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/README b/README
index 784b1cb13ea9abfc852cf790b1ed40c579305619..680986bf6146b9ddc77a092e6dcc6d4c09dd6b8e 100644
--- a/README
+++ b/README
@@ -36,7 +36,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started:
-doc/Manual.html the LAMMPS manual
-doc/Section_intro.html hi-level introduction to LAMMPS
-doc/Section_start.html how to build and use LAMMPS
-doc/Developer.pdf LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html hi-level introduction
+http://lammps.sandia.gov/doc/Build.html how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html # creates HTML pages in doc/html
+% make pdf # creates Manual.pdf and Developer.pdf
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 0d8a4894bd8d014cb44559960a9c89bd73675f03..3ef3e8d7f48d31f1e0e02d748d4482801ef801e7 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -276,11 +276,14 @@ endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
- if(NOT LAPACK_FOUND)
+ find_package(BLAS)
+ if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
set(LAPACK_LIBRARIES linalg)
+ else()
+ list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
endif()
@@ -377,6 +380,9 @@ endif()
if(PKG_LATTE)
option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
if(DOWNLOAD_LATTE)
+ if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+ message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+ endif()
message(STATUS "LATTE not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
@@ -479,6 +485,9 @@ if(PKG_MSCG)
find_package(GSL REQUIRED)
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
if(DOWNLOAD_MSCG)
+ if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+ message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+ endif()
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
@@ -669,7 +678,9 @@ 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
@@ -1002,7 +1013,9 @@ 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()
@@ -1052,6 +1065,7 @@ if(BUILD_EXE)
set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+ install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1)
if(ENABLE_TESTING)
add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
endif()
@@ -1121,7 +1135,7 @@ 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)
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/README.md b/cmake/README.md
index 85375cd2aa49ca9ddb0bc97b0fa50d048a344f4a..21e728c1f02a696ede20bf6fe632200acd05f69e 100644
--- a/cmake/README.md
+++ b/cmake/README.md
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl>
</td>
</tr>
+<tr>
+ <td><code>BUILD_EXE</code></td>
+ <td>control whether to build LAMMPS executable</td>
+ <td>
+ <dl>
+ <dt><code>on</code> (default)</dt>
+ <dt><code>off</code></dt>
+ </dl>
+ </td>
+</tr>
<tr>
<td><code>BUILD_SHARED_LIBS</code></td>
<td>control whether to build LAMMPS as a shared-library</td>
diff --git a/doc/Makefile b/doc/Makefile
index 81f362349950be2123d2da4bd14255e7f9f27739..9069fa1d60dacb7484f54dda7b310e495d0c73ea 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
-.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
# ------------------------------------------
@@ -42,6 +42,8 @@ help:
@echo " old create old-style HTML doc pages in old dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
+ @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
+ @echo " (requires ebook-convert tool from calibre)"
@echo " clean remove all intermediate RST files"
@echo " clean-all reset the entire build environment"
@echo " txt2html build txt2html tool"
@@ -106,6 +108,11 @@ epub: $(OBJECTS)
@rm -rf epub
@echo "Build finished. The ePUB manual file is created."
+mobi: epub
+ @rm -f LAMMPS.mobi
+ @ebook-convert LAMMPS.epub LAMMPS.mobi
+ @echo "Conversion finished. The MOBI manual file is created."
+
pdf: utils/txt2html/txt2html.exe
@(\
set -e; \
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.txt b/doc/src/Build.txt
index 1046171de1c58ecd8c1fc358bc4b598d661ecc38..df30af36f5df45a7621e10f7f3832be49e6e622d 100644
--- a/doc/src/Build.txt
+++ b/doc/src/Build.txt
@@ -28,6 +28,7 @@ as described on the "Install"_Install.html doc page.
Build_settings
Build_package
Build_extras
+ Build_windows
END_RST -->
@@ -39,7 +40,8 @@ END_RST -->
"Basic build options"_Build_basics.html
"Optional build settings"_Build_settings.html
"Include packages in build"_Build_package.html
-"Packages with extra build options"_Build_extras.html :all(b)
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html :all(b)
If you have problems building LAMMPS, it is often due to software
issues on your local machine. If you can, find a local expert to
diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt
index cee78aced3faafce24586e4543d344185500fc7d..6924e7341782e7e782300f4201c988dc4724763f 100644
--- a/doc/src/Build_basics.txt
+++ b/doc/src/Build_basics.txt
@@ -61,7 +61,7 @@ library files. Failing this, these 3 variables can be used to specify
where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
are found, and the name of the library files (MPI_LIB).
-For a serial build, you need to specify the 3 varaibles, as shown
+For a serial build, you need to specify the 3 variables, as shown
above.
For a serial LAMMPