+void FixEDPDSource::post_force(int /*vflag*/)
{
double **x = atom->x;
double *edpd_flux = atom->edpd_flux;
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index c97a2d779c0de1595e13a5e09f2a3809d4057fa1..f663165f78d834d4aec55b51bb23e9f0e63a7c5f 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -72,7 +72,7 @@ void FixMvvDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvDPD::initial_integrate(int vflag)
+void FixMvvDPD::initial_integrate(int /*vflag*/)
{
double dtfm;
double **x = atom->x;
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index 89a831e121b9a37fbdb8271f9db554b2fa6d2d07..8719d0d262d35e3f20eb0e0d57f031141ed69981 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -78,7 +78,7 @@ void FixMvvEDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvEDPD::initial_integrate(int vflag)
+void FixMvvEDPD::initial_integrate(int /*vflag*/)
{
double dtfm,dtT;
// update v and x and cc of atoms in group
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index e16171800b1b61bc44899fc0895adff7a52637a3..24b1bbcf48bc2ed85d27fbf8e80893794689bdfc 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -76,7 +76,7 @@ void FixMvvTDPD::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMvvTDPD::initial_integrate(int vflag)
+void FixMvvTDPD::initial_integrate(int /*vflag*/)
{
double dtfm;
// update v and x and cc of atoms in group
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index 64964a4c983ebb5ef8fb5cd27df15079f8860464..89e8005b43500bedefeee55078c3fe5b914ebec3 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -88,7 +88,7 @@ void FixTDPDSource::init()
/* ---------------------------------------------------------------------- */
-void FixTDPDSource::post_force(int vflag)
+void FixTDPDSource::post_force(int /*vflag*/)
{
double **x = atom->x;
double **cc_flux = atom->cc_flux;
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index 351637a842018c6469c09a1929e5552487c20695..5ed63a2a8b3dca4ad4a10fde95ed79ba9f185ac9 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -530,7 +530,7 @@ void PairEDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairEDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
double *T = atom->edpd_temp;
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index 1264d03ed3b5dd9404fef9ba6a5eac0acb28b16d..806a63f898685c731b6a79d1937e102a1e184a26 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -186,7 +186,7 @@ void PairMDPDRhoSum::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairMDPDRhoSum::settings(int narg, char **arg) {
+void PairMDPDRhoSum::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,"Illegal number of setting arguments for pair_style mdpd/rhosum");
}
@@ -236,8 +236,8 @@ double PairMDPDRhoSum::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce) {
+double PairMDPDRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
+ double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
@@ -246,7 +246,7 @@ double PairMDPDRhoSum::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
int PairMDPDRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc) {
+ int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index b8bbf6d622f51e16f15813cbeb1af08a692adceb..821d8c0486b60928ba9f075daf1ad2a242b10da5 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -465,8 +465,8 @@ void PairTDPD::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairTDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairTDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wc,phi;
diff --git a/src/USER-MGPT/mgpt_linalg.cpp b/src/USER-MGPT/mgpt_linalg.cpp
index 94a4e21ea6a3cb185a556459e30dd98b3cbab0e4..68701037f4a52bbdfeba238004f67d7900d2cb72 100644
--- a/src/USER-MGPT/mgpt_linalg.cpp
+++ b/src/USER-MGPT/mgpt_linalg.cpp
@@ -81,8 +81,8 @@
#define const
#endif
static void transprod_generic(const double * restrict A,
- const double * restrict B,
- double * restrict C) {
+ const double * restrict B,
+ double * restrict C) {
const int lda = 8,n = mgpt_linalg::matrix_size;
int i,j,k;
double s;
@@ -90,15 +90,15 @@ static void transprod_generic(const double * restrict A,
for(j = 0; j<n; j++) {
s = 0.0;
for(k = 1; k<=n; k++)
- s = s + A[i*lda+k]*B[j*lda+k];
+ s = s + A[i*lda+k]*B[j*lda+k];
C[i*lda+(j+1)] = s;
}
}
static void transtrace3_generic(const double * restrict A,
- const double * restrict B0,double * restrict tout0,
- const double * restrict B1,double * restrict tout1,
- const double * restrict B2,double * restrict tout2) {
+ const double * restrict B0,double * restrict tout0,
+ const double * restrict B1,double * restrict tout1,
+ const double * restrict B2,double * restrict tout2) {
const int lda = 8,n = mgpt_linalg::matrix_size;
double t0 = 0.0,t1 = 0.0,t2 = 0.0;
int i,j;
@@ -116,16 +116,16 @@ static void transtrace3_generic(const double * restrict A,
*tout2 = t2;
}
-static void transprod_error(const double * restrict A,
- const double * restrict B,
- double * restrict C) {
+static void transprod_error(const double * restrict /*A*/,
+ const double * restrict /*B*/,
+ double * restrict /*C*/) {
printf("Linear algebra subroutines not initialized (transprod).\n");
exit(1);
}
-static void transtrace3_error(const double * restrict A,
- const double * restrict B0,double * restrict tout0,
- const double * restrict B1,double * restrict tout1,
- const double * restrict B2,double * restrict tout2) {
+static void transtrace3_error(const double * restrict /*A*/,
+ const double * restrict /*B0*/,double * restrict /*tout0*/,
+ const double * restrict /*B1*/,double * restrict /*tout1*/,
+ const double * restrict /*B2*/,double * restrict /*tout2*/) {
printf("Linear algebra subroutines not initialized (transtrace3).\n");
exit(1);
}
diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp
index bac405bcbbd59b5482eb0ee83f2f7da663c52f23..347bc9cc691a2c482c0b54fdca1c5760728bdff9 100644
--- a/src/USER-MGPT/pair_mgpt.cpp
+++ b/src/USER-MGPT/pair_mgpt.cpp
@@ -79,7 +79,7 @@ static double gettime(int x = 0) {
return 0.0;
}
#else
-static double gettime(int x = 0) { return 0.0; }
+static double gettime(int /*x*/ = 0) { return 0.0; }
#endif
@@ -1805,7 +1805,7 @@ void PairMGPT::allocate()
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
-void PairMGPT::settings(int narg, char **arg)
+void PairMGPT::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(__FILE__,__LINE__,"Illegal pair_style command");
}
@@ -2025,7 +2025,7 @@ void PairMGPT::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMGPT::init_one(int i, int j)
+double PairMGPT::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index bcb631c61f065353cbb60761a4e693c28800693a..c4186da472b58d51c2a1ae5ec94518ae40065c5a 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -229,7 +229,7 @@ void AngleDipole::write_data(FILE *fp)
used by ComputeAngleLocal
------------------------------------------------------------------------- */
-double AngleDipole::single(int type, int iRef, int iDip, int iDummy)
+double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
{
double **x = atom->x; // position vector
double **mu = atom->mu; // point-dipole components and moment magnitude
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index 7148c5438d1d4ff200915edbb5c1fda345bd3d01..b34f71e8885ffce2e25154a7e2985eb739a1dfd3 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -203,7 +203,7 @@ void BondHarmonicShift::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonicShift::single(int type, double rsq, int i, int j,
+double BondHarmonicShift::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index 20c8a1a30019fb5cb3bdb99b597e91c6fd116778..a58df7087818de4a2c48f4624c3915d3b0988311 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -205,7 +205,7 @@ void BondHarmonicShiftCut::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondHarmonicShiftCut::single(int type, double rsq, int i, int j,
+double BondHarmonicShiftCut::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
fforce = 0.0;
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index a17aefe71b46b0dd435473c9d917eb6a74561365..bcf41591ebb1b29fb2ed173fde0fa8c1cc9b5259 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -105,7 +105,7 @@ void ComputeAcklandAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeAcklandAtom::init_list(int id, NeighList *ptr)
+void ComputeAcklandAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index 4d8627a11fb66534b0e982413790156d4efaf524..3b9b38343d2aabe3ea67ffa737973d74cda24f71 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -85,7 +85,7 @@ void ComputeBasalAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeBasalAtom::init_list(int id, NeighList *ptr)
+void ComputeBasalAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp
index 51cf3ab07a43628ba454f708400d386bdffdb54f..6fa16f1a9ac5b6f82a35eac3a9d792c9dedabe30 100644
--- a/src/USER-MISC/compute_cnp_atom.cpp
+++ b/src/USER-MISC/compute_cnp_atom.cpp
@@ -121,7 +121,7 @@ void ComputeCNPAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCNPAtom::init_list(int id, NeighList *ptr)
+void ComputeCNPAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp
index 922f2aaf5ee9d53b50bbadb3485142ab1bc88961..4946bc437e7960bba7e9f054d298d191c69f2711 100644
--- a/src/USER-MISC/compute_entropy_atom.cpp
+++ b/src/USER-MISC/compute_entropy_atom.cpp
@@ -151,7 +151,7 @@ void ComputeEntropyAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeEntropyAtom::init_list(int id, NeighList *ptr)
+void ComputeEntropyAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index 654911769c271bce9c23c7488d5fa35ca88370e0..2cd1ac7527f063fb28dc9080000321126f7a00e4 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -164,7 +164,7 @@ void FixAddTorque::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddTorque::post_force(int vflag)
+void FixAddTorque::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -252,7 +252,7 @@ void FixAddTorque::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddTorque::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAddTorque::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index da6d041287df6904548cd4fa0070ca2a58b7a86e..0ce6121bf9950f404951d95ebad7761bf0222ecb 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -412,7 +412,7 @@ void FixAveCorrelateLong::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveCorrelateLong::setup(int vflag)
+void FixAveCorrelateLong::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index f369a9a10f5d4a3860ee6830a91ee3806632ac9b..469e1d6347a3c073c0ffbecd5c26a905a85dcaf8 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -588,7 +588,7 @@ void FixBondReact::init()
/* ---------------------------------------------------------------------- */
-void FixBondReact::init_list(int id, NeighList *ptr)
+void FixBondReact::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -1558,7 +1558,6 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
for (int i = 0; i < twomol->natoms; i++) {
if (landlocked_atoms[i][myrxn] == 0) {
- int twomol_atomi = i+1;
for (int j = 0; j < twomol->num_bond[i]; j++) {
int twomol_atomj = twomol->bond_atom[i][j];
if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
@@ -2632,7 +2631,7 @@ double FixBondReact::compute_vector(int n)
/* ---------------------------------------------------------------------- */
-void FixBondReact::post_integrate_respa(int ilevel, int iloop)
+void FixBondReact::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -2640,7 +2639,7 @@ void FixBondReact::post_integrate_respa(int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index 91c70335133e4fdf6a37c0ec212d5d38dc9501fb..56ab2b3df9698edd26898fe0c1cbacb8001eebe0 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -705,7 +705,7 @@ double FixFilterCorotate::compute_array(int,int)
return 1;
}
-void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixFilterCorotate::pre_force_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1)
{
@@ -717,7 +717,7 @@ void FixFilterCorotate::pre_force_respa(int vflag, int ilevel, int iloop)
}
}
-void FixFilterCorotate::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFilterCorotate::post_force_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1)
{
@@ -1699,7 +1699,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
}
int FixFilterCorotate::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
double**f = atom->f;
@@ -1839,7 +1839,7 @@ double FixFilterCorotate::memory_usage()
* copy values within local atom-based arrays
* ------------------------------------------------------------------------- */
-void FixFilterCorotate::copy_arrays(int i, int j, int delflag)
+void FixFilterCorotate::copy_arrays(int i, int j, int /*delflag*/)
{
int flag = shake_flag[j] = shake_flag[i];
if (flag == 1) {
diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp
index 6a1e508030c16857aa282e0089c920bfdbbe8796..b6366ec509cd356990aff55b10d19c9ebb1baefe 100644
--- a/src/USER-MISC/fix_flow_gauss.cpp
+++ b/src/USER-MISC/fix_flow_gauss.cpp
@@ -155,7 +155,7 @@ void FixFlowGauss::setup(int vflag)
/* ----------------------------------------------------------------------
this is where Gaussian dynamics constraint is applied
------------------------------------------------------------------------- */
-void FixFlowGauss::post_force(int vflag)
+void FixFlowGauss::post_force(int /*vflag*/)
{
double **f = atom->f;
double **v = atom->v;
@@ -222,7 +222,7 @@ void FixFlowGauss::post_force(int vflag)
}
-void FixFlowGauss::post_force_respa(int vflag, int ilevel, int iloop)
+void FixFlowGauss::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 584b33bfe7da1bc93d041ee15388d7e72ebe36d5..0b08fab4cada24c97730d0354ea9a8602e4aea6a 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -582,7 +582,7 @@ void FixGLE::gle_integrate()
energy += deltae*0.5*force->mvv2e;
}
-void FixGLE::initial_integrate(int vflag)
+void FixGLE::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -685,7 +685,7 @@ void FixGLE::final_integrate()
}
/* ---------------------------------------------------------------------- */
-void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixGLE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -699,7 +699,7 @@ void FixGLE::initial_integrate_respa(int vflag, int ilevel, int iloop)
else { final_integrate();}
}
-void FixGLE::final_integrate_respa(int ilevel, int iloop)
+void FixGLE::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -793,7 +793,7 @@ void FixGLE::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixGLE::copy_arrays(int i, int j, int delflag)
+void FixGLE::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < 3*ns; k++) gle_s[j][k] = gle_s[i][k];
}
@@ -868,7 +868,7 @@ void FixGLE::unpack_restart(int nlocal, int nth)
fixes on a given processor.
------------------------------------------------------------------------- */
-int FixGLE::size_restart(int nlocal)
+int FixGLE::size_restart(int /*nlocal*/)
{
return 3*ns+1;
}
diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp
index a5f8c344488864f80eb160d44c26c21b9ae7890a..635acf705c93bfc758bde45dc14b1e77276ae22a 100644
--- a/src/USER-MISC/fix_grem.cpp
+++ b/src/USER-MISC/fix_grem.cpp
@@ -256,7 +256,7 @@ void FixGrem::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGrem::post_force(int vflag)
+void FixGrem::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index abf9e7cb0ba59629d5d1f65524dbea82b2f0db74..1c3eafdc46cf1ca42b451bd33e5b2e8f3e058890 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -811,7 +811,7 @@ void FixIMD::ioworker()
/* ---------------------------------------------------------------------- */
/* Main IMD protocol handler:
* Send coodinates, energies, and add IMD forces to atoms. */
-void FixIMD::post_force(int vflag)
+void FixIMD::post_force(int /*vflag*/)
{
/* check for reconnect */
if (imd_inactive) {
@@ -1153,7 +1153,7 @@ void FixIMD::post_force(int vflag)
}
/* ---------------------------------------------------------------------- */
-void FixIMD::post_force_respa(int vflag, int ilevel, int iloop)
+void FixIMD::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
/* only process IMD on the outmost RESPA level. */
if (ilevel == nlevels_respa-1) post_force(vflag);
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index c4750ce49e211b22c6f3b1ddc8e8d812f1843402..32892d87a8edd81945e7b613567b3998a5eb03cd 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -269,7 +269,7 @@ void FixIPI::init()
neighbor->every = 1;
}
-void FixIPI::initial_integrate(int vflag)
+void FixIPI::initial_integrate(int /*vflag*/)
{
/* This is called at the beginning of the integration loop,
* and will be used to read positions from the socket. Then,
diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp
index dbf7b56fe22048745d10b71dad15e8def74fa30e..2ac2a7c9fca3ad1b2218ab6127def276a8cca14d 100644
--- a/src/USER-MISC/fix_nvk.cpp
+++ b/src/USER-MISC/fix_nvk.cpp
@@ -94,7 +94,7 @@ void FixNVK::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVK::initial_integrate(int vflag)
+void FixNVK::initial_integrate(int /*vflag*/)
{
double sm;
double a,b,sqtb,s,sdot;
@@ -190,7 +190,7 @@ void FixNVK::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVK::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel];
@@ -204,7 +204,7 @@ void FixNVK::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVK::final_integrate_respa(int ilevel, int iloop)
+void FixNVK::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel];
final_integrate();
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index e65ae6ae28168acf3a766798f4028f5c7fca700a..eba8ed5d0c7d86477c8ba288931ef7b2357abddb 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -214,7 +214,7 @@ void FixPIMD::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPIMD::initial_integrate(int vflag)
+void FixPIMD::initial_integrate(int /*vflag*/)
{
nhc_update_v();
nhc_update_x();
@@ -229,7 +229,7 @@ void FixPIMD::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixPIMD::post_force(int flag)
+void FixPIMD::post_force(int /*flag*/)
{
for(int i=0; i<atom->nlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np;
@@ -686,7 +686,7 @@ void FixPIMD::comm_exec(double **ptr)
/* ---------------------------------------------------------------------- */
int FixPIMD::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
@@ -744,7 +744,7 @@ void FixPIMD::grow_arrays(int nmax)
/* ---------------------------------------------------------------------- */
-void FixPIMD::copy_arrays(int i, int j, int delflag)
+void FixPIMD::copy_arrays(int i, int j, int /*delflag*/)
{
int i_pos = i*3;
int j_pos = j*3;
@@ -832,7 +832,7 @@ int FixPIMD::maxsize_restart()
/* ---------------------------------------------------------------------- */
-int FixPIMD::size_restart(int nlocal)
+int FixPIMD::size_restart(int /*nlocal*/)
{
return size_peratom_cols+1;
}
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
index bbc4ce417a460d194bf3014b61cadc802c763a8d..78d63b79a82fbd39c78c3100b5460fae971d5e76 100644
--- a/src/USER-MISC/fix_rhok.cpp
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -144,7 +144,7 @@ FixRhok::min_setup( int inVFlag )
// Modify the forces calculated in the main force loop of ordinary MD
void
-FixRhok::post_force( int inVFlag )
+FixRhok::post_force( int /*inVFlag*/ )
{
double **x = atom->x;
double **f = atom->f;
@@ -206,7 +206,7 @@ FixRhok::post_force( int inVFlag )
// Forces in RESPA loop
void
-FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop )
+FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ )
{
if( inILevel == mNLevelsRESPA - 1 )
post_force( inVFlag );
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index a42690c280f960d55ef482f4f7d9c85a04af0d31..cbebdebdbf920bce5ba705ff4630f24892f32b23 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -461,7 +461,7 @@ void FixSMD::restart(char *buf)
/* ---------------------------------------------------------------------- */
-void FixSMD::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSMD::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index e4d85e867418b3d3173b1883d79aa567d7129278..ebc161ff99b31c32431df6cfbf21f478f3276014 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -145,7 +145,7 @@ void FixSRP::init()
insert bond particles
------------------------------------------------------------------------- */
-void FixSRP::setup_pre_force(int zz)
+void FixSRP::setup_pre_force(int /*zz*/)
{
double **x = atom->x;
double **xold;
@@ -394,7 +394,7 @@ void FixSRP::grow_arrays(int nmax)
called when move to new proc
------------------------------------------------------------------------- */
-void FixSRP::copy_arrays(int i, int j, int delflag)
+void FixSRP::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2; m++)
array[j][m] = array[i][m];
@@ -589,7 +589,7 @@ int FixSRP::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixSRP::size_restart(int nlocal)
+int FixSRP::size_restart(int /*nlocal*/)
{
return 3;
}
@@ -632,7 +632,7 @@ void FixSRP::restart(char *buf)
pair srp sets the bond type in this fix
------------------------------------------------------------------------- */
-int FixSRP::modify_param(int narg, char **arg)
+int FixSRP::modify_param(int /*narg*/, char **arg)
{
if (strcmp(arg[0],"btype") == 0) {
btype = atoi(arg[1]);
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 5812142763f82c44e9b9cab16595d579e5483701..305e29e0339ea754984caa3977b07ccf32ea9732 100644
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -167,7 +167,7 @@ void FixTISpring::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::post_force(int vflag)
+void FixTISpring::post_force(int /*vflag*/)
{
// do not calculate forces during equilibration
if ((update->ntimestep - t0) < t_equil) return;
@@ -200,7 +200,7 @@ void FixTISpring::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTISpring::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -214,7 +214,7 @@ void FixTISpring::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTISpring::initial_integrate(int vflag)
+void FixTISpring::initial_integrate(int /*vflag*/)
{
// Update the coupling parameter value if needed
if ((update->ntimestep - t0) < t_equil) return;
@@ -278,7 +278,7 @@ void FixTISpring::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixTISpring::copy_arrays(int i, int j, int delflag)
+void FixTISpring::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -354,7 +354,7 @@ int FixTISpring::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTISpring::size_restart(int nlocal)
+int FixTISpring::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index 1e1e62b638595c9e2aabcb3e690c2d64517dab80..65f8e90ec3d2304a96314a9b3f6afed3fc474612 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -357,7 +357,7 @@ void FixTTMMod::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force(int vflag)
+void FixTTMMod::post_force(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
@@ -451,7 +451,7 @@ void FixTTMMod::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_setup(int vflag)
+void FixTTMMod::post_force_setup(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -468,14 +468,14 @@ void FixTTMMod::post_force_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_respa(int vflag, int ilevel, int iloop)
+void FixTTMMod::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
-void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int iloop)
+void FixTTMMod::post_force_respa_setup(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force_setup(vflag);
}
@@ -916,7 +916,7 @@ int FixTTMMod::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixTTMMod::size_restart(int nlocal)
+int FixTTMMod::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp
index 82a78d3e73bc2d757ca2399c6a3ebc8726ad99af..33bf636e640e2aa81c795fbeb417a7341b044b50 100644
--- a/src/USER-MISC/fix_wall_region_ees.cpp
+++ b/src/USER-MISC/fix_wall_region_ees.cpp
@@ -149,7 +149,7 @@ void FixWallRegionEES::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegionEES::post_force(int vflag)
+void FixWallRegionEES::post_force(int /*vflag*/)
{
//sth is needed here, but I dont know what
//that is calculation of sn
@@ -246,7 +246,7 @@ void FixWallRegionEES::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 785146a0d6fef2646333d30f6c7f6fd5cfe67f0e..998582f619d2667a984d82446e5e8ed1fe65295a 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -246,7 +246,7 @@ void PairAGNI::allocate()
global settings
------------------------------------------------------------------------- */
-void PairAGNI::settings(int narg, char **arg)
+void PairAGNI::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index 457d75bc7712907bd06caab711216947e2bcc270..61d32892fcf7b5282a3c4bdb475dde78e14e3afc 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -391,8 +391,8 @@ void PairBuckMDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBuckMDF::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBuckMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index 3f07df3d9861dbc0cb5af1bf6a3766d5ccebb38d..0154e8973171fe2675fa349235ba50507fdb2727 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -326,7 +326,7 @@ void PairCoulDiel::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulDiel::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r, rarg,forcedielec,phidielec;
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index deec7da81faaa4a2557f7e40bd21c1389c6aa0e2..11df975c1903acf861bd16c7d8749dc03bfab0f8 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -341,7 +341,7 @@ void PairCoulShield::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairCoulShield::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r, rarg,Vc,fvc,forcecoul,phishieldec;
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 2976d7ad73c994fcb4237e6d05edd642f0f2c749..4716e271d7feaeda271c1d4d0ee23355c1deba82 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -621,7 +621,7 @@ void PairEDIP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEDIP::settings(int narg, char **arg)
+void PairEDIP::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index 6be57eee74c9c32ffb92f28f27391b225e10d6ed..fc76aadb0b92d5b08bfa2c074348aa12226c5bab 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -516,7 +516,7 @@ void PairEDIPMulti::allocate()
global settings
------------------------------------------------------------------------- */
-void PairEDIPMulti::settings(int narg, char **arg)
+void PairEDIPMulti::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index 5a8cdf28841cf2f7fa61b4f184867a2f8465ff7f..49c562471ffd9f5453df9eb333f033e618e9804a 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -442,7 +442,7 @@ void PairExTeP::allocate()
global settings
------------------------------------------------------------------------- */
-void PairExTeP::settings(int narg, char **arg)
+void PairExTeP::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index 85f7c02887a1d0c1a9a6841d69df6c17a754b5e6..a000eff028ccb7e153f4837e04c5512905f8bad1 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -374,8 +374,8 @@ void PairGaussCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGaussCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r, rexp,ugauss,phigauss;
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 30ee2e7a5ae3c3aa42843f2ba07c1c8f36b7dbb9..7e11cdff4f567b769e17d9a0f12316c05ad529f7 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -1010,8 +1010,8 @@ void PairILPGrapheneHBN::read_file(char *filename)
/* ---------------------------------------------------------------------- */
-double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairILPGrapheneHBN::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,r2inv,r6inv,r8inv,forcelj,philj,fpair;
@@ -1047,7 +1047,7 @@ double PairILPGrapheneHBN::single(int i, int j, int itype, int jtype, double rsq
/* ---------------------------------------------------------------------- */
int PairILPGrapheneHBN::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m,id,ip,l;
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index be0e81d48d9e986e38247aae32bb60b0ac4fb377..bc3bfaeba91e8fe8ee733ad43c71d5150605faad 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -1015,8 +1015,8 @@ void PairKolmogorovCrespiFull::read_file(char *filename)
/* ---------------------------------------------------------------------- */
-double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairKolmogorovCrespiFull::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,r2inv,r6inv,r8inv,forcelj,philj;
@@ -1050,7 +1050,7 @@ double PairKolmogorovCrespiFull::single(int i, int j, int itype, int jtype, doub
/* ---------------------------------------------------------------------- */
int PairKolmogorovCrespiFull::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m,l,ip,id;
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index f6e7f7f56b0084b8fe5115e0424fce3909bde8c4..45d0da4d83e03d2bea53c7ab2ca62f57ede9c802 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -352,9 +352,9 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJ_AB_MDF::single(int i, int j, int itype, int jtype,
+double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index d43a6c30862165ea7cd6d0a801e7e285902feb0c..891239016bc09c5829aa53566da2c4fe55a2ab2a 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -352,9 +352,9 @@ void PairLJMDF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJMDF::single(int i, int j, int itype, int jtype,
+double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 750f6ac5bbaee20ffcdffbaf8dccecf28576701b..e6ea6c2ae445f30bcb99a4f7667fdee093dbcc70 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -360,7 +360,7 @@ void PairMEAMSpline::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMSpline::settings(int narg, char **arg)
+void PairMEAMSpline::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -592,7 +592,7 @@ void PairMEAMSpline::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMSpline::init_one(int i, int j)
+double PairMEAMSpline::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
@@ -600,7 +600,7 @@ double PairMEAMSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairMEAMSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -618,14 +618,14 @@ void PairMEAMSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSpline::pack_reverse_comm(int n, int first, double *buf)
+int PairMEAMSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSpline::unpack_reverse_comm(int n, int *list, double *buf)
+void PairMEAMSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/)
{
}
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index f6b7212f9cfd9ee124eed653d2cf588b77d502a0..891913ccfcf5e95e83b0a709ce0a9c857e7c4994 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -372,7 +372,7 @@ void PairMEAMSWSpline::allocate()
global settings
------------------------------------------------------------------------- */
-void PairMEAMSWSpline::settings(int narg, char **arg)
+void PairMEAMSWSpline::settings(int narg, char **/*arg*/)
{
if(narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -552,7 +552,7 @@ void PairMEAMSWSpline::init_list(int id, NeighList *ptr)
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairMEAMSWSpline::init_one(int i, int j)
+double PairMEAMSWSpline::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
@@ -560,7 +560,7 @@ double PairMEAMSWSpline::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairMEAMSWSpline::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int* list_iter = list;
int* list_iter_end = list + n;
@@ -578,14 +578,14 @@ void PairMEAMSWSpline::unpack_forward_comm(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int PairMEAMSWSpline::pack_reverse_comm(int n, int first, double *buf)
+int PairMEAMSWSpline::pack_reverse_comm(int /*n*/, int /*first*/, double * /*buf*/)
{
return 0;
}
/* ---------------------------------------------------------------------- */
-void PairMEAMSWSpline::unpack_reverse_comm(int n, int *list, double *buf)
+void PairMEAMSWSpline::unpack_reverse_comm(int /*n*/, int * /*list*/, double * /*buf*/)
{
}
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index 12a40bb08beb6ce981920f5dbba5dc041564deb8..927181ebf6362a0982de2ad8875fbd7dba85bb83 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -365,8 +365,8 @@ void PairMomb::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMomb::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMomb::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 8a9c89cf6945afbba59a7509d936f0ecf526c4a8..328c1bd27b655e3d8226a80b59fefd25b00f2fef 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -337,8 +337,8 @@ void PairMorseSmoothLinear::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorseSmoothLinear::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorseSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index c2362b8de9ce0c186636d91d324f406b5bdadfd4..d7e28a1e40778cd0e19eb51185d4e731e5f39fc9 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -719,7 +719,7 @@ void PairTersoffTable::allocate()
global settings
------------------------------------------------------------------------- */
-void PairTersoffTable::settings(int narg, char **arg)
+void PairTersoffTable::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index b5800db2beb9a398eaa2fd8d314a8ae5566df1a9..3f87aeb7574a00b0fa5b83e8a76d038202fc329d 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -56,7 +56,7 @@ AngleCosineBuck6d::~AngleCosineBuck6d()
void AngleCosineBuck6d::compute(int eflag, int vflag)
{
- int i,i1,i2,i3,n,type,itype,jtype;
+ int i1,i2,i3,n,type,itype,jtype;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
@@ -309,7 +309,7 @@ void AngleCosineBuck6d::init_style()
/* ---------------------------------------------------------------------- */
-double AngleCosineBuck6d::equilibrium_angle(int i)
+double AngleCosineBuck6d::equilibrium_angle(int /*i*/)
{
return MY_PI;
}
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 53a7b4729a990c6adacf7b69c8a57558e586e465..9608d58054fa49d99443f915dbe5c78af055d34a 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -139,7 +139,6 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
double upx,upy,upz,upn,rup,umx,umy,umz,umn,rum,wwr;
double rucb,rudb,rvcb,rvdb,rupupn,rumumn;
- double **x = atom->x;
double **f = atom->f;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
@@ -242,7 +241,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
f[i4][2] += f4[2];
}
- double rb1x, rb1y, rb1z, rb2x, rb2y, rb2z, rb3x, rb3y, rb3z;
+ double rb3x, rb3y, rb3z;
if (evflag)
rb3x = vb1x - vb2x;
@@ -253,7 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
vb3x,vb3y,vb3z,
vb2x,vb2y,vb2z,
rb3x,rb3y,rb3z);
- }
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index 3a37c67a3871f1e044ba568e256c8c57a56620c8..cdbe4068bc9d96de79e52b02c4f6a09bacf5d23d 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -299,7 +299,7 @@ void FixPhonon::init()
/* ---------------------------------------------------------------------- */
-void FixPhonon::setup(int flag)
+void FixPhonon::setup(int /*flag*/)
{
// initialize accumulating variables
for (int i = 0; i < sysdim; ++i) TempSum[i] = 0.;
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index fa5ee75bcb8852fb6ea3e24f229d0ffdd1bb8812..e8a4f85eaa5edec07fc81d1ffdb6c4e4221758e3 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -424,7 +424,7 @@ void FixQBMSST::init()
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixQBMSST::setup(int vflag)
+void FixQBMSST::setup(int /*vflag*/)
{
lagrangian_position = 0.0;
@@ -507,7 +507,7 @@ void FixQBMSST::setup(int vflag)
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixQBMSST::initial_integrate(int vflag)
+void FixQBMSST::initial_integrate(int /*vflag*/)
{
int sd;
sd = direction;
@@ -1157,7 +1157,7 @@ void FixQBMSST::grow_arrays(int nmax)
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixQBMSST::copy_arrays(int i, int j, int delflag)
+void FixQBMSST::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2*N_f; m++) {
random_array_0[j][m] = random_array_0[i][m];
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index 7f9a6510bed1d6223d5afa71863f14fb24c91664..015f953b8e1438682d39c9df6f7cbfaf677e0adf 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -239,7 +239,7 @@ void FixQTB::setup(int vflag)
/* ----------------------------------------------------------------------
post_force
------------------------------------------------------------------------- */
-void FixQTB::post_force(int vflag)
+void FixQTB::post_force(int /*vflag*/)
{
double gamma1,gamma3;
@@ -334,7 +334,7 @@ void FixQTB::post_force(int vflag)
/* ----------------------------------------------------------------------
post_force_respa
------------------------------------------------------------------------- */
-void FixQTB::post_force_respa(int vflag, int ilevel, int iloop)
+void FixQTB::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -392,7 +392,7 @@ void FixQTB::grow_arrays(int nmax)
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixQTB::copy_arrays(int i, int j, int delflag)
+void FixQTB::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < 2*N_f; m++) {
random_array_0[j][m] = random_array_0[i][m];
diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp
index 0c00a5ef59309b824e1c534d58a6fcff9df79ceb..6f5040d037869c75973a12d34297491a14c144bd 100644
--- a/src/USER-QUIP/pair_quip.cpp
+++ b/src/USER-QUIP/pair_quip.cpp
@@ -212,7 +212,7 @@ 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)
@@ -315,7 +315,7 @@ void PairQUIP::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairQUIP::init_one(int i, int j)
+double PairQUIP::init_one(int /*i*/, int /*j*/)
{
return cutoff;
}
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index a2f4d3d0e936c70674d1340e2c883cbb3a0c79be..6f0b93235fe7b3094786182791ec6857783cf604 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -381,7 +381,7 @@ void FixQEqReax::init()
/* ---------------------------------------------------------------------- */
-void FixQEqReax::init_list(int id, NeighList *ptr)
+void FixQEqReax::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -485,7 +485,7 @@ void FixQEqReax::init_storage()
/* ---------------------------------------------------------------------- */
-void FixQEqReax::pre_force(int vflag)
+void FixQEqReax::pre_force(int /*vflag*/)
{
double t_start, t_end;
@@ -518,7 +518,7 @@ void FixQEqReax::pre_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixQEqReax::pre_force_respa(int vflag, int ilevel, int iloop)
+void FixQEqReax::pre_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) pre_force(vflag);
}
@@ -833,7 +833,7 @@ void FixQEqReax::calculate_Q()
/* ---------------------------------------------------------------------- */
int FixQEqReax::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int m;
@@ -952,7 +952,7 @@ void FixQEqReax::grow_arrays(int nmax)
copy values within fictitious charge arrays
------------------------------------------------------------------------- */
-void FixQEqReax::copy_arrays(int i, int j, int delflag)
+void FixQEqReax::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nprev; m++) {
s_hist[j][m] = s_hist[i][m];
diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp
index df06217993da53bc31492e1ea85957883a4ef475..c4701736631b1a345bda3e23f3ffe0d10f8aafb5 100644
--- a/src/USER-REAXC/fix_reaxc.cpp
+++ b/src/USER-REAXC/fix_reaxc.cpp
@@ -105,7 +105,7 @@ void FixReaxC::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixReaxC::copy_arrays(int i, int j, int delflag)
+void FixReaxC::copy_arrays(int i, int j, int /*delflag*/)
{
num_bonds[j] = num_bonds[i];
num_hbonds[j] = num_hbonds[i];
@@ -136,7 +136,7 @@ int FixReaxC::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
int FixReaxC::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index b38d137412b16d18130ed32dcaf82cd0ead7ab94..fb40b2042ecd9cc35c17352645cfe82b8c34a205 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -112,7 +112,7 @@ int FixReaxCBonds::setmask()
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::setup(int vflag)
+void FixReaxCBonds::setup(int /*vflag*/)
{
end_of_step();
}
@@ -137,7 +137,7 @@ void FixReaxCBonds::end_of_step()
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
+void FixReaxCBonds::Output_ReaxC_Bonds(bigint /*ntimestep*/, FILE * /*fp*/)
{
int i, j;
@@ -185,7 +185,7 @@ void FixReaxCBonds::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
/* ---------------------------------------------------------------------- */
-void FixReaxCBonds::FindBond(struct _reax_list *lists, int &numbonds)
+void FixReaxCBonds::FindBond(struct _reax_list * /*lists*/, int &numbonds)
{
int *ilist, i, ii, inum;
int j, pj, nj;
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 61b4cebf966592ff2a8a73ce708647d639ac8951..8ec7f4174f918b6cb95e04f6ded0f637903be1db 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -281,7 +281,7 @@ int FixReaxCSpecies::setmask()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::setup(int vflag)
+void FixReaxCSpecies::setup(int /*vflag*/)
{
ntotal = static_cast<int> (atom->natoms);
if (Name == NULL)
@@ -427,7 +427,7 @@ void FixReaxCSpecies::create_fix()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::init_list(int id, NeighList *ptr)
+void FixReaxCSpecies::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -442,7 +442,7 @@ void FixReaxCSpecies::post_integrate()
/* ---------------------------------------------------------------------- */
-void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
+void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE * /*fp*/)
{
int Nmole, Nspec;
@@ -946,7 +946,7 @@ int FixReaxCSpecies::nint(const double &r)
/* ---------------------------------------------------------------------- */
int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp
index 7f77d875bc8cea1c45a613c6a1f87bc68222de6f..378d20952c7186c0fbab9456df53cc1ea1d00f55 100644
--- a/src/USER-REAXC/pair_reaxc.cpp
+++ b/src/USER-REAXC/pair_reaxc.cpp
@@ -751,7 +751,7 @@ int PairReaxC::write_reax_lists()
/* ---------------------------------------------------------------------- */
-void PairReaxC::read_reax_forces(int vflag)
+void PairReaxC::read_reax_forces(int /*vflag*/)
{
for( int i = 0; i < system->N; ++i ) {
system->my_atoms[i].f[0] = workspace->f[i][0];
diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp
index a07f090f92a8c712c301444d6c0aac6941e2723d..c6c103b6f4a989c3a55638699e0fbc5ad6e1c458 100644
--- a/src/USER-REAXC/reaxc_allocate.cpp
+++ b/src/USER-REAXC/reaxc_allocate.cpp
@@ -39,8 +39,8 @@
important: we cannot know the exact number of atoms that will fall into a
process's box throughout the whole simulation. therefore
we need to make upper bound estimates for various data structures */
-int PreAllocate_Space( reax_system *system, control_params *control,
- storage *workspace, MPI_Comm comm )
+int PreAllocate_Space( reax_system *system, control_params * /*control*/,
+ storage * workspace, MPI_Comm comm )
{
int mincap = system->mincap;
double safezone = system->safezone;
@@ -60,6 +60,8 @@ int PreAllocate_Space( reax_system *system, control_params *control,
workspace->forceReduction = NULL;
workspace->valence_angle_atom_myoffset = NULL;
workspace->my_ext_pressReduction = NULL;
+#else
+ LMP_UNUSED_PARAM(workspace);
#endif
return SUCCESS;
@@ -68,8 +70,8 @@ int PreAllocate_Space( reax_system *system, control_params *control,
/************* system *************/
-int Allocate_System( reax_system *system, int local_cap, int total_cap,
- char *msg )
+int Allocate_System( reax_system *system, int /*local_cap*/, int total_cap,
+ char * /*msg*/ )
{
system->my_atoms = (reax_atom*)
realloc( system->my_atoms, total_cap*sizeof(reax_atom) );
@@ -116,7 +118,7 @@ void DeAllocate_System( reax_system *system )
/************* workspace *************/
-void DeAllocate_Workspace( control_params *control, storage *workspace )
+void DeAllocate_Workspace( control_params * /*control*/, storage *workspace )
{
int i;
@@ -204,9 +206,9 @@ void DeAllocate_Workspace( control_params *control, storage *workspace )
}
-int Allocate_Workspace( reax_system *system, control_params *control,
+int Allocate_Workspace( reax_system * /*system*/, control_params * control,
storage *workspace, int local_cap, int total_cap,
- MPI_Comm comm, char *msg )
+ MPI_Comm comm, char * /*msg*/ )
{
int i, total_real, total_rvec, local_rvec;
@@ -307,6 +309,8 @@ int Allocate_Workspace( reax_system *system, control_params *control,
workspace->valence_angle_atom_myoffset = (int *) scalloc(sizeof(int), total_cap, "valence_angle_atom_myoffset", comm);
workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads);
+#else
+ LMP_UNUSED_PARAM(control);
#endif
return SUCCESS;
diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp
index 468164a2c0007ad7bb16a0ab778082f9f6348ffa..572d27526cbb8aa4d118e9e23cb00771d0ef62f7 100644
--- a/src/USER-REAXC/reaxc_bond_orders.cpp
+++ b/src/USER-REAXC/reaxc_bond_orders.cpp
@@ -359,8 +359,8 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut,
}
-void BO( reax_system *system, control_params *control, simulation_data *data,
- storage *workspace, reax_list **lists, output_controls *out_control )
+void BO( reax_system *system, control_params * /*control*/, simulation_data * /*data*/,
+ storage *workspace, reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index;
diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp
index 9678addd6bfe5ec7f4982049641d909f22284009..6fde18e5c2485f979d6bdaa595742330ced40789 100644
--- a/src/USER-REAXC/reaxc_bonds.cpp
+++ b/src/USER-REAXC/reaxc_bonds.cpp
@@ -31,9 +31,9 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-void Bonds( reax_system *system, control_params *control,
+void Bonds( reax_system *system, control_params * /*control*/,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+ output_controls * /*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp
index 00b29824eae5cd9c92fb1d3e2fc9a2de92dc4b6a..dfcc9fd4ae4e11bc6351f549bc9c7b0a4a941ee0 100644
--- a/src/USER-REAXC/reaxc_forces.cpp
+++ b/src/USER-REAXC/reaxc_forces.cpp
@@ -41,9 +41,9 @@
interaction_function Interaction_Functions[NUM_INTRS];
-void Dummy_Interaction( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/,
+ simulation_data * /*data*/, storage * /*workspace*/,
+ reax_list **/*lists*/, output_controls * /*out_control*/ )
{
}
@@ -68,7 +68,7 @@ void Init_Force_Functions( control_params *control )
void Compute_Bonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+ MPI_Comm /*comm*/ )
{
int i;
@@ -83,7 +83,7 @@ void Compute_Bonded_Forces( reax_system *system, control_params *control,
void Compute_NonBonded_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
- MPI_Comm comm )
+ MPI_Comm /*comm*/ )
{
/* van der Waals and Coulomb interactions */
@@ -98,7 +98,7 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, mpi_datatypes *mpi_data )
+ reax_list **lists, mpi_datatypes * /*mpi_data*/ )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
@@ -114,8 +114,8 @@ void Compute_Total_Force( reax_system *system, control_params *control,
}
-void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
- int step, int n, int N, int numH, MPI_Comm comm )
+void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists,
+ int step, int /*n*/, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
@@ -173,7 +173,7 @@ void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control,
+ reax_list **lists, output_controls * /*out_control*/,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
@@ -317,7 +317,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
- int *bond_top, int *num_3body, MPI_Comm comm )
+ int *bond_top, int *num_3body, MPI_Comm /*comm*/ )
{
int i, j, pj;
int start_i, end_i;
diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
index cb516b24f7dd3f370ebd5ce8883853208334f1e2..6442dd47e944b332e979aaacfe755c5c4e6583a9 100644
--- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
+++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp
@@ -33,7 +33,7 @@
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp
index 4af21284f2bfd97028cc32832f8c20231ea4abeb..88fb9cf17fdbb2ecc88eac5b336de42135e96bdb 100644
--- a/src/USER-REAXC/reaxc_init_md.cpp
+++ b/src/USER-REAXC/reaxc_init_md.cpp
@@ -36,7 +36,7 @@
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
-int Init_System( reax_system *system, control_params *control, char *msg )
+int Init_System( reax_system *system, control_params *control, char * /*msg*/ )
{
int i;
reax_atom *atom;
@@ -66,7 +66,7 @@ int Init_System( reax_system *system, control_params *control, char *msg )
int Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, char *msg )
+ simulation_data *data, char * /*msg*/ )
{
Reset_Simulation_Data( data, control->virial );
@@ -139,8 +139,8 @@ int Init_Workspace( reax_system *system, control_params *control,
/************** setup communication data structures **************/
-int Init_MPI_Datatypes( reax_system *system, storage *workspace,
- mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
+int Init_MPI_Datatypes( reax_system *system, storage * /*workspace*/,
+ mpi_datatypes *mpi_data, MPI_Comm comm, char * /*msg*/ )
{
/* setup the world */
@@ -151,8 +151,8 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
}
int Init_Lists( reax_system *system, control_params *control,
- simulation_data *data, storage *workspace, reax_list **lists,
- mpi_datatypes *mpi_data, char *msg )
+ simulation_data * /*data*/, storage * /*workspace*/, reax_list **lists,
+ mpi_datatypes *mpi_data, char * /*msg*/ )
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp
index 4d58f7514de5eefc6910fb9e345e9fb16ad64459..b63fee23098f5fef833c7a99dae84ffa9d1302a4 100644
--- a/src/USER-REAXC/reaxc_io_tools.cpp
+++ b/src/USER-REAXC/reaxc_io_tools.cpp
@@ -88,7 +88,7 @@ int Init_Output_Files( reax_system *system, control_params *control,
/************************ close output files ************************/
int Close_Output_Files( reax_system *system, control_params *control,
- output_controls *out_control, mpi_datatypes *mpi_data )
+ output_controls *out_control, mpi_datatypes * /*mpi_data*/ )
{
if( out_control->write_steps > 0 )
End_Traj( system->my_rank, out_control );
diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp
index 9db8b7b9f650105c9c6c9d5bed90634a49b2e29f..918099a6319403b3a425d955582db3f797902c5d 100644
--- a/src/USER-REAXC/reaxc_lookup.cpp
+++ b/src/USER-REAXC/reaxc_lookup.cpp
@@ -151,7 +151,7 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double
int Init_Lookup_Tables( reax_system *system, control_params *control,
- storage *workspace, mpi_datatypes *mpi_data, char *msg )
+ storage *workspace, mpi_datatypes *mpi_data, char * /*msg*/ )
{
int i, j, r;
int num_atom_types;
diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp
index ce5b966529e0d0db5b69d0e03ebfcd2bfd808812..360a9431cf6c9b49637daf1bad8693393894f0e6 100644
--- a/src/USER-REAXC/reaxc_multi_body.cpp
+++ b/src/USER-REAXC/reaxc_multi_body.cpp
@@ -32,7 +32,7 @@
void Atom_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
- output_controls *out_control )
+ output_controls * /*out_control*/ )
{
int i, j, pj, type_i, type_j;
double Delta_lpcorr, dfvl;
diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp
index 9c223428a68dfe386c52345a3a89193b2d2161f1..b44632ec29d8e387ba0669d2a693ccaa78ad6065 100644
--- a/src/USER-REAXC/reaxc_nonbonded.cpp
+++ b/src/USER-REAXC/reaxc_nonbonded.cpp
@@ -33,7 +33,7 @@
void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pj, natoms;
int start_i, end_i, flag;
@@ -206,7 +206,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
- output_controls *out_control )
+ output_controls * /*out_control*/ )
{
int i, j, pj, r, natoms;
int type_i, type_j, tmin, tmax;
diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp
index 4ec744e7b1c0a9ff1f823951690d6f86de0b4cc4..1b16f10aeee1786e732bf7b6613f602b356ff0fb 100644
--- a/src/USER-REAXC/reaxc_reset_tools.cpp
+++ b/src/USER-REAXC/reaxc_reset_tools.cpp
@@ -87,7 +87,7 @@ void Reset_Pressures( simulation_data *data )
}
-void Reset_Simulation_Data( simulation_data* data, int virial )
+void Reset_Simulation_Data( simulation_data* data, int /*virial*/ )
{
Reset_Energies( &data->my_en );
Reset_Energies( &data->sys_en );
diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp
index c5a7f23b301c6f3a51ea1ed0439ea489b0878a8a..2abfbde61de915d461bdb2c12a64bc19eceb2583 100644
--- a/src/USER-REAXC/reaxc_torsion_angles.cpp
+++ b/src/USER-REAXC/reaxc_torsion_angles.cpp
@@ -41,7 +41,7 @@ double Calculate_Omega( rvec dvec_ij, double r_ij,
three_body_interaction_data *p_jkl,
rvec dcos_omega_di, rvec dcos_omega_dj,
rvec dcos_omega_dk, rvec dcos_omega_dl,
- output_controls *out_control )
+ output_controls * /*out_control*/ )
{
double unnorm_cos_omega, unnorm_sin_omega, omega;
double sin_ijk, cos_ijk, sin_jkl, cos_jkl;
diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp
index ae2bba2150673f13cf3523fcb4ca1e78ab8d81e4..c1f3e8ae8f17b0ebc5a668858a9c3c6953d96171 100644
--- a/src/USER-REAXC/reaxc_traj.cpp
+++ b/src/USER-REAXC/reaxc_traj.cpp
@@ -48,7 +48,7 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space,
}
-void Write_Skip_Line( output_controls *out_control, mpi_datatypes *mpi_data,
+void Write_Skip_Line( output_controls *out_control, mpi_datatypes * /*mpi_data*/,
int my_rank, int skip, int num_section )
{
if( my_rank == MASTER_NODE )
@@ -259,7 +259,7 @@ int Write_Header( reax_system *system, control_params *control,
}
-int Write_Init_Desc( reax_system *system, control_params *control,
+int Write_Init_Desc( reax_system *system, control_params * /*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, cnt, buffer_len, buffer_req;
@@ -482,7 +482,7 @@ int Write_Frame_Header( reax_system *system, control_params *control,
-int Write_Atoms( reax_system *system, control_params *control,
+int Write_Atoms( reax_system *system, control_params * /*control*/,
output_controls *out_control, mpi_datatypes *mpi_data )
{
int i, me, np, line_len, buffer_len, buffer_req, cnt;
diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp
index c92996e56b9a776735bbe2eab7fa06819ef18eb2..118735fbbdec0177efd32025bd8d831c439f1153 100644
--- a/src/USER-REAXC/reaxc_valence_angles.cpp
+++ b/src/USER-REAXC/reaxc_valence_angles.cpp
@@ -76,7 +76,7 @@ void Calculate_dCos_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk,
void Valence_Angles( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
- reax_list **lists, output_controls *out_control )
+ reax_list **lists, output_controls * /*out_control*/ )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index e99f3c51694eb609944461f44a495bca88187e1e..020284312b2164bd01c126a4695a65b28b010f78 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -208,7 +208,7 @@ void AtomVecSMD::copy(int i, int j, int delflag) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int AtomVecSMD::pack_comm(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -333,7 +333,7 @@ int AtomVecSMD::pack_comm_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_comm(int n, int first, double *buf) {
+void AtomVecSMD::unpack_comm(int /*n*/, int /*first*/, double * /*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -441,7 +441,7 @@ int AtomVecSMD::unpack_reverse_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-int AtomVecSMD::pack_border(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int AtomVecSMD::pack_border(int /*n*/, int * /*list*/, double * /*buf*/, int /*pbc_flag*/, int * /*pbc*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
return -1;
}
@@ -633,7 +633,7 @@ int AtomVecSMD::pack_border_hybrid(int n, int *list, double *buf) {
/* ---------------------------------------------------------------------- */
-void AtomVecSMD::unpack_border(int n, int first, double *buf) {
+void AtomVecSMD::unpack_border(int /*n*/, int /*first*/, double * /*buf*/) {
error->one(FLERR, "atom vec tlsph can only be used with ghost velocities turned on");
}
@@ -1098,7 +1098,7 @@ void AtomVecSMD::data_atom(double *coord, imageint imagetmp, char **values) {
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
-int AtomVecSMD::data_atom_hybrid(int nlocal, char **values) {
+int AtomVecSMD::data_atom_hybrid(int /*nlocal*/, char **/*values*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1120,7 +1120,7 @@ void AtomVecSMD::data_vel(int m, char **values) {
unpack hybrid quantities from one line in Velocities section of data file
------------------------------------------------------------------------- */
-int AtomVecSMD::data_vel_hybrid(int m, char **values) {
+int AtomVecSMD::data_vel_hybrid(int /*m*/, char **/*values*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1158,7 +1158,7 @@ void AtomVecSMD::pack_data(double **buf) {
pack hybrid atom info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_data_hybrid(int i, double *buf) {
+int AtomVecSMD::pack_data_hybrid(int /*i*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1180,7 +1180,7 @@ void AtomVecSMD::write_data(FILE *fp, int n, double **buf) {
write hybrid atom info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_data_hybrid(FILE *fp, double *buf) {
+int AtomVecSMD::write_data_hybrid(FILE * /*fp*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return -1;
}
@@ -1203,7 +1203,7 @@ void AtomVecSMD::pack_vel(double **buf) {
pack hybrid velocity info for data file
------------------------------------------------------------------------- */
-int AtomVecSMD::pack_vel_hybrid(int i, double *buf) {
+int AtomVecSMD::pack_vel_hybrid(int /*i*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 0;
}
@@ -1222,7 +1222,7 @@ void AtomVecSMD::write_vel(FILE *fp, int n, double **buf) {
write hybrid velocity info to data file
------------------------------------------------------------------------- */
-int AtomVecSMD::write_vel_hybrid(FILE *fp, double *buf) {
+int AtomVecSMD::write_vel_hybrid(FILE * /*fp*/, double * /*buf*/) {
error->one(FLERR, "hybrid atom style functionality not yet implemented for atom style smd");
return 3;
}
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index 3685248d5e556fa7aa08f09b1f5fa42d252e08e7..f015c6c4dfdbe4357e1714bdcd4bfc10e6017630 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -86,13 +86,13 @@ void FixSMDTlsphDtReset::init() {
/* ---------------------------------------------------------------------- */
-void FixSMDTlsphDtReset::setup(int vflag) {
+void FixSMDTlsphDtReset::setup(int /*vflag*/) {
end_of_step();
}
/* ---------------------------------------------------------------------- */
-void FixSMDTlsphDtReset::initial_integrate(int vflag) {
+void FixSMDTlsphDtReset::initial_integrate(int /*vflag*/) {
//printf("in adjust_dt: dt = %20.10f\n", update->dt);
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index 4668e673fca68d72dd4c1ece19fecacc8ed94228..1eae45161f44451a4327754c933cfcc9480a1fd7 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -125,7 +125,7 @@ void FixSMDIntegrateTlsph::init() {
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
-void FixSMDIntegrateTlsph::initial_integrate(int vflag) {
+void FixSMDIntegrateTlsph::initial_integrate(int /*vflag*/) {
double dtfm, vsq, scale;
// update v and x of atoms in group
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index a145deeb61ce90733aafd5d54c32d1aadaca5dd5..685d6af5a86840ce6433b28aeda8ab7410b328ff 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -158,7 +158,7 @@ void FixSMDIntegrateUlsph::init() {
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixSMDIntegrateUlsph::initial_integrate(int vflag) {
+void FixSMDIntegrateUlsph::initial_integrate(int /*vflag*/) {
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index d4afbe0535e4445709914d7ea71a9d1867a1eee5..b0944f1186cc13977e2f89a6b33ca1ff166bf415 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -248,7 +248,7 @@ void FixSMDMoveTriSurf::init() {
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
-void FixSMDMoveTriSurf::initial_integrate(int vflag) {
+void FixSMDMoveTriSurf::initial_integrate(int /*vflag*/) {
double **x = atom->x;
double **x0 = atom->x0;
double **v = atom->v;
@@ -461,7 +461,7 @@ void FixSMDMoveTriSurf::reset_dt() {
/* ---------------------------------------------------------------------- */
-int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int FixSMDMoveTriSurf::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double **x0 = atom->x0;
double **smd_data_9 = atom->smd_data_9;
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 5e7cdbad3807dc15e1a535bb81b6db24d331ced8..4bc8b5127b07251a8f5492f4e919ca3077445074 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -231,7 +231,7 @@ void FixSMDSetVel::min_setup(int vflag) {
/* ---------------------------------------------------------------------- */
//void FixSMDSetVel::initial_integrate(int vflag) {
-void FixSMDSetVel::post_force(int vflag) {
+void FixSMDSetVel::post_force(int /*vflag*/) {
double **x = atom->x;
double **f = atom->f;
double **v = atom->v;
diff --git a/src/USER-SMD/fix_smd_setvel.h b/src/USER-SMD/fix_smd_setvel.h
index b987a56f6cc1bc9603d72113139f0d27986d3d58..a3e650e682dcecc5eb29d6049ad7b5e9e505fbd6 100644
--- a/src/USER-SMD/fix_smd_setvel.h
+++ b/src/USER-SMD/fix_smd_setvel.h
@@ -56,7 +56,6 @@ class FixSMDSetVel : public Fix {
int xvar,yvar,zvar,xstyle,ystyle,zstyle;
double foriginal[3],foriginal_all[3];
int force_flag;
- int nlevels_respa;
int maxatom;
double **sforce;
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index 3e2812aa12e29a1f3e6d57ff3867d987676b361c..a2813cc3cae52d8a7b3bd1f09fec1ef333823d1d 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -149,7 +149,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
if (updateFlag > 0) {
if (comm->me == 0) {
- printf("**** updating ref config at step: %ld\n", update->ntimestep);
+ printf("**** updating ref config at step: " BIGINT_FORMAT "\n", update->ntimestep);
}
for (i = 0; i < nlocal; i++) {
@@ -199,7 +199,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::pre_exchange() {
so can be migrated or stored with atoms
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::setup(int vflag) {
+void FixSMD_TLSPH_ReferenceConfiguration::setup(int /*vflag*/) {
int i, j, ii, jj, n, inum, jnum;
int *ilist, *jlist, *numneigh, **firstneigh;
double r, h, wf, wfd;
@@ -386,7 +386,7 @@ void FixSMD_TLSPH_ReferenceConfiguration::grow_arrays(int nmax) {
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int delflag) {
+void FixSMD_TLSPH_ReferenceConfiguration::copy_arrays(int i, int j, int /*delflag*/) {
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
@@ -470,7 +470,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::pack_restart(int i, double *buf) {
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
-void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int nlocal, int nth) {
+void FixSMD_TLSPH_ReferenceConfiguration::unpack_restart(int /*nlocal*/, int /*nth*/) {
// ipage = NULL if being called from granular pair style init()
// skip to Nth set of extra values
@@ -512,7 +512,7 @@ int FixSMD_TLSPH_ReferenceConfiguration::size_restart(int nlocal) {
/* ---------------------------------------------------------------------- */
-int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int FixSMD_TLSPH_ReferenceConfiguration::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *radius = atom->radius;
double *vfrac = atom->vfrac;
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 97c2ead5fc79d8b913173d09d709a34294888120..4dd415f53ec02dae9605779585afc4162b00553c 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -110,7 +110,7 @@ void FixSMDWallSurface::min_setup(int vflag) {
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
-void FixSMDWallSurface::setup(int vflag) {
+void FixSMDWallSurface::setup(int /*vflag*/) {
if (!first)
return;
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index 815db4a4508a297d779a8a4499f21aa073fa17d4..13f48e995eb73e3fa39cfe96b43f9bdf34489d90 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -373,7 +373,7 @@ double PairHertz::memory_usage() {
return 0.0;
}
-void *PairHertz::extract(const char *str, int &i) {
+void *PairHertz::extract(const char *str, int &/*i*/) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 4dd16c4d83a4ee212491da430dc37f34fe49b751..09fe3b11805464ceac5867d063a75d792569adb8 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -1802,7 +1802,7 @@ double PairTlsph::memory_usage() {
extract method to provide access to this class' data structures
------------------------------------------------------------------------- */
-void *PairTlsph::extract(const char *str, int &i) {
+void *PairTlsph::extract(const char *str, int &/*i*/) {
//printf("in PairTlsph::extract\n");
if (strcmp(str, "smd/tlsph/Fincr_ptr") == 0) {
return (void *) Fincr;
@@ -1839,7 +1839,7 @@ void *PairTlsph::extract(const char *str, int &i) {
/* ---------------------------------------------------------------------- */
-int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int PairTlsph::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
tagint *mol = atom->molecule;
double *damage = atom->damage;
@@ -1928,7 +1928,7 @@ void PairTlsph::unpack_forward_comm(int n, int first, double *buf) {
------------------------------------------------------------------------- */
void PairTlsph::effective_longitudinal_modulus(const int itype, const double dt, const double d_iso, const double p_rate,
- const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double damage, double &K_eff, double &mu_eff, double &M_eff) {
+ const Matrix3d d_dev, const Matrix3d sigma_dev_rate, const double /*damage*/, double &K_eff, double &mu_eff, double &M_eff) {
double M0; // initial longitudinal modulus
double shear_rate_sq;
@@ -2094,7 +2094,7 @@ void PairTlsph::ComputeStressDeviator(const int i, const Matrix3d sigmaInitial_d
/* ----------------------------------------------------------------------
Compute damage. Called from AssembleStress().
------------------------------------------------------------------------- */
-void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &stress_damaged) {
+void PairTlsph::ComputeDamage(const int i, const Matrix3d strain, const Matrix3d stress, Matrix3d &/*stress_damaged*/) {
double *eff_plastic_strain = atom->eff_plastic_strain;
double *eff_plastic_strain_rate = atom->eff_plastic_strain_rate;
double *radius = atom->radius;
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index b8bff7e799948c73a47ecc71c44da5c15e068dd3..e40c876ec3de098739dbdb56ef5b07786c725fba 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -834,7 +834,7 @@ double PairTriSurf::clamp(const double a, const double min, const double max) {
}
}
-void *PairTriSurf::extract(const char *str, int &i) {
+void *PairTriSurf::extract(const char *str, int &/*i*/) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/tri_surface/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index 96eb912faec26a2e7b18a888eebd359f68771fa2..ff3720b2ff3637f9ccc6589d6dfd138bed0d3b5c 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -1487,7 +1487,7 @@ double PairULSPH::memory_usage() {
/* ---------------------------------------------------------------------- */
-int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) {
+int PairULSPH::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) {
double *vfrac = atom->vfrac;
double *eff_plastic_strain = atom->eff_plastic_strain;
int i, j, m;
@@ -1562,7 +1562,7 @@ void PairULSPH::unpack_forward_comm(int n, int first, double *buf) {
* EXTRACT
*/
-void *PairULSPH::extract(const char *str, int &i) {
+void *PairULSPH::extract(const char *str, int &/*i*/) {
//printf("in extract\n");
if (strcmp(str, "smd/ulsph/smoothVel_ptr") == 0) {
return (void *) smoothVel;
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index e3deb199b650be86b37fc7998152a57cfa6c22e1..42134288720406df76ebabdce03393bdfe6df019 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -97,7 +97,7 @@ void ShockEOS(double rho, double rho0, double e, double e0, double c0, double S,
final pressure pFinal
------------------------------------------------------------------------- */
-void polynomialEOS(double rho, double rho0, double e, double C0, double C1, double C2, double C3, double C4, double C5, double C6,
+void polynomialEOS(double rho, double rho0, double /*e*/, double C0, double C1, double C2, double C3, double /*C4*/, double /*C5*/, double /*C6*/,
double pInitial, double dt, double &pFinal, double &p_rate) {
double mu = rho / rho0 - 1.0;
@@ -307,7 +307,7 @@ void LinearPlasticStrength(const double G, const double yieldStress, const Matri
output: sigmaFinal_dev, sigmaFinal_dev_rate__: final stress deviator and its rate.
------------------------------------------------------------------------- */
void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a,
- const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep,
+ const double C, const double epdot0, const double T0, const double Tmelt, const double /*M*/, const double dt, const double ep,
const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__,
Matrix3d &sigma_dev_rate__, double &plastic_strain_increment) {
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 1028d8a8972117568e8670f101296a1db25703db..a8cce49749f9b55f8896c224668b6a2591a83bee 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -242,7 +242,7 @@ void PairSMTBQ::allocate()
global settings
------------------------------------------------------------------------- */
-void PairSMTBQ::settings(int narg, char **arg)
+void PairSMTBQ::settings(int narg, char **/*arg*/)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
@@ -1592,7 +1592,7 @@ void PairSMTBQ::tabqeq()
/* ---------------------------------------------------------------------*/
void PairSMTBQ::potqeq(int i, int j, double qi, double qj, double rsq,
- double &fforce, int eflag, double &eng)
+ double &fforce, int /*eflag*/, double &eng)
{
/* ===================================================================
@@ -1840,7 +1840,7 @@ void PairSMTBQ::pot_ES2 (int i, int j, double rsq, double &pot)
-------------------------------------------------------------------- */
void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
- int eflag, double &eng)
+ int /*eflag*/, double &eng)
{
double r,tmp_exp,tmp;
double A = intparam->abuck ;
@@ -1858,7 +1858,7 @@ void PairSMTBQ::rep_OO(Intparam *intparam, double rsq, double &fforce,
void PairSMTBQ::Attr_OO(Intparam *intparam, double rsq, double &fforce,
- int eflag, double &eng)
+ int /*eflag*/, double &eng)
{
double r,tmp_exp;
double aOO = intparam->aOO ;
@@ -1980,8 +1980,8 @@ void PairSMTBQ::tabsm()
/* -------------------------------------------------------------- */
-void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
- double &fforce, int eflag, double &eng)
+void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int /*i*/, int /*j*/,
+ double &fforce, int /*eflag*/, double &eng)
{
/* ================================================
@@ -2031,7 +2031,7 @@ void PairSMTBQ::repulsive(Intparam *intparam, double rsq, int i, int j,
void PairSMTBQ::attractive(Intparam *intparam, double rsq,
- int eflag, int i, double iq, int j, double jq)
+ int /*eflag*/, int i, double /*iq*/, int /*j*/, double /*jq*/)
{
int itype,l;
double r,t1,t2,xi,sds;
@@ -3334,7 +3334,7 @@ void PairSMTBQ::groupQEqAllParallel_QEq()
/* ---------------------------------------------------------------------- */
-void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
+void PairSMTBQ::Init_charge(int * /*nQEq*/, int * /*nQEqa*/, int * /*nQEqc*/)
{
int ii,i,gp,itype;
int *ilist,test[nteam],init[nteam];
@@ -3391,7 +3391,7 @@ void PairSMTBQ::Init_charge(int *nQEq, int *nQEqa, int *nQEqc)
* COMMUNICATION
* ---------------------------------------------------------------------- */
-int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+int PairSMTBQ::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index d7a5d81517600583101303174793d37f29ec27ae..b688eccfea4bff3003db9db77d77d15db7349abe 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -64,7 +64,7 @@ void FixMeso::init() {
dtf = 0.5 * update->dt * force->ftm2v;
}
-void FixMeso::setup_pre_force(int vflag)
+void FixMeso::setup_pre_force(int /*vflag*/)
{
// set vest equal to v
double **v = atom->v;
@@ -87,7 +87,7 @@ void FixMeso::setup_pre_force(int vflag)
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMeso::initial_integrate(int vflag) {
+void FixMeso::initial_integrate(int /*vflag*/) {
// update v and x and rho and e of atoms in group
double **x = atom->x;
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index f5fc306320d1951078cd122500705898a30f6262..29e8a1554c7abcb08175a27763e8846865d8e99c 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -67,7 +67,7 @@ void FixMesoStationary::init() {
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixMesoStationary::initial_integrate(int vflag) {
+void FixMesoStationary::initial_integrate(int /*vflag*/) {
double *rho = atom->rho;
double *drho = atom->drho;
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
index 6f0cf7eca2f734b4e19bb3c69246aeae71996874..4a8990d6fdc05950bc9e29ce889f4c118c1ac20c 100644
--- a/src/USER-SPH/pair_sph_heatconduction.cpp
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -155,7 +155,7 @@ void PairSPHHeatConduction::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHHeatConduction::settings(int narg, char **arg) {
+void PairSPHHeatConduction::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/heatconduction");
@@ -211,8 +211,8 @@ double PairSPHHeatConduction::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHHeatConduction::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHHeatConduction::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
index 99fba05917ae35dbf71836cf10c5c568c10a5278..32b3e612332dca166a5f239a91ff6bca007d618e 100644
--- a/src/USER-SPH/pair_sph_idealgas.cpp
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -197,7 +197,7 @@ void PairSPHIdealGas::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHIdealGas::settings(int narg, char **arg) {
+void PairSPHIdealGas::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/idealgas");
@@ -252,8 +252,8 @@ double PairSPHIdealGas::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHIdealGas::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHIdealGas::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
index 5cefdf87c43645e32be21de131ce1d8ec2046ee7..c382833baff7d6b92c669f5fcc432d3a933bc833 100644
--- a/src/USER-SPH/pair_sph_lj.cpp
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -204,7 +204,7 @@ void PairSPHLJ::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHLJ::settings(int narg, char **arg) {
+void PairSPHLJ::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/lj");
@@ -261,8 +261,8 @@ double PairSPHLJ::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHLJ::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHLJ::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 605187d3a733115254fe3a74967442c63de0afa2..7a3c78efd022a7959acf96bf21396a994a8698e8 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -278,8 +278,8 @@ double PairSPHRhoSum::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj, double &fforce) {
+double PairSPHRhoSum::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
+ double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
@@ -288,7 +288,7 @@ double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
/* ---------------------------------------------------------------------- */
int PairSPHRhoSum::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc) {
+ int /*pbc_flag*/, int * /*pbc*/) {
int i, j, m;
double *rho = atom->rho;
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
index 00500b940de1803c47982e2b4936ddbd005cc915..42b318f2c95008631d27c4eab3db8c0e06e50c10 100644
--- a/src/USER-SPH/pair_sph_taitwater.cpp
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -225,7 +225,7 @@ void PairSPHTaitwater::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHTaitwater::settings(int narg, char **arg) {
+void PairSPHTaitwater::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/taitwater");
@@ -293,8 +293,8 @@ double PairSPHTaitwater::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHTaitwater::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHTaitwater::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
index 80607cb333b2cd882c1b276c703e4c5d173c9b94..8012895af8ed147dcb5596160b3ac29396451958 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.cpp
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -225,7 +225,7 @@ void PairSPHTaitwaterMorris::allocate() {
global settings
------------------------------------------------------------------------- */
-void PairSPHTaitwaterMorris::settings(int narg, char **arg) {
+void PairSPHTaitwaterMorris::settings(int narg, char **/*arg*/) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/taitwater/morris");
@@ -289,8 +289,8 @@ double PairSPHTaitwaterMorris::init_one(int i, int j) {
/* ---------------------------------------------------------------------- */
-double PairSPHTaitwaterMorris::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj, double &fforce) {
+double PairSPHTaitwaterMorris::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/,
+ double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) {
fforce = 0.0;
return 0.0;
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index bfa45492864ff4708fb0e22167b04b69ca95cbc1..bffcd7849f7535ae9f486fb7664b1722718b79b3 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -348,7 +348,7 @@ void FixNHUef::final_integrate()
* at outer level: call this->final_integrate()
* at other levels: rotate -> 2nd verlet step -> rotate back
* ---------------------------------------------------------------------- */
-void FixNHUef::final_integrate_respa(int ilevel, int iloop)
+void FixNHUef::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h
index 8bbb6c4788c4bc17ea32a34424abc508d646b2ca..e64bde24bedc6796eea607735144662e3c644024 100644
--- a/src/accelerator_kokkos.h
+++ b/src/accelerator_kokkos.h
@@ -66,8 +66,8 @@ class AtomKokkos : public Atom {
tagint **k_special;
AtomKokkos(class LAMMPS *lmp) : Atom(lmp) {}
~AtomKokkos() {}
- void sync(const ExecutionSpace space, unsigned int mask) {}
- void modified(const ExecutionSpace space, unsigned int mask) {}
+ void sync(const ExecutionSpace /*space*/, unsigned int /*mask*/) {}
+ void modified(const ExecutionSpace /*space*/, unsigned int /*mask*/) {}
};
class CommKokkos : public CommBrick {
diff --git a/src/accelerator_omp.h b/src/accelerator_omp.h
index 6caa0826fe8e48fe7da7b99525ea6668fc84105c..25910ae800972c95669aca2ca7f8d1cdc272192a 100644
--- a/src/accelerator_omp.h
+++ b/src/accelerator_omp.h
@@ -17,47 +17,6 @@
// true interface to USER-OMP
-// this part is used inside the neighbor.h header file to
-// add functions to the Neighbor class definition
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
-
- void half_nsq_no_newton_omp(class NeighList *);
- void half_nsq_no_newton_ghost_omp(class NeighList *);
- void half_nsq_newton_omp(class NeighList *);
-
- void half_bin_no_newton_omp(class NeighList *);
- void half_bin_no_newton_ghost_omp(class NeighList *);
- void half_bin_newton_omp(class NeighList *);
- void half_bin_newton_tri_omp(class NeighList *);
-
- void half_multi_no_newton_omp(class NeighList *);
- void half_multi_newton_omp(class NeighList *);
- void half_multi_newton_tri_omp(class NeighList *);
-
- void full_nsq_omp(class NeighList *);
- void full_nsq_ghost_omp(class NeighList *);
- void full_bin_omp(class NeighList *);
- void full_bin_ghost_omp(class NeighList *);
- void full_multi_omp(class NeighList *);
-
- void half_from_full_no_newton_omp(class NeighList *);
- void half_from_full_newton_omp(class NeighList *);
-
- void granular_nsq_no_newton_omp(class NeighList *);
- void granular_nsq_newton_omp(class NeighList *);
- void granular_bin_no_newton_omp(class NeighList *);
- void granular_bin_newton_omp(class NeighList *);
- void granular_bin_newton_tri_omp(class NeighList *);
-
- void respa_nsq_no_newton_omp(class NeighList *);
- void respa_nsq_newton_omp(class NeighList *);
- void respa_bin_no_newton_omp(class NeighList *);
- void respa_bin_newton_omp(class NeighList *);
- void respa_bin_newton_tri_omp(class NeighList *);
-
-#else /* !LMP_INSIDE_NEIGHBOR_H */
-
// provide a DomainOMP class with some overrides for Domain
#include "domain.h"
@@ -68,8 +27,8 @@ namespace LAMMPS_NS {
class DomainOMP : public Domain {
public:
- DomainOMP(class LAMMPS *lmp) : Domain(lmp) {};
- virtual ~DomainOMP() {};
+ DomainOMP(class LAMMPS *lmp) : Domain(lmp) {}
+ virtual ~DomainOMP() {}
// multi-threaded versions
virtual void pbc();
@@ -81,48 +40,5 @@ class DomainOMP : public Domain {
}
#endif /* LMP_DOMAIN_OMP_H */
-#endif /* !LMP_INSIDE_NEIGHBOR_H */
-
-#else /* !LMP_USER_OMP */
-
-// dummy interface to USER-OMP
-// needed for compiling when USER-OMP is not installed
-
-#ifdef LMP_INSIDE_NEIGHBOR_H
-
- void half_nsq_no_newton_omp(class NeighList *) {}
- void half_nsq_no_newton_ghost_omp(class NeighList *) {}
- void half_nsq_newton_omp(class NeighList *) {}
-
- void half_bin_no_newton_omp(class NeighList *) {}
- void half_bin_no_newton_ghost_omp(class NeighList *) {}
- void half_bin_newton_omp(class NeighList *) {}
- void half_bin_newton_tri_omp(class NeighList *) {}
-
- void half_multi_no_newton_omp(class NeighList *) {}
- void half_multi_newton_omp(class NeighList *) {}
- void half_multi_newton_tri_omp(class NeighList *) {}
-
- void full_nsq_omp(class NeighList *) {}
- void full_nsq_ghost_omp(class NeighList *) {}
- void full_bin_omp(class NeighList *) {}
- void full_bin_ghost_omp(class NeighList *) {}
- void full_multi_omp(class NeighList *) {}
-
- void half_from_full_no_newton_omp(class NeighList *) {}
- void half_from_full_newton_omp(class NeighList *) {}
-
- void granular_nsq_no_newton_omp(class NeighList *) {}
- void granular_nsq_newton_omp(class NeighList *) {}
- void granular_bin_no_newton_omp(class NeighList *) {}
- void granular_bin_newton_omp(class NeighList *) {}
- void granular_bin_newton_tri_omp(class NeighList *) {}
-
- void respa_nsq_no_newton_omp(class NeighList *) {}
- void respa_nsq_newton_omp(class NeighList *) {}
- void respa_bin_no_newton_omp(class NeighList *) {}
- void respa_bin_newton_omp(class NeighList *) {}
- void respa_bin_newton_tri_omp(class NeighList *) {}
-#endif
#endif /* !LMP_USER_OMP */
diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp
index e5191c4fb22d6ceaaa0f4a562abe5b103364cefe..d7b7c9cdb5546eda86753439a5cd37079fc1801a 100644
--- a/src/angle_zero.cpp
+++ b/src/angle_zero.cpp
@@ -148,7 +148,7 @@ void AngleZero::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double AngleZero::single(int type, int i1, int i2, int i3)
+double AngleZero::single(int /*type*/, int /*i1*/, int /*i2*/, int /*i3*/)
{
return 0.0;
}
diff --git a/src/atom.cpp b/src/atom.cpp
index cf4d20a71e30914a6405f9c2e84fd0e3c4fb0510..95f5406d95906c2ea7162188ec978c6cdaaf0e59 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -99,7 +99,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// SPIN package
sp = fm = NULL;
-
+
// USER-DPD
uCond = uMech = uChem = uCG = uCGnew = NULL;
@@ -1516,7 +1516,7 @@ void Atom::set_mass(const char *file, int line, int itype, double value)
called from reading of input script
------------------------------------------------------------------------- */
-void Atom::set_mass(const char *file, int line, int narg, char **arg)
+void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
{
if (mass == NULL) error->all(file,line,"Cannot set mass for this atom style");
@@ -1533,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int narg, char **arg)
}
/* ----------------------------------------------------------------------
- set all masses as read in from restart file
+ set all masses
+ called from reading of restart file, also from ServerMD
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index b04bfba34c91295b0858c6f0833d75172fed20c9..a7ca6fcb19313e0c5d26e7fb6e8a3641a6a95ff4 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -66,7 +66,7 @@ void AtomVec::store_args(int narg, char **arg)
no additional args by default
------------------------------------------------------------------------- */
-void AtomVec::process_args(int narg, char **arg)
+void AtomVec::process_args(int narg, char ** /*arg*/)
{
if (narg) error->all(FLERR,"Invalid atom_style command");
}
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index 4d3b5643aea121a788d41345f2a1be43e2e0a667..5a277627ee86f557f7060cbaf069426dee58264d 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -82,6 +82,9 @@ AtomVecBody::~AtomVecBody()
void AtomVecBody::process_args(int narg, char **arg)
{
+ // suppress unused parameter warning dependent on style_body.h
+ (void)(arg);
+
if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
if (0) bptr = NULL;
diff --git a/src/body.cpp b/src/body.cpp
index 42f4ccbdd3fcaf9491d7656a7e138c1f7efe4ebe..78e2f5d71b3637db3a71a0176325bf6ef4b2b969 100644
--- a/src/body.cpp
+++ b/src/body.cpp
@@ -21,7 +21,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Body::Body(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Body::Body(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
int n = strlen(arg[0]) + 1;
style = new char[n];
diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp
index 9fd9d4a580c5d83cf4c69a431330975a116ee330..9fcf300b21bef3f2fc6efacdb9215d964d09e349 100644
--- a/src/bond_zero.cpp
+++ b/src/bond_zero.cpp
@@ -149,8 +149,8 @@ void BondZero::write_data(FILE *fp)
/* ---------------------------------------------------------------------- */
-double BondZero::single(int type, double rsq, int i, int j,
- double &fforce)
+double BondZero::single(int /*type*/, double /*rsq*/, int /*i*/, int /*j*/,
+ double & /*fforce*/)
{
return 0.0;
}
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index d1794753450d98373a6925a84d393e2aa8ccdf98..4015240af890523eb23ef7acfd1143a72880f87c 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -90,7 +90,7 @@ CommBrick::~CommBrick()
// The call to Comm::copy_arrays() then converts the shallow copy
// into a deep copy of the class with the new layout.
-CommBrick::CommBrick(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
+CommBrick::CommBrick(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm)
{
if (oldcomm->layout == Comm::LAYOUT_TILED)
error->all(FLERR,"Cannot change to comm_style brick from tiled layout");
@@ -459,7 +459,7 @@ int CommBrick::updown(int dim, int dir, int loc,
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-void CommBrick::forward_comm(int dummy)
+void CommBrick::forward_comm(int /*dummy*/)
{
int n;
MPI_Request request;
diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp
index 584be94bf3f32f8bc91451f545fef888e3f54bc6..d7d2e4725d10f67b13e62c5437a73ffebaa43748 100644
--- a/src/comm_tiled.cpp
+++ b/src/comm_tiled.cpp
@@ -55,7 +55,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
// The call to Comm::copy_arrays() then converts the shallow copy
// into a deep copy of the class with the new layout.
-CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
+CommTiled::CommTiled(LAMMPS * /*lmp*/, Comm *oldcomm) : Comm(*oldcomm)
{
style = 1;
layout = oldcomm->layout;
@@ -438,7 +438,7 @@ void CommTiled::setup()
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
-void CommTiled::forward_comm(int dummy)
+void CommTiled::forward_comm(int /*dummy*/)
{
int i,irecv,n,nsend,nrecv;
AtomVec *avec = atom->avec;
@@ -1164,7 +1164,7 @@ void CommTiled::reverse_comm_fix(Fix *fix, int size)
NOTE: how to setup one big buf recv with correct offsets ??
------------------------------------------------------------------------- */
-void CommTiled::reverse_comm_fix_variable(Fix *fix)
+void CommTiled::reverse_comm_fix_variable(Fix * /*fix*/)
{
error->all(FLERR,"Reverse comm fix variable not yet supported by CommTiled");
}
@@ -1428,7 +1428,7 @@ void CommTiled::forward_comm_array(int nsize, double **array)
NOTE: this method is currently not used
------------------------------------------------------------------------- */
-int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
+int CommTiled::exchange_variable(int n, double * /*inbuf*/, double *& /*outbuf*/)
{
int nrecv = n;
return nrecv;
@@ -1509,7 +1509,7 @@ void CommTiled::box_drop_brick(int idim, double *lo, double *hi, int &indexme)
no need to split lo/hi box as recurse b/c OK if box extends outside RCB box
------------------------------------------------------------------------- */
-void CommTiled::box_drop_tiled(int idim, double *lo, double *hi, int &indexme)
+void CommTiled::box_drop_tiled(int /*idim*/, double *lo, double *hi, int &indexme)
{
box_drop_tiled_recurse(lo,hi,0,nprocs-1,indexme);
}
@@ -1601,7 +1601,7 @@ void CommTiled::box_other_brick(int idim, int idir,
return other box owned by proc as lo/hi corner pts
------------------------------------------------------------------------- */
-void CommTiled::box_other_tiled(int idim, int idir,
+void CommTiled::box_other_tiled(int /*idim*/, int /*idir*/,
int proc, double *lo, double *hi)
{
double (*split)[2] = rcbinfo[proc].mysplit;
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index 56855fcc29720bf8db93b8a2a6a52f8c1818fd45..6c8c8e5d9ad0aac6b2fdfc34777b13a87361aa24 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -98,7 +98,7 @@ void ComputeAggregateAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeAggregateAtom::init_list(int id, NeighList *ptr)
+void ComputeAggregateAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -231,7 +231,7 @@ void ComputeAggregateAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 985e3ef0756260c9b6e9f258a5d3ab1b080f4605..56abb9b07113722f9fdf39e6cc6368c89334e352 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -337,7 +337,7 @@ int ComputeBondLocal::compute_bonds(int flag)
/* ---------------------------------------------------------------------- */
int ComputeBondLocal::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 48af45363598ab0ed8fd8e1b3b9aff5d9c996be3..5096879b32bbeebd8cfc8392e0cbcb01a71b3d09 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -110,7 +110,7 @@ void ComputeCentroAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCentroAtom::init_list(int id, NeighList *ptr)
+void ComputeCentroAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 85934c5e6d20df3a6eaa915d8269d32988147120..0c34b426719ddaa0446b82cd3ad95a1eb4b69a54 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -89,7 +89,7 @@ void ComputeClusterAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeClusterAtom::init_list(int id, NeighList *ptr)
+void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -209,7 +209,7 @@ void ComputeClusterAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index a1b97d94043dc537102f98cb3a05cbb7555a26a1..b8ad3f0f644eb3a7bd11d32d45808e9fabcb919e 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -100,7 +100,7 @@ void ComputeCNAAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCNAAtom::init_list(int id, NeighList *ptr)
+void ComputeCNAAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp
index f3c4513b0152a2edd090c31d07a46f832d925021..e60a51832a063e78c4ec22b3d8cf36765565716e 100644
--- a/src/compute_contact_atom.cpp
+++ b/src/compute_contact_atom.cpp
@@ -80,7 +80,7 @@ void ComputeContactAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeContactAtom::init_list(int id, NeighList *ptr)
+void ComputeContactAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index b86d818d0608d99468658adb982df1afaccf7472..33b318ea17247718049eda4c4230df46f4f4dec9 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -153,7 +153,7 @@ void ComputeCoordAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeCoordAtom::init_list(int id, NeighList *ptr)
+void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -311,7 +311,7 @@ void ComputeCoordAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,m=0,j;
for (i = 0; i < n; ++i) {
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index b9fb2331ecf35bca18a9f5803baad10c0273eaa2..bb273f3bdb11d6262d7f465851fc9144b956ade5 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -159,7 +159,7 @@ void ComputeFragmentAtom::compute_peratom()
/* ---------------------------------------------------------------------- */
int ComputeFragmentAtom::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index dc94db50f645ee35f9c1e5b928881aa5a584f155..51f84b020dba81007416e89aad5bd0308379d027 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -173,7 +173,7 @@ void ComputeGroupGroup::init()
/* ---------------------------------------------------------------------- */
-void ComputeGroupGroup::init_list(int id, NeighList *ptr)
+void ComputeGroupGroup::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index cb2946beba8e7833feb9115566f38505108360cb..6d17ae15bd5eaf1ea29f503d469181c5511b4cb0 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -129,7 +129,7 @@ void ComputeHexOrderAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeHexOrderAtom::init_list(int id, NeighList *ptr)
+void ComputeHexOrderAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index f263fdfaed0caa3cdeea54cf149b080c716bf7be..8a0a525fdc7a133cfc513cdc2e02b7ecad0dfae0 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -187,7 +187,7 @@ void ComputeOrientOrderAtom::init()
/* ---------------------------------------------------------------------- */
-void ComputeOrientOrderAtom::init_list(int id, NeighList *ptr)
+void ComputeOrientOrderAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
@@ -542,4 +542,3 @@ double ComputeOrientOrderAtom::associated_legendre(int l, int m, double x)
return p;
}
-
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 3f1147ed2778c3640c749ee76c7db66b28f9ca24..e4cbabfd3d34496498f9e122f0384c84cd90a0c8 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -139,7 +139,7 @@ void ComputePairLocal::init()
/* ---------------------------------------------------------------------- */
-void ComputePairLocal::init_list(int id, NeighList *ptr)
+void ComputePairLocal::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index ad68459650a500a513f9d9e7718377f7a2870247..ddcf5913ca003bd9938974d196625d4de3381b8d 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -308,7 +308,7 @@ void ComputePropertyLocal::init()
/* ---------------------------------------------------------------------- */
-void ComputePropertyLocal::init_list(int id, NeighList *ptr)
+void ComputePropertyLocal::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index f2635c09485ea9770b4adcd0770d207a5be83330..0a0e8fb684a921f3a2faa096ccad69f3d5b71f87 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -213,7 +213,7 @@ void ComputeRDF::init()
/* ---------------------------------------------------------------------- */
-void ComputeRDF::init_list(int id, NeighList *ptr)
+void ComputeRDF::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index 35f4512ab2b76e8c7b16d1de171588b6c2a547f6..f2ad40ea43361af4968a1d6bde367904ebc27d29 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -163,7 +163,7 @@ void ComputeTempCOM::compute_vector()
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempCOM::remove_bias(int i, double *v)
+void ComputeTempCOM::remove_bias(int /*i*/, double *v)
{
v[0] -= vbias[0];
v[1] -= vbias[1];
@@ -204,7 +204,7 @@ void ComputeTempCOM::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempCOM::restore_bias(int i, double *v)
+void ComputeTempCOM::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index 8729204e700d5bd105ed4ac35f4468068dfb8547..39780b5cf6fe724c64a82ead4dc70c773742e12e 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -277,7 +277,7 @@ void ComputeTempDeform::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempDeform::restore_bias(int i, double *v)
+void ComputeTempDeform::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
@@ -289,7 +289,7 @@ void ComputeTempDeform::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempDeform::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempDeform::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[0] += b[0];
v[1] += b[1];
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index 4b87a2249ed1f96593a901d264b1b9bd61f20621..4425aebdda76a45cc9eacb959c2e122aac464d5e 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -90,7 +90,7 @@ void ComputeTempPartial::dof_compute()
/* ---------------------------------------------------------------------- */
-int ComputeTempPartial::dof_remove(int i)
+int ComputeTempPartial::dof_remove(int /*i*/)
{
int nper = xflag+yflag+zflag;
return (domain->dimension - nper);
@@ -169,7 +169,7 @@ void ComputeTempPartial::compute_vector()
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempPartial::remove_bias(int i, double *v)
+void ComputeTempPartial::remove_bias(int /*i*/, double *v)
{
if (!xflag) {
vbias[0] = v[0];
@@ -189,7 +189,7 @@ void ComputeTempPartial::remove_bias(int i, double *v)
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
-void ComputeTempPartial::remove_bias_thr(int i, double *v, double *b)
+void ComputeTempPartial::remove_bias_thr(int /*i*/, double *v, double *b)
{
if (!xflag) {
b[0] = v[0];
@@ -275,7 +275,7 @@ void ComputeTempPartial::reapply_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempPartial::restore_bias(int i, double *v)
+void ComputeTempPartial::restore_bias(int /*i*/, double *v)
{
if (!xflag) v[0] += vbias[0];
if (!yflag) v[1] += vbias[1];
@@ -287,7 +287,7 @@ void ComputeTempPartial::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempPartial::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempPartial::restore_bias_thr(int /*i*/, double *v, double *b)
{
if (!xflag) v[0] += b[0];
if (!yflag) v[1] += b[1];
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index 42d258d8b2fe626d68524fc21af9b427dd477baf..ba572645f34f22c144f612ab1d29ccae1e2628b1 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -279,7 +279,7 @@ void ComputeTempRamp::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRamp::restore_bias(int i, double *v)
+void ComputeTempRamp::restore_bias(int /*i*/, double *v)
{
v[v_dim] += vbias[v_dim];
}
@@ -289,7 +289,7 @@ void ComputeTempRamp::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempRamp::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempRamp::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[v_dim] += b[v_dim];
}
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index bde70a20f0c44058961dab409ca605bfe4e7a81e..4aa4dac0a11c36437bbfac84898553de73c439f0 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -253,7 +253,7 @@ void ComputeTempRegion::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
-void ComputeTempRegion::restore_bias(int i, double *v)
+void ComputeTempRegion::restore_bias(int /*i*/, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
@@ -265,7 +265,7 @@ void ComputeTempRegion::restore_bias(int i, double *v)
assume remove_bias_thr() was previously called with the same buffer b
------------------------------------------------------------------------- */
-void ComputeTempRegion::restore_bias_thr(int i, double *v, double *b)
+void ComputeTempRegion::restore_bias_thr(int /*i*/, double *v, double *b)
{
v[0] += b[0];
v[1] += b[1];
diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp
index bdd2eaadd3d484e5f709531be0ac43635b826ed1..46facdb6dbe716471f4004c7d646b49f60cdee01 100644
--- a/src/dihedral_zero.cpp
+++ b/src/dihedral_zero.cpp
@@ -99,13 +99,13 @@ void DihedralZero::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
-void DihedralZero::write_restart(FILE *fp) {}
+void DihedralZero::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
-void DihedralZero::read_restart(FILE *fp)
+void DihedralZero::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
@@ -119,4 +119,3 @@ void DihedralZero::write_data(FILE *fp) {
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d\n",i);
}
-
diff --git a/src/domain.cpp b/src/domain.cpp
index 4c1d12018b1b6076819e3938239e70129c61d989..8238ab7eead9f2b7a21761b91f6b9b95bb17b519 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1176,12 +1176,12 @@ int Domain::closest_image(int i, int j)
if J is not a valid index like -1, just return it
------------------------------------------------------------------------- */
-int Domain::closest_image(double *pos, int j)
+int Domain::closest_image(const double * const pos, int j)
{
if (j < 0) return j;
- int *sametag = atom->sametag;
- double **x = atom->x;
+ const int * const sametag = atom->sametag;
+ const double * const * const x = atom->x;
int closest = j;
double delx = pos[0] - x[j][0];
@@ -1208,13 +1208,10 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
- not currently used (Jan 2017):
- used to be called by pair TIP4P styles but no longer,
- due to use of other closest_image() method
+ called by ServerMD class and LammpsInterface in lib/atc.
------------------------------------------------------------------------- */
-void Domain::closest_image(const double * const xi, const double * const xj,
- double * const xjimage)
+void Domain::closest_image(const double * const xi, const double * const xj, double * const xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];
@@ -1618,7 +1615,7 @@ void Domain::image_flip(int m, int n, int p)
called from create_atoms() in library.cpp
------------------------------------------------------------------------- */
-int Domain::ownatom(int id, double *x, imageint *image, int shrinkexceed)
+int Domain::ownatom(int /*id*/, double *x, imageint *image, int shrinkexceed)
{
double lamda[3];
double *coord,*blo,*bhi,*slo,*shi;
diff --git a/src/domain.h b/src/domain.h
index 5581f9a45fc85eb2a5d79f353e5bc53e41ba2e89..9ebdd6ae9477cec5739992096ea7d5bf5655355a 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -115,9 +115,8 @@ class Domain : protected Pointers {
void minimum_image(double *);
void minimum_image_once(double *);
int closest_image(int, int);
- int closest_image(double *, int);
- void closest_image(const double * const, const double * const,
- double * const);
+ int closest_image(const double * const, int);
+ void closest_image(const double * const, const double * const, double * const);
void remap(double *, imageint &);
void remap(double *);
void remap_near(double *, double *);
diff --git a/src/dump.cpp b/src/dump.cpp
index 7c171015bb4e201f8a8602294ad53c2c9937fbf6..7cd80dcf71ac2cc7a964389674983cbcabb7c274 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -45,7 +45,7 @@ enum{ASCEND,DESCEND};
/* ---------------------------------------------------------------------- */
-Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 4c3950c0992deacc6b7741f1da30d42239b53265..17ad4b89ef2a1eec6782165f024426173d70f1ad 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -1023,12 +1023,12 @@ int DumpCustom::count()
} else if (thresh_op[ithresh] == XOR) {
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
+ if ((choose[i] && *ptr == 0.0 && values[i] == 0.0) ||
(*ptr != 0.0 && values[i] != 0.0))
choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
+ if ((choose[i] && *ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
}
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 60a1f545c9715d951d07590891e4f31888b3746c..a488f65161909a05b598832c3d15a109f346eb21 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -1193,7 +1193,7 @@ void DumpImage::create_image()
/* ---------------------------------------------------------------------- */
int DumpImage::pack_forward_comm(int n, int *list, double *buf,
- int pbc_flag, int *pbc)
+ int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,m;
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 0d5172b5c1bdaf0de61828a464bc0e7b09a61006..8dc055469064c4751a5d3b1a0b7586de417c5a95 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -326,7 +326,7 @@ int DumpLocal::count()
/* ---------------------------------------------------------------------- */
-void DumpLocal::pack(tagint *dummy)
+void DumpLocal::pack(tagint * /*dummy*/)
{
for (int n = 0; n < size_one; n++) (this->*pack_choice[n])(n);
}
diff --git a/src/fix.cpp b/src/fix.cpp
index a54e2957985207ee6c5a27f59ae70483763d251b..051ac12bbea99e4a6439b8e564f01862a18fb395 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -31,7 +31,7 @@ int Fix::instance_total = 0;
/* ---------------------------------------------------------------------- */
-Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
+Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
Pointers(lmp),
id(NULL), style(NULL), extlist(NULL), vector_atom(NULL), array_atom(NULL),
vector_local(NULL), array_local(NULL), eatom(NULL), vatom(NULL)
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 42cd1bd1992de2c9d474b018634bd33052e8b03f..950bc242534893b23ada9ae57203f428cd467ba0 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -476,7 +476,7 @@ void FixAdapt::init()
/* ---------------------------------------------------------------------- */
-void FixAdapt::setup_pre_force(int vflag)
+void FixAdapt::setup_pre_force(int /*vflag*/)
{
change_settings();
}
@@ -491,7 +491,7 @@ void FixAdapt::setup_pre_force_respa(int vflag, int ilevel)
/* ---------------------------------------------------------------------- */
-void FixAdapt::pre_force(int vflag)
+void FixAdapt::pre_force(int /*vflag*/)
{
if (nevery == 0) return;
if (update->ntimestep % nevery) return;
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index c2eedccd6151e6306bcf11d6f7a380413434850a..d66457a1f19ef1a903d22c87099d6c5cb75d01bb 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -361,7 +361,7 @@ void FixAddForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAddForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAddForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index a8c3be07af55fe5eab76b1c35fbd3afe0b2340f4..c8cbad75c969adc32517e122f6da84e5ba3236f6 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -283,7 +283,7 @@ void FixAveAtom::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveAtom::setup(int vflag)
+void FixAveAtom::setup(int /*vflag*/)
{
end_of_step();
}
@@ -432,7 +432,7 @@ void FixAveAtom::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixAveAtom::copy_arrays(int i, int j, int delflag)
+void FixAveAtom::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++)
array[j][m] = array[i][m];
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 5f727fd3f747f6c9ec21cf7fcdf873cf57ecf5cb..1aead7064447c3faa023bf7db237600f60cebfce 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -557,7 +557,7 @@ void FixAveChunk::init()
that nchunk may not track it
------------------------------------------------------------------------- */
-void FixAveChunk::setup(int vflag)
+void FixAveChunk::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index 418464a2484b4884e58a2966a410eb9e092b1d38..198caf151409301e2ca7308a7026ff1af79b3d39 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -404,7 +404,7 @@ void FixAveCorrelate::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveCorrelate::setup(int vflag)
+void FixAveCorrelate::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index 7aa599389979bac8cdfe48614a5302c7834a2bac..ce32167b745ffbfe9374bdf3855b226cba79e550 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -559,7 +559,7 @@ void FixAveHisto::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveHisto::setup(int vflag)
+void FixAveHisto::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index c3ace296842b0cb3738c62b635ed7fb48854e48a..53354ee06617157de389060cce0e22f5cc4b8172 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -529,7 +529,7 @@ void FixAveTime::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixAveTime::setup(int vflag)
+void FixAveTime::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 4432a5dd36d8aeb369a34c0523bc1592a83050a7..1c87ba57851a0e5de4864b1ba3be8d6f845aae8e 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -194,7 +194,7 @@ void FixAveForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAveForce::post_force(int vflag)
+void FixAveForce::post_force(int /*vflag*/)
{
// update region if necessary
@@ -259,7 +259,7 @@ void FixAveForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixAveForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixAveForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// ave + extra force on selected RESPA level
// just ave on all other levels
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index e748e0ae31c0fd0e550d35dff5b5f3898daeccac..8995a57afe0d6fd7a22bd66a3f6f89e9b5cc6ef0 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -160,7 +160,7 @@ void FixBalance::init()
/* ---------------------------------------------------------------------- */
-void FixBalance::setup(int vflag)
+void FixBalance::setup(int /*vflag*/)
{
// compute final imbalance factor if setup_pre_exchange() invoked balancer
// this is called at end of run setup, before output
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index 6a69dddbf5d744a8028c3aac143def239e3991cf..e4cf12d1ffcc2215ece204d559aa4ab943b5b23f 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -90,7 +90,7 @@ void FixDrag::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixDrag::post_force(int vflag)
+void FixDrag::post_force(int /*vflag*/)
{
// apply drag force to atoms in group of magnitude f_mag
// apply in direction (r-r0) if atom is further than delta away
@@ -132,7 +132,7 @@ void FixDrag::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixDrag::post_force_respa(int vflag, int ilevel, int iloop)
+void FixDrag::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index f2a50fd6d1c416ee9b8c1f551a1ef56305a3b945..7566094b48050d21cd6f281e9b8582706d8a7de2 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -129,7 +129,7 @@ void FixDtReset::init()
/* ---------------------------------------------------------------------- */
-void FixDtReset::setup(int vflag)
+void FixDtReset::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index 791a52c50cb39e13c61d2d8159820c71c03dbb87..ef7eb3a0ef1a2972cb632bbee55e73e14f1ca77b 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -112,7 +112,7 @@ void FixEnforce2D::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEnforce2D::post_force(int vflag)
+void FixEnforce2D::post_force(int /*vflag*/)
{
double **v = atom->v;
double **f = atom->f;
@@ -164,7 +164,7 @@ void FixEnforce2D::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixEnforce2D::post_force_respa(int vflag, int ilevel, int iloop)
+void FixEnforce2D::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index 4fcc842f899401eebc0f21e2fdf0abe86a7f3e41..5ac9206e7fae6630bf4bf76284df1173432f8f9a 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -129,7 +129,7 @@ void FixExternal::min_setup(int vflag)
store eflag, so can use it in post_force to tally per-atom energies
------------------------------------------------------------------------- */
-void FixExternal::pre_reverse(int eflag, int vflag)
+void FixExternal::pre_reverse(int eflag, int /*vflag*/)
{
eflag_caller = eflag;
}
@@ -305,7 +305,7 @@ void FixExternal::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixExternal::copy_arrays(int i, int j, int delflag)
+void FixExternal::copy_arrays(int i, int j, int /*delflag*/)
{
fexternal[j][0] = fexternal[i][0];
fexternal[j][1] = fexternal[i][1];
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 9ace9d45ffcad6a3a6b86f3111e503ec3237b764..c3e73d86c935dfbe497f9285004ea588162d1675 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -247,7 +247,7 @@ void FixGravity::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGravity::post_force(int vflag)
+void FixGravity::post_force(int /*vflag*/)
{
// update gravity due to variables
@@ -300,7 +300,7 @@ void FixGravity::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
+void FixGravity::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 10736964e788d5b76d47ea392737c35f714fedb9..0980ff5456089ad2936049fdbfab70fe335bb1f7 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -176,7 +176,7 @@ void FixGroup::init()
assign atoms to group
------------------------------------------------------------------------- */
-void FixGroup::setup(int vflag)
+void FixGroup::setup(int /*vflag*/)
{
set_group();
}
@@ -192,7 +192,7 @@ void FixGroup::post_integrate()
/* ---------------------------------------------------------------------- */
-void FixGroup::post_integrate_respa(int ilevel, int iloop)
+void FixGroup::post_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_integrate();
}
@@ -259,7 +259,7 @@ void FixGroup::set_group()
/* ---------------------------------------------------------------------- */
-void *FixGroup::extract(const char *str, int &unused)
+void *FixGroup::extract(const char *str, int &/*unused*/)
{
if (strcmp(str,"property") == 0 && propflag) return (void *) idprop;
if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar;
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index 7de09a0fa4b9add400543a97a62f2f8a73ad2f74..983f993ae8b617afab02823f2768a3dbb087a3eb 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -184,7 +184,7 @@ void FixHalt::end_of_step()
// print message with ID of fix halt in case multiple instances
char str[128];
- sprintf(str,"Fix halt %s condition met on step %ld with value %g",
+ sprintf(str,"Fix halt %s condition met on step " BIGINT_FORMAT " with value %g",
id,update->ntimestep,attvalue);
if (eflag == HARD) {
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index ade8cee5328d711ddbfd6ccb4088fe49120f7b88..b8e07dfd53f358cdf1f305ab3a16864e0ed8c8f5 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -182,7 +182,7 @@ void FixIndent::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixIndent::post_force(int vflag)
+void FixIndent::post_force(int /*vflag*/)
{
// indenter values, 0 = energy, 1-3 = force components
// wrap variable evaluations with clear/add
@@ -357,7 +357,7 @@ void FixIndent::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixIndent::post_force_respa(int vflag, int ilevel, int iloop)
+void FixIndent::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index e4c36cc73917fe0f7d6b8b7ad094741d94cb1f8d..d829982274e9431c30368c5362e228b954ec9b8d 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -298,7 +298,7 @@ void FixLangevin::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLangevin::post_force(int vflag)
+void FixLangevin::post_force(int /*vflag*/)
{
double *rmass = atom->rmass;
@@ -441,7 +441,7 @@ void FixLangevin::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLangevin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
@@ -896,7 +896,7 @@ void FixLangevin::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixLangevin::copy_arrays(int i, int j, int delflag)
+void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++)
franprev[j][m] = franprev[i][m];
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index e90152c4e1092ef95b94df1371f6131f94e8d979..aea1a2a25bc3c4b54ca6428ed17dec3baca36a49 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -80,7 +80,7 @@ void FixLineForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLineForce::post_force(int vflag)
+void FixLineForce::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -98,7 +98,7 @@ void FixLineForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixLineForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixLineForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index 06a3ac900d7cd28209682056d923b6889ecc37d2..fa39643a1bc9beba894349396b1e325ec59a208d 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -184,7 +184,7 @@ void FixMinimize::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixMinimize::copy_arrays(int i, int j, int delflag)
+void FixMinimize::copy_arrays(int i, int j, int /*delflag*/)
{
int m,iper,nper,ni,nj;
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 9eadfa5ab4c7c9b2a41102e9997f90178633d9bc..2f9fb0ebaa596bdbc37553f6e2f2344c49e6f515 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -453,7 +453,7 @@ void FixMove::init()
set x,v of particles
------------------------------------------------------------------------- */
-void FixMove::initial_integrate(int vflag)
+void FixMove::initial_integrate(int /*vflag*/)
{
int flag;
double ddotr,dx,dy,dz;
@@ -945,7 +945,7 @@ void FixMove::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixMove::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
// outermost level - update v and x
// all other levels - nothing
@@ -955,7 +955,7 @@ void FixMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixMove::final_integrate_respa(int ilevel, int iloop)
+void FixMove::final_integrate_respa(int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) final_integrate();
}
@@ -1019,7 +1019,7 @@ void FixMove::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixMove::copy_arrays(int i, int j, int delflag)
+void FixMove::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -1238,7 +1238,7 @@ int FixMove::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixMove::size_restart(int nlocal)
+int FixMove::size_restart(int /*nlocal*/)
{
return nrestart;
}
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index 3329b604efa4a0e2f6310e34cce95d7ca6902a14..9661409a6a1cbde20beacd3e3f1ff63605273b7b 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -35,7 +35,7 @@ enum{DEFAULT,NPARTNER,PERPARTNER}; // also set in fix neigh/history/omp
FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- npartner(NULL), partner(NULL), valuepartner(NULL), pair(NULL),
+ pair(NULL), npartner(NULL), partner(NULL), valuepartner(NULL),
ipage_atom(NULL), dpage_atom(NULL), ipage_neigh(NULL), dpage_neigh(NULL)
{
if (narg != 4) error->all(FLERR,"Illegal fix NEIGH_HISTORY command");
@@ -686,7 +686,7 @@ void FixNeighHistory::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixNeighHistory::copy_arrays(int i, int j, int delflag)
+void FixNeighHistory::copy_arrays(int i, int j, int /*delflag*/)
{
// just copy pointers for partner and valuepartner
// b/c can't overwrite chunk allocation inside ipage_atom,dpage_atom
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 73c70420c5bc84e001d448a5d580b1fe10ce9ece..a1a562f2bb078602875e8b8581891e891c9736d3 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -742,7 +742,7 @@ void FixNH::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixNH::setup(int vflag)
+void FixNH::setup(int /*vflag*/)
{
// tdof needed by compute_temp_target()
@@ -827,7 +827,7 @@ void FixNH::setup(int vflag)
1st half of Verlet update
------------------------------------------------------------------------- */
-void FixNH::initial_integrate(int vflag)
+void FixNH::initial_integrate(int /*vflag*/)
{
// update eta_press_dot
@@ -922,7 +922,7 @@ void FixNH::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNH::initial_integrate_respa(int /*vflag*/, int ilevel, int /*iloop*/)
{
// set timesteps by level
@@ -991,7 +991,7 @@ void FixNH::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNH::final_integrate_respa(int ilevel, int iloop)
+void FixNH::final_integrate_respa(int ilevel, int /*iloop*/)
{
// set timesteps by level
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index 58e33b9744b7c84eac6ca72b6d05ae7b502b571d..959483230e5753b43c802c0755605e4789803c85 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -62,7 +62,7 @@ void FixNVE::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVE::initial_integrate(int vflag)
+void FixNVE::initial_integrate(int /*vflag*/)
{
double dtfm;
@@ -143,7 +143,7 @@ void FixNVE::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVE::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -157,7 +157,7 @@ void FixNVE::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVE::final_integrate_respa(int ilevel, int iloop)
+void FixNVE::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index f659597af7aeeb0d35081ed02aa43736d58fe8a1..b4fb43e56fc5b95aea196875028d905208877041 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -83,7 +83,7 @@ void FixNVELimit::init()
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
-void FixNVELimit::initial_integrate(int vflag)
+void FixNVELimit::initial_integrate(int /*vflag*/)
{
double dtfm,vsq,scale;
@@ -202,7 +202,7 @@ void FixNVELimit::final_integrate()
/* ---------------------------------------------------------------------- */
-void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -213,7 +213,7 @@ void FixNVELimit::initial_integrate_respa(int vflag, int ilevel, int iloop)
/* ---------------------------------------------------------------------- */
-void FixNVELimit::final_integrate_respa(int ilevel, int iloop)
+void FixNVELimit::final_integrate_respa(int ilevel, int /*iloop*/)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index 3403f4f5ec6b7f2eb7b71229159c18f3136b252e..d4fca9e6760444e23db32386a7d181e08e742e3f 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -54,7 +54,7 @@ void FixNVENoforce::init()
/* ---------------------------------------------------------------------- */
-void FixNVENoforce::initial_integrate(int vflag)
+void FixNVENoforce::initial_integrate(int /*vflag*/)
{
double **x = atom->x;
double **v = atom->v;
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index fe37324cfbac2164ea0bd04940df8145f12f7e7f..0bee8b868538ccf11f9c92e556e38dd009ad3c06 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -97,7 +97,7 @@ void FixNVESphere::init()
/* ---------------------------------------------------------------------- */
-void FixNVESphere::initial_integrate(int vflag)
+void FixNVESphere::initial_integrate(int /*vflag*/)
{
double dtfm,dtirotate,msq,scale,s2,inv_len_mu;
double g[3];
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index f90be6a233a330a9687ce56b7864d2bdda6128e6..45dc782fcf086da5fd4bf8c586a04f7ec383d58f 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -80,7 +80,7 @@ void FixPlaneForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPlaneForce::post_force(int vflag)
+void FixPlaneForce::post_force(int /*vflag*/)
{
double **f = atom->f;
int *mask = atom->mask;
@@ -98,7 +98,7 @@ void FixPlaneForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixPlaneForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPlaneForce::post_force_respa(int vflag, int /*ilevel*/, int /*iloop*/)
{
post_force(vflag);
}
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index 792154e93fe6dc222d1e9902019297731f48a486..95db004436a512a5d00f5a8aa506202d53084907 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -334,7 +334,7 @@ void FixPressBerendsen::init()
compute T,P before integrator starts
------------------------------------------------------------------------- */
-void FixPressBerendsen::setup(int vflag)
+void FixPressBerendsen::setup(int /*vflag*/)
{
// trigger virial computation on next timestep
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 5ad4dfa4ba1bf2a3d4cee54695d80d28aa98bc71..5b12b6def21bf29b71c113929a6ff23ca2de7b95 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -292,7 +292,7 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf,
return # of lines in section of data file labeled by keyword
------------------------------------------------------------------------- */
-bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
+bigint FixPropertyAtom::read_data_skip_lines(char * /*keyword*/)
{
return atom->natoms;
}
@@ -304,7 +304,7 @@ bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
ny = columns = tag + nvalues
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
+void FixPropertyAtom::write_data_section_size(int /*mth*/, int &nx, int &ny)
{
nx = atom->nlocal;
ny = nvalue + 1;
@@ -315,7 +315,7 @@ void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
buf allocated by caller as Nlocal by Nvalues+1
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
+void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
{
int i;
@@ -354,7 +354,7 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
only called by proc 0
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
+void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
{
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
@@ -368,8 +368,8 @@ void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
only called by proc 0
------------------------------------------------------------------------- */
-void FixPropertyAtom::write_data_section(int mth, FILE *fp,
- int n, double **buf, int index)
+void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp,
+ int n, double **buf, int /*index*/)
{
int m;
@@ -443,7 +443,7 @@ void FixPropertyAtom::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
+void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
@@ -644,7 +644,7 @@ int FixPropertyAtom::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixPropertyAtom::size_restart(int nlocal)
+int FixPropertyAtom::size_restart(int /*nlocal*/)
{
return nvalue+1;
}
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index b384234b99973c51aa8c8a8ce765e99257bc5b0d..3c3178f4af3e6d05866eea3e1ce3d81108100618 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -96,7 +96,7 @@ void FixReadRestart::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixReadRestart::copy_arrays(int i, int j, int delflag)
+void FixReadRestart::copy_arrays(int i, int j, int /*delflag*/)
{
count[j] = count[i];
for (int m = 0; m < count[i]; m++) extra[j][m] = extra[i][m];
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index 49e370ac806ead4df1a1845dacdd1341503d9630..75b383d67a2f46ef99e7d721c70964c9d47b654b 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -149,7 +149,7 @@ void FixRecenter::init()
/* ---------------------------------------------------------------------- */
-void FixRecenter::initial_integrate(int vflag)
+void FixRecenter::initial_integrate(int /*vflag*/)
{
// target COM
// bounding box around domain works for both orthogonal and triclinic
@@ -211,7 +211,7 @@ void FixRecenter::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixRecenter::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/)
{
// outermost level - operate recenter
// all other levels - nothing
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index 3b9aad1286c4e62dbab97e505cdd3afcd7ab6cee..64461ba7ca2044277ab86fc5ccc83a7fbcbf2f6a 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -93,7 +93,7 @@ void FixRespa::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixRespa::copy_arrays(int i, int j, int delflag)
+void FixRespa::copy_arrays(int i, int j, int /*delflag*/)
{
for (int k = 0; k < nlevels; k++) {
f_level[j][k][0] = f_level[i][k][0];
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index 6ad229fea7e70e16099b90cf9aee1e7b615e0ed3..bb09116374d0f03572f9b5f2da5ddc2588af435f 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -188,7 +188,7 @@ void FixRestrain::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRestrain::post_force(int vflag)
+void FixRestrain::post_force(int /*vflag*/)
{
energy = 0.0;
@@ -204,7 +204,7 @@ void FixRestrain::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRestrain::post_force_respa(int vflag, int ilevel, int iloop)
+void FixRestrain::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index 89b340b0ae422558e666f81190bb3c4055abf69c..fc8b7aeb59862fb78860b507f31f9477fa3888a0 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -219,7 +219,7 @@ void FixSetForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSetForce::post_force(int vflag)
+void FixSetForce::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -293,7 +293,7 @@ void FixSetForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSetForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSetForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
// set force to desired value on requested level, 0.0 on other levels
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index ecb84eeb0f0ead6b4aec161ae43b8a38d6e8fc89..328a0eeafda12cf3f71efffb8d8168b6e27fe9ae 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -159,7 +159,7 @@ void FixSpring::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpring::post_force(int vflag)
+void FixSpring::post_force(int /*vflag*/)
{
if (styleflag == TETHER) spring_tether();
else spring_couple();
@@ -335,7 +335,7 @@ void FixSpring::spring_couple()
/* ---------------------------------------------------------------------- */
-void FixSpring::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpring::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp
index 53e9285a9c7ddd4869bb760c8b5cc60be790b073..5b5d95b111b5d7eb8eb8b3049217be5272be3d3a 100644
--- a/src/fix_spring_chunk.cpp
+++ b/src/fix_spring_chunk.cpp
@@ -144,7 +144,7 @@ void FixSpringChunk::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringChunk::post_force(int vflag)
+void FixSpringChunk::post_force(int /*vflag*/)
{
int i,m;
double dx,dy,dz,r;
@@ -231,7 +231,7 @@ void FixSpringChunk::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringChunk::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringChunk::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index c2e226a343dc657b5661f24b6991d390cac4f1ff..28c89690061eb2c92c3a6b587e9833f052b0be3f 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -95,7 +95,7 @@ void FixSpringRG::setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringRG::post_force(int vflag)
+void FixSpringRG::post_force(int /*vflag*/)
{
// compute current Rg and center-of-mass
@@ -142,7 +142,7 @@ void FixSpringRG::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringRG::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index 1a5c89c6a15b43832f190d7f73dcfeaef3cf6383..670883af41b3bc29f865789e0d57a0b7decc5de2 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -148,7 +148,7 @@ void FixSpringSelf::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringSelf::post_force(int vflag)
+void FixSpringSelf::post_force(int /*vflag*/)
{
double **x = atom->x;
double **f = atom->f;
@@ -181,7 +181,7 @@ void FixSpringSelf::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixSpringSelf::post_force_respa(int vflag, int ilevel, int iloop)
+void FixSpringSelf::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
@@ -227,7 +227,7 @@ void FixSpringSelf::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixSpringSelf::copy_arrays(int i, int j, int delflag)
+void FixSpringSelf::copy_arrays(int i, int j, int /*delflag*/)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@@ -303,7 +303,7 @@ int FixSpringSelf::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixSpringSelf::size_restart(int nlocal)
+int FixSpringSelf::size_restart(int /*nlocal*/)
{
return 4;
}
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 350e12097270c1e64f80313af5665ca60e719963..9db65d0987be99c813071c5a827ec8361e98fba8 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -229,7 +229,7 @@ void FixStore::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixStore::copy_arrays(int i, int j, int delflag)
+void FixStore::copy_arrays(int i, int j, int /*delflag*/)
{
if (disable) return;
@@ -324,7 +324,7 @@ int FixStore::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixStore::size_restart(int nlocal)
+int FixStore::size_restart(int /*nlocal*/)
{
if (disable) return 1;
return nvalues+1;
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index 5e2150f68d004cdd6a82d0f416ddbd00311520d7..a841714098e1f808217afcf13d7335a7a4fd3199 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -95,7 +95,7 @@ void FixStoreForce::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixStoreForce::post_force(int vflag)
+void FixStoreForce::post_force(int /*vflag*/)
{
if (atom->nmax > nmax) {
nmax = atom->nmax;
@@ -118,7 +118,7 @@ void FixStoreForce::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixStoreForce::post_force_respa(int vflag, int ilevel, int iloop)
+void FixStoreForce::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 3195e983e35019adb4c627f20a62bffa18dae2e3..da899a173cc22fe837d9e177064b343159d901a5 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -446,7 +446,7 @@ void FixStoreState::init()
/* ---------------------------------------------------------------------- */
-void FixStoreState::setup(int vflag)
+void FixStoreState::setup(int /*vflag*/)
{
// if first invocation, store current values for compute, fix, variable
@@ -580,7 +580,7 @@ void FixStoreState::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
-void FixStoreState::copy_arrays(int i, int j, int delflag)
+void FixStoreState::copy_arrays(int i, int j, int /*delflag*/)
{
for (int m = 0; m < nvalues; m++) values[j][m] = values[i][m];
}
@@ -646,7 +646,7 @@ int FixStoreState::maxsize_restart()
size of atom nlocal's restart data
------------------------------------------------------------------------- */
-int FixStoreState::size_restart(int nlocal)
+int FixStoreState::size_restart(int /*nlocal*/)
{
return nvalues+1;
}
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index 39d4173a63a058a40030512287d7441123266d63..dd11dfd0c7dc3e917f83306c6aa0da7d6a59edb4 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -170,7 +170,7 @@ void FixTMD::init()
/* ---------------------------------------------------------------------- */
-void FixTMD::initial_integrate(int vflag)
+void FixTMD::initial_integrate(int /*vflag*/)
{
double a,b,c,d,e;
double dx,dy,dz,dxkt,dykt,dzkt;
@@ -335,7 +335,7 @@ void FixTMD::grow_arrays(int nmax)
copy values within local atom-based arrays
------------------------------------------------------------------------- */
-void FixTMD::copy_arrays(int i, int j, int delflag)
+void FixTMD::copy_arrays(int i, int j, int /*delflag*/)
{
xf[j][0] = xf[i][0];
xf[j][1] = xf[i][1];
@@ -412,7 +412,7 @@ void FixTMD::readfile(char *file)
m++;
}
- MPI_Bcast(&eof,sizeof(char *)/sizeof(char),MPI_CHAR,0,world);
+ MPI_Bcast(&eof,sizeof(char *),MPI_CHAR,0,world);
MPI_Bcast(&nlines,1,MPI_INT,0,world);
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 9b7f01697084ce3e705dc1920de8b11f0b024a62..6387af767606cac35b701410c5a4cbf8fabdf50d 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -239,7 +239,7 @@ void FixVector::init()
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
-void FixVector::setup(int vflag)
+void FixVector::setup(int /*vflag*/)
{
end_of_step();
}
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index 1d2609c8b68ff782ba1e41c7798f4e944a6ed646..e8451423227decc258780ff3b65a76a66e11f9eb 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -109,7 +109,7 @@ void FixViscous::min_setup(int vflag)
/* ---------------------------------------------------------------------- */
-void FixViscous::post_force(int vflag)
+void FixViscous::post_force(int /*vflag*/)
{
// apply drag force to atoms in group
// direction is opposed to velocity vector
@@ -134,7 +134,7 @@ void FixViscous::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixViscous::post_force_respa(int vflag, int ilevel, int iloop)
+void FixViscous::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index 096bbe618a5a9b3fa234292807912f32642d210c..e84d01191d43bc800b115e89cfb2ae9636461635 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -343,7 +343,7 @@ void FixWall::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWall::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWall::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index ea1b62bfa5e160688cd7913e9cad106e5db60535..ff147d74463827b410f6c7bb9b92a90eb83bc93d 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -287,7 +287,7 @@ void FixWallRegion::post_force(int vflag)
/* ---------------------------------------------------------------------- */
-void FixWallRegion::post_force_respa(int vflag, int ilevel, int iloop)
+void FixWallRegion::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
diff --git a/src/group.cpp b/src/group.cpp
index dd5e53bb3c58234655c8fcf76c171dc84cf386b1..3bc3f3d7bf9e7c47275a50b53bf31f07b4da7174 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -629,7 +629,7 @@ int Group::find_unused()
do not include molID = 0
------------------------------------------------------------------------- */
-void Group::add_molecules(int igroup, int bit)
+void Group::add_molecules(int /*igroup*/, int bit)
{
// hash = unique molecule IDs of atoms already in group
diff --git a/src/image.cpp b/src/image.cpp
index 301a2af88f23588dfcdea129fe2c283ae6269cb0..3df167bbf60b519184a128d9bceb0ba258ab0a72 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -1017,6 +1017,8 @@ void Image::write_JPG(FILE *fp)
jpeg_finish_compress(&cinfo);
jpeg_destroy_compress(&cinfo);
+#else
+ LMP_UNUSED_PARAM(fp);
#endif
}
@@ -1074,6 +1076,8 @@ void Image::write_PNG(FILE *fp)
png_destroy_write_struct(&png_ptr, &info_ptr);
delete[] row_pointers;
+#else
+ LMP_UNUSED_PARAM(fp);
#endif
}
diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp
index acb3da8d1370ed6215549effa3a340abd492f82c..e089b1df0ce3e522dbd518b128cd1a867e429668 100644
--- a/src/imbalance_var.cpp
+++ b/src/imbalance_var.cpp
@@ -52,7 +52,7 @@ int ImbalanceVar::options(int narg, char **arg)
/* -------------------------------------------------------------------- */
-void ImbalanceVar::init(int flag)
+void ImbalanceVar::init(int /*flag*/)
{
id = input->variable->find(name);
if (id < 0) {
diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp
index 25ab3e7bbafa554104b440245c07dda93a18f924..8a1fa529c6dc1658c5d268d3acc268d2da5b7af7 100644
--- a/src/improper_zero.cpp
+++ b/src/improper_zero.cpp
@@ -99,13 +99,13 @@ void ImproperZero::coeff(int narg, char **arg)
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
-void ImproperZero::write_restart(FILE *fp) {}
+void ImproperZero::write_restart(FILE * /*fp*/) {}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
-void ImproperZero::read_restart(FILE *fp)
+void ImproperZero::read_restart(FILE * /*fp*/)
{
allocate();
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 97d28d6d7c2b6bccbc70d6f973017f31d86cc6d4..d6b27e042d2ee7042d10d0af4bf4376423efc054 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Integrate::Integrate(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+Integrate::Integrate(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)
{
elist_global = elist_atom = NULL;
vlist_global = vlist_atom = NULL;
diff --git a/src/kspace.cpp b/src/kspace.cpp
index fc8b12288ba0679f17d0cbca31287c24208f142b..ad5c9e42f24ec2323fa68319480d3f41ab59a239 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -30,7 +30,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-KSpace::KSpace(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+KSpace::KSpace(LAMMPS *lmp, int /*narg*/, char **/*arg*/) : Pointers(lmp)
{
order_allocated = 0;
energy = 0.0;
diff --git a/src/lammps.cpp b/src/lammps.cpp
index df6519f9f4b899c5c5c26cb13ea93eca601f695d..fcdfecf30a83795d742504e43ae12a9e0dd7bdc3 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -47,8 +47,8 @@
#include "accelerator_omp.h"
#include "timer.h"
#include "python.h"
-#include "memory.h"
#include "version.h"
+#include "memory.h"
#include "error.h"
#include "lmpinstalledpkgs.h"
@@ -73,12 +73,46 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
output = NULL;
python = NULL;
+ clientserver = 0;
+ cslib = NULL;
+ cscomm = 0;
+
screen = NULL;
logfile = NULL;
infile = NULL;
initclock = MPI_Wtime();
+ // 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
+ // e.g. for client/server coupling with another code
+ // in the future LAMMPS might leverage this in other ways
+ // universe communicator needs to shrink to be just LAMMPS
+ // syntax: -mpi color
+ // color = integer for this app, different than other app(s)
+ // do the following:
+ // perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
+ // NOTE: this assumes other app(s) does same thing, else will hang!
+ // re-create universe with subcomm
+ // store full multi-app comm in cscomm
+ // cscomm is used by CSLIB package to exchange messages w/ other app
+
+ int iarg = 1;
+ if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0)) {
+ int me,nprocs;
+ MPI_Comm_rank(communicator,&me);
+ MPI_Comm_size(communicator,&nprocs);
+ int color = atoi(arg[iarg+1]);
+ MPI_Comm subcomm;
+ MPI_Comm_split(communicator,color,me,&subcomm);
+ cscomm = communicator;
+ communicator = subcomm;
+ delete universe;
+ universe = new Universe(this,communicator);
+ }
+
// parse input switches
int inflag = 0;
@@ -107,59 +141,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int *pfirst = NULL;
int *plast = NULL;
- int iarg = 1;
+ iarg = 1;
while (iarg < narg) {
- if (strcmp(arg[iarg],"-partition") == 0 ||
- strcmp(arg[iarg],"-p") == 0) {
- universe->existflag = 1;
+
+ if (strcmp(arg[iarg],"-echo") == 0 ||
+ strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- iarg++;
- while (iarg < narg && arg[iarg][0] != '-') {
- universe->add_world(arg[iarg]);
- iarg++;
- }
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-help") == 0 ||
+ strcmp(arg[iarg],"-h") == 0) {
+ if (iarg+1 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ helpflag = 1;
+ citeflag = 0;
+ iarg += 1;
+
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
- } else if (strcmp(arg[iarg],"-screen") == 0 ||
- strcmp(arg[iarg],"-sc") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- screenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-log") == 0 ||
- strcmp(arg[iarg],"-l") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- logflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-var") == 0 ||
- strcmp(arg[iarg],"-v") == 0) {
- if (iarg+3 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 3;
- while (iarg < narg && arg[iarg][0] != '-') iarg++;
- } else if (strcmp(arg[iarg],"-echo") == 0 ||
- strcmp(arg[iarg],"-e") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- iarg += 2;
- } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
- strcmp(arg[iarg],"-ps") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partscreenflag = iarg + 1;
- iarg += 2;
- } else if (strcmp(arg[iarg],"-plog") == 0 ||
- strcmp(arg[iarg],"-pl") == 0) {
- if (iarg+2 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- partlogflag = iarg + 1;
- iarg += 2;
+
} else if (strcmp(arg[iarg],"-kokkos") == 0 ||
strcmp(arg[iarg],"-k") == 0) {
if (iarg+2 > narg)
@@ -172,6 +177,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
kkfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
kklast = iarg;
+
+ } else if (strcmp(arg[iarg],"-log") == 0 ||
+ strcmp(arg[iarg],"-l") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ logflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-mpi") == 0 ||
+ strcmp(arg[iarg],"-m") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-nocite") == 0 ||
+ strcmp(arg[iarg],"-nc") == 0) {
+ citeflag = 0;
+ iarg++;
+
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@@ -188,31 +213,32 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
else break;
}
plast[npack++] = iarg;
- } else if (strcmp(arg[iarg],"-suffix") == 0 ||
- strcmp(arg[iarg],"-sf") == 0) {
+
+ } else if (strcmp(arg[iarg],"-partition") == 0 ||
+ strcmp(arg[iarg],"-p") == 0) {
+ universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- delete [] suffix;
- delete [] suffix2;
- suffix2 = NULL;
- suffix_enable = 1;
- // hybrid option to set fall-back for suffix2
- if (strcmp(arg[iarg+1],"hybrid") == 0) {
- if (iarg+4 > narg)
- error->universe_all(FLERR,"Invalid command-line argument");
- int n = strlen(arg[iarg+2]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+2]);
- n = strlen(arg[iarg+3]) + 1;
- suffix2 = new char[n];
- strcpy(suffix2,arg[iarg+3]);
- iarg += 4;
- } else {
- int n = strlen(arg[iarg+1]) + 1;
- suffix = new char[n];
- strcpy(suffix,arg[iarg+1]);
- iarg += 2;
+ iarg++;
+ while (iarg < narg && arg[iarg][0] != '-') {
+ universe->add_world(arg[iarg]);
+ iarg++;
}
+
+ } else if (strcmp(arg[iarg],"-plog") == 0 ||
+ strcmp(arg[iarg],"-pl") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partlogflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-pscreen") == 0 ||
+ strcmp(arg[iarg],"-ps") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ partscreenflag = iarg + 1;
+ iarg += 2;
+
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
if (iarg+3 > narg)
@@ -221,6 +247,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
+
} else if (strcmp(arg[iarg],"-restart") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
@@ -241,17 +268,47 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
wdfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wdlast = iarg;
- } else if (strcmp(arg[iarg],"-nocite") == 0 ||
- strcmp(arg[iarg],"-nc") == 0) {
- citeflag = 0;
- iarg++;
- } else if (strcmp(arg[iarg],"-help") == 0 ||
- strcmp(arg[iarg],"-h") == 0) {
- if (iarg+1 > narg)
+
+ } else if (strcmp(arg[iarg],"-screen") == 0 ||
+ strcmp(arg[iarg],"-sc") == 0) {
+ if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
- helpflag = 1;
- citeflag = 0;
- iarg += 1;
+ screenflag = iarg + 1;
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"-suffix") == 0 ||
+ strcmp(arg[iarg],"-sf") == 0) {
+ if (iarg+2 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ delete [] suffix;
+ delete [] suffix2;
+ suffix2 = NULL;
+ suffix_enable = 1;
+ // hybrid option to set fall-back for suffix2
+ if (strcmp(arg[iarg+1],"hybrid") == 0) {
+ if (iarg+4 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ int n = strlen(arg[iarg+2]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+2]);
+ n = strlen(arg[iarg+3]) + 1;
+ suffix2 = new char[n];
+ strcpy(suffix2,arg[iarg+3]);
+ iarg += 4;
+ } else {
+ int n = strlen(arg[iarg+1]) + 1;
+ suffix = new char[n];
+ strcpy(suffix,arg[iarg+1]);
+ iarg += 2;
+ }
+
+ } else if (strcmp(arg[iarg],"-var") == 0 ||
+ strcmp(arg[iarg],"-v") == 0) {
+ if (iarg+3 > narg)
+ error->universe_all(FLERR,"Invalid command-line argument");
+ iarg += 3;
+ while (iarg < narg && arg[iarg][0] != '-') iarg++;
+
} else error->universe_all(FLERR,"Invalid command-line argument");
}
@@ -595,6 +652,14 @@ LAMMPS::~LAMMPS()
delete [] suffix;
delete [] suffix2;
+ // free the MPI comm created by -mpi command-line arg processed in constructor
+ // it was passed to universe as if original universe world
+ // may have been split later by partitions, universe will free the splits
+ // free a copy of uorig here, so check in universe destructor will still work
+
+ MPI_Comm copy = universe->uorig;
+ if (cscomm) MPI_Comm_free(©);
+
delete input;
delete universe;
delete error;
@@ -814,6 +879,7 @@ void LAMMPS::help()
"-in filename : read input from file, not stdin (-i)\n"
"-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n"
"-log none/filename : where to send log output (-l)\n"
+ "-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n"
"-nocite : disable writing log.cite file (-nc)\n"
"-package style ... : invoke package command (-pk)\n"
"-partition size1 size2 ... : assign partition sizes (-p)\n"
diff --git a/src/lammps.h b/src/lammps.h
index b2c867347108edee9814906e42185db56a9a21f9..5ccef3026ed068ba2d10c291d629f652d30c3321 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -51,6 +51,10 @@ class LAMMPS {
int num_package; // number of cmdline package commands
int cite_enable; // 1 if generating log.cite, 0 if disabled
+ int clientserver; // 0 = neither, 1 = client, 2 = server
+ void *cslib; // client/server messaging via CSlib
+ MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode
+
class KokkosLMP *kokkos; // KOKKOS accelerator class
class AtomKokkos *atomKK; // KOKKOS version of Atom class
class MemoryKokkos *memoryKK; // KOKKOS version of Memory class
diff --git a/src/library.cpp b/src/library.cpp
index 13e07568667d6319bd52b2c9fe6166decf292953..a46689da09a39fd999111a63cef48c7baf6ec839 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -336,7 +336,7 @@ void lammps_free(void *ptr)
customize by adding names
------------------------------------------------------------------------- */
-int lammps_extract_setting(void *ptr, char *name)
+int lammps_extract_setting(void * /*ptr*/, char *name)
{
if (strcmp(name,"bigint") == 0) return sizeof(bigint);
if (strcmp(name,"tagint") == 0) return sizeof(tagint);
@@ -1515,7 +1515,8 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type,
if (lmp->atom->natoms != natoms_prev + n) {
char str[128];
sprintf(str,"Library warning in lammps_create_atoms, "
- "invalid total atoms %ld %ld",lmp->atom->natoms,natoms_prev+n);
+ "invalid total atoms " BIGINT_FORMAT " " BIGINT_FORMAT,
+ lmp->atom->natoms,natoms_prev+n);
if (lmp->comm->me == 0)
lmp->error->warning(FLERR,str);
}
diff --git a/src/lmptype.h b/src/lmptype.h
index 7e359d2abeda05c1b0ec992cb7b113b9be7e67ab..7c3dbc1c3dad802948b6abc189422e811e54d496 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -213,4 +213,8 @@ typedef int bigint;
#include "lmpwindows.h"
#endif
+// suppress unused parameter warning
+
+#define LMP_UNUSED_PARAM(x) (void)(x)
+
#endif
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index b70986ce914904edc8b3a2cbf41fb3b3e9ade210..0bba2ad40125e7ffa6a65f8fa22552e77bba8371 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -590,7 +590,7 @@ void inertia_triangle(double *v0, double *v1, double *v2,
return symmetric inertia tensor as 6-vector in Voigt notation
------------------------------------------------------------------------- */
-void inertia_triangle(double *idiag, double *quat, double mass,
+void inertia_triangle(double *idiag, double *quat, double /*mass*/,
double *inertia)
{
double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3];
diff --git a/src/memory.h b/src/memory.h
index f2faecf6e177587e4aaf9dfc14991c6ef4f94f58..20ea426f909c0aabe619398e44f9b72bbaf40216 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -50,7 +50,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **create(TYPE **&array, int n, const char *name)
+ TYPE **create(TYPE **& /*array*/, int /*n*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -68,7 +68,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **grow(TYPE **&array, int n, const char *name)
+ TYPE **grow(TYPE **& /*array*/, int /*n*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -96,7 +96,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE **create1d_offset(TYPE **&array, int nlo, int nhi, const char *name)
+ TYPE **create1d_offset(TYPE **& /*array*/, int /*nlo*/, int /*nhi*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -131,7 +131,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create(TYPE ***&array, int n1, int n2, const char *name)
+ TYPE ***create(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -158,7 +158,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***grow(TYPE ***&array, int n1, int n2, const char *name)
+ TYPE ***grow(TYPE ***& /*array*/, int /*n1*/, int /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -198,7 +198,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create_ragged(TYPE ***&array, int n1, int *n2, const char *name)
+ TYPE ***create_ragged(TYPE ***& /*array*/, int /*n1*/, int * /*n2*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -217,7 +217,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ***create2d_offset(TYPE ***&array, int n1, int n2lo, int n2hi,
+ TYPE ***create2d_offset(TYPE ***& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/,
const char *name) {fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -262,7 +262,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****create(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -297,7 +297,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, const char *name)
+ TYPE ****grow(TYPE ****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -330,8 +330,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2, int n3, const char *name)
+ TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/,
+ int /*n2*/, int /*n3*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
@@ -374,8 +374,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create3d_offset(TYPE ****&array, int n1lo, int n1hi,
- int n2lo, int n2hi, int n3lo, int n3hi,
+ TYPE ****create3d_offset(TYPE ****& /*array*/, int /*n1lo*/, int /*n1hi*/,
+ int /*n2lo*/, int /*n2hi*/, int /*n3lo*/, int /*n3hi*/,
const char *name)
{fail(name); return NULL;}
@@ -432,7 +432,7 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4,
+ TYPE *****create(TYPE *****& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/,
const char *name)
{fail(name); return NULL;}
@@ -478,8 +478,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ****create4d_offset(TYPE *****&array, int n1, int n2lo, int n2hi,
- int n3lo, int n3hi, int n4lo, int n4hi,
+ TYPE ****create4d_offset(TYPE *****& /*array*/, int /*n1*/, int /*n2lo*/, int /*n2hi*/,
+ int /*n3lo*/, int /*n3hi*/, int /*n4lo*/, int /*n4hi*/,
const char *name)
{fail(name); return NULL;}
@@ -546,8 +546,8 @@ class Memory : protected Pointers {
}
template <typename TYPE>
- TYPE ******create(TYPE ******&array, int n1, int n2, int n3, int n4,
- int n5, const char *name)
+ TYPE ******create(TYPE ******& /*array*/, int /*n1*/, int /*n2*/, int /*n3*/, int /*n4*/,
+ int /*n5*/, const char *name)
{fail(name); return NULL;}
/* ----------------------------------------------------------------------
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 912a636227b84b0fb81a549a7297698bbd98c1b0..759f84e29f92406bace3bfb5ea5715be2f0c7e73 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -2193,7 +2193,7 @@ void Neighbor::set(int narg, char **arg)
ditto for lastcall and last_setup_bins
------------------------------------------------------------------------- */
-void Neighbor::reset_timestep(bigint ntimestep)
+void Neighbor::reset_timestep(bigint /*ntimestep*/)
{
for (int i = 0; i < nbin; i++)
neigh_bin[i]->last_bin = -1;
diff --git a/src/pair.cpp b/src/pair.cpp
index 5c308cc7ce51e840713abfaeacdcbd8190ce95e9..18d561bdb55230ef2f63f6fc01f600916bcad8ab 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -301,7 +301,7 @@ void Pair::init_style()
specific pair style can override this function
------------------------------------------------------------------------- */
-void Pair::init_list(int which, NeighList *ptr)
+void Pair::init_list(int /*which*/, NeighList *ptr)
{
list = ptr;
}
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index cc8e14bf2c6c93164a1795b79352a7568f24f515..d9c0fb902c9f833a128344fd9944c205e50518e3 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -327,9 +327,9 @@ void PairBeck::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBeck::single(int i, int j, int itype, int jtype,
+double PairBeck::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double phi_beck,r,rinv;
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index ce7a255fd4935a41e1a20d00fe4ea8757894600f..1a1db9dd905822810dc6cc201c1bf2bc8c006d8e 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -407,8 +407,8 @@ void PairBorn::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBorn::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBorn::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forceborn,phiborn;
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index 450ce291cb9814629e0ade5d1398cd595744d95c..8b6d79234bb174ff3fffc26ad5278c563d3f40c0 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -380,8 +380,8 @@ void PairBuck::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairBuck::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairBuck::single(int /*i*/, int /*j*/, int itype, int jtype,
+ double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,rexp,forcebuck,phibuck;
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index edcf26bffe990d91219eaeaa60d53e20bf57181a..8741abdb895893da53453faff9466ffdd0ee7d3d 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -284,8 +284,8 @@ void PairCoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulCut::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,rinv,forcecoul,phicoul;
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index ee08ab3294909b1865bc16100b3a390468fa31d3..432a0155982b67189228de7d978fc6eeb632e725 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -163,8 +163,8 @@ void PairCoulDebye::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulDebye::single(int i, int j, int itype, int jtype,
- double rsq, double factor_coul, double factor_lj,
+double PairCoulDebye::single(int i, int j, int /*itype*/, int /*jtype*/,
+ double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,rinv,forcecoul,phicoul,screening;
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index f20eae43bdbdde3fe252d25f3f6194404e8e81bb..8cd5f7feceff4366d4cfc5ef24275889fc8aea0e 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -221,7 +221,7 @@ void PairCoulDSF::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairCoulDSF::init_one(int i, int j)
+double PairCoulDSF::init_one(int /*i*/, int /*j*/)
{
return cut_coul;
}
@@ -291,8 +291,8 @@ void PairCoulDSF::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairCoulDSF::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairCoulDSF::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,erfcc,erfcd,prefactor,t;
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index cd582f0693abaafffb3d04af52996cf7ea033c8a..762491166efe79abd0a87478921429568e1fccfe 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -219,7 +219,7 @@ void PairCoulWolf::init_style()
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairCoulWolf::init_one(int i, int j)
+double PairCoulWolf::init_one(int /*i*/, int /*j*/)
{
return cut_coul;
}
@@ -290,8 +290,8 @@ void PairCoulWolf::read_restart_settings(FILE *fp)
only the pair part is calculated here
------------------------------------------------------------------------- */
-double PairCoulWolf::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairCoulWolf::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
+ double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r,prefactor;
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index c209de87ed15e7aad81c1e1c01322509d4045720..5c5fc4254b4005baaf3ca9b57cf9b6445be00e2b 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -390,8 +390,8 @@ void PairDPD::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairDPD::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_dpd, double &fforce)
+double PairDPD::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_dpd, double &fforce)
{
double r,rinv,wd,phi;
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index fe53bcc9e1b2af7b61b3074170521887b8166252..426389753b79ecbc215e1d9f9d157c61751abc95 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -347,8 +347,8 @@ void PairGauss::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairGauss::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double /*factor_lj*/,
double &fforce)
{
double philj =
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index dc74dd040dde23f9b72fe87ab39417a54de263a6..03747e1de3faa91f7e142372de7922904c522d28 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -844,7 +844,7 @@ void PairHybrid::modify_params(int narg, char **arg)
store a local per pair style override for special_lj and special_coul
------------------------------------------------------------------------- */
-void PairHybrid::modify_special(int m, int narg, char **arg)
+void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
{
double special[4];
int i;
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index 28677a393ef3745a969ae3ca03dcb47f09ed5e53..457eba0e7958d401fb9f1ee24226408e6455fe26 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -678,8 +678,8 @@ void PairLJ96Cut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJ96Cut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJ96Cut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r3inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index 4b140e5f05d416fce943890c9412d8f1962a5a3e..770caa6359b850b2944ebaa9f304b108fb56f20f 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -175,7 +175,7 @@ void PairLJCubic::allocate()
global settings
------------------------------------------------------------------------- */
-void PairLJCubic::settings(int narg, char **arg)
+void PairLJCubic::settings(int narg, char **/*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
@@ -321,9 +321,9 @@ void PairLJCubic::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCubic::single(int i, int j, int itype, int jtype,
+double PairLJCubic::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index bb2db6aa2fc025cbec62d10111ee2d838caf1715..13a546f5a5411ca5c19f425defc0f4e9605141d7 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -672,8 +672,8 @@ void PairLJCut::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index ba72d7d45f39884c80c061d3b6a3b9bc6b5157dd..9aa58b3b88adb1f9257cac3ff9ed94f15032c3a9 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -396,8 +396,8 @@ void PairLJExpand::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJExpand::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index 6b2219d2c5cef92f4da305e343e4111eb4fc751b..495e96c3680388e44add0f6ac4ae537db44b1be1 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -414,9 +414,9 @@ void PairLJGromacs::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJGromacs::single(int i, int j, int itype, int jtype,
+double PairLJGromacs::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj;
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 23256d486ed09fcf2a48e31ebefd65aead569372..a12046bb3bf9783892d20617e0700d959f88689c 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -425,8 +425,8 @@ void PairLJSmooth::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJSmooth::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairLJSmooth::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,t,tsq,fskin;
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index 592a7f6f41a1ad75eae1a537e3e02e5c88b29bfb..17c789bceed7c2ac3de4881a9924e4971b9198dd 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -326,9 +326,9 @@ void PairLJSmoothLinear::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairLJSmoothLinear::single(int i, int j, int itype, int jtype,
+double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq,
- double factor_coul, double factor_lj,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r6inv,forcelj,philj,r,rinv;
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 1f9267ca30898ed75de80279c23bb3b74d670e88..c1e1c1ff507cd36b769b34577423fe2951d76d45 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -682,8 +682,8 @@ void PairMIECut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMIECut::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_mie,
+double PairMIECut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_mie,
double &fforce)
{
double r2inv,rgamR,rgamA,forcemie,phimie;
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index 32ddd723b2c0dcf062a2f3f1261651786b092bbc..c1031343e19e40d63b37a2cf0371f3a117d32109 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -334,8 +334,8 @@ void PairMorse::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairMorse::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairMorse::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index f428893fd107a0726dcf9532a49d55ddb288b8b3..d1c51ac6006cdb83be753bec80f64783b2048133 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -307,8 +307,8 @@ void PairSoft::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairSoft::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,arg,philj;
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 9e9e41a54c6eac3671c7260937d9ca401254b35b..5c43761cab7ab4fa6ec1d73858a62f9d95c88762 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -993,8 +993,8 @@ void PairTable::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairTable::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairTable::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
int itable;
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index 965fe0204e739a526f5f7ebe13e981f2b5c22984..a9f076f504a3303f83d96ad545f7f0ca8315450a 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -353,8 +353,8 @@ void PairUFM::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairUFM::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairUFM::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double expuf,phiuf;
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 040664abec071e8b776a9315f2e33521d6221f2a..af520fd3da793056af62a4907e48a56b5154dd7e 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -319,8 +319,8 @@ void PairYukawa::write_data_all(FILE *fp)
/* ---------------------------------------------------------------------- */
-double PairYukawa::single(int i, int j, int itype, int jtype, double rsq,
- double factor_coul, double factor_lj,
+double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index 98048f61d0751393e4a23b672b84c6698e669db2..f23a1e5d56c210c08efb0f1bbd7f18a9a6a28c9f 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -267,8 +267,8 @@ double PairZBL::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
-double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
- double dummy1, double dummy2,
+double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
+ double /*dummy1*/, double /*dummy2*/,
double &fforce)
{
double phi,r,t,eswitch,fswitch;
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 13e27b6fbfda836c53b381db8171f59f4b921e0d..630cef309a581c5da789d2d659783139573427c6 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -1108,7 +1108,7 @@ void RCB::compute_old(int dimension, int n, double **x, double *wt,
merge of each component of an RCB bounding box
------------------------------------------------------------------------- */
-void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
+void box_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/)
{
RCB::BBox *box1 = (RCB::BBox *) in;
@@ -1138,7 +1138,7 @@ void box_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
all procs must get same proclo,prochi
------------------------------------------------------------------------- */
-void median_merge(void *in, void *inout, int *len, MPI_Datatype *dptr)
+void median_merge(void *in, void *inout, int * /*len*/, MPI_Datatype * /*dptr*/)
{
RCB::Median *med1 = (RCB::Median *) in;
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index 5cb3476510f093abbe51f745043e0d063356fe29..37d30bd740992e1d78d6f9573b8431fe9bf5f471 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -117,9 +117,9 @@ void ReaderXYZ::skip()
only called by proc 0
------------------------------------------------------------------------- */
-bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
+bigint ReaderXYZ::read_header(double /*box*/[3][3], int &triclinic,
int fieldinfo, int nfield,
- int *fieldtype, char **fieldlabel,
+ int *fieldtype, char **/*fieldlabel*/,
int scaleflag, int wrapflag, int &fieldflag,
int &xflag, int &yflag, int &zflag)
{
diff --git a/src/region.cpp b/src/region.cpp
index 88a414b13438fb2acc8008c7e635645fb1026c30..c52c0181aaf6e6dbeef9c204f60f7f4f796a661b 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -28,7 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-Region::Region(LAMMPS *lmp, int narg, char **arg) :
+Region::Region(LAMMPS *lmp, int /*narg*/, char **arg) :
Pointers(lmp),
id(NULL), style(NULL), contact(NULL), list(NULL),
xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp
index fd898bd3ab63db79f7b45e659ae346e6d19bdab9..b2cf7a9bbce2a5286c5415a8e34148bef37d9aad 100644
--- a/src/reset_ids.cpp
+++ b/src/reset_ids.cpp
@@ -28,7 +28,7 @@ ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
-void ResetIDs::command(int narg, char **arg)
+void ResetIDs::command(int narg, char **/*arg*/)
{
if (domain->box_exist == 0)
error->all(FLERR,"Reset_ids command before simulation box is defined");
diff --git a/src/respa.cpp b/src/respa.cpp
index 73e280b03d806fa038d388e2943d067465cce3d2..26bae5a1cb3c7be8c5cc160e90d209b2d09b5359 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -774,7 +774,7 @@ void Respa::recurse(int ilevel)
clear other arrays as needed
------------------------------------------------------------------------- */
-void Respa::force_clear(int newtonflag)
+void Respa::force_clear(int /*newtonflag*/)
{
if (external_force_clear) return;
diff --git a/src/variable.cpp b/src/variable.cpp
index f005221400509f76fd5887f0323fa11cc8f30a32..3c54eac1efe2e1be4b9c95a0ffc69358f0624ade 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -733,7 +733,7 @@ int Variable::find(char *name)
called when atom is created
------------------------------------------------------------------------- */
-void Variable::set_arrays(int i)
+void Variable::set_arrays(int /*i*/)
{
for (int i = 0; i < nvar; i++)
if (reader[i] && style[i] == ATOMFILE)
@@ -3733,7 +3733,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
if (strcmp(word,"count") == 0) {
if (narg == 1) value = group->count(igroup);
- else if (narg == 2)
+ else if (narg == 2)
value = group->count(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
@@ -3744,7 +3744,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"charge") == 0) {
if (narg == 1) value = group->charge(igroup);
- else if (narg == 2)
+ else if (narg == 2)
value = group->charge(igroup,region_function(args[1],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
@@ -3795,7 +3795,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
} else if (strcmp(word,"bound") == 0) {
double minmax[6];
if (narg == 2) group->bounds(igroup,minmax);
- else if (narg == 3)
+ else if (narg == 3)
group->bounds(igroup,minmax,region_function(args[2],ivar));
else print_var_error(FLERR,"Invalid group function in variable formula",ivar);
if (strcmp(args[1],"xmin") == 0) value = minmax[0];
@@ -3959,7 +3959,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
double *argstack, int &nargstack, int ivar)
{
bigint sx,sxx;
- double value,xvalue,sy,sxy;
+ double value,sy,sxy;
// word not a match to any special function
@@ -4055,7 +4055,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
} else index = 0;
int ifix = modify->find_fix(&args[0][2]);
- if (ifix < 0)
+ if (ifix < 0)
print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
fix = modify->fix[ifix];
if (index == 0 && fix->vector_flag) {
diff --git a/src/velocity.cpp b/src/velocity.cpp
index f83f778f8b15dfecfbd7b755da0fc7dfb19f93d7..3a0b95fb4da91ea6e77d6ff24a012e493137d610 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -410,7 +410,7 @@ void Velocity::create(double t_desired, int seed)
/* ---------------------------------------------------------------------- */
-void Velocity::set(int narg, char **arg)
+void Velocity::set(int /*narg*/, char **arg)
{
int xstyle,ystyle,zstyle,varflag;
double vx,vy,vz;
@@ -579,7 +579,7 @@ void Velocity::set(int narg, char **arg)
rescale velocities of a group after computing its temperature
------------------------------------------------------------------------- */
-void Velocity::scale(int narg, char **arg)
+void Velocity::scale(int /*narg*/, char **arg)
{
double t_desired = force->numeric(FLERR,arg[0]);
@@ -628,7 +628,7 @@ void Velocity::scale(int narg, char **arg)
apply a ramped set of velocities
------------------------------------------------------------------------- */
-void Velocity::ramp(int narg, char **arg)
+void Velocity::ramp(int /*narg*/, char **arg)
{
// set scale factors
@@ -705,7 +705,7 @@ void Velocity::ramp(int narg, char **arg)
zero linear or angular momentum of a group
------------------------------------------------------------------------- */
-void Velocity::zero(int narg, char **arg)
+void Velocity::zero(int /*narg*/, char **arg)
{
if (strcmp(arg[0],"linear") == 0) {
if (rfix < 0) zero_momentum();
diff --git a/src/version.h b/src/version.h
index 2192b25d9147aef94706956d2c16eea09c51e2b9..fbeeabff8d77922d9f4eaafd6aa50c59ae215a61 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "22 Aug 2018"
+#define LAMMPS_VERSION "31 Aug 2018"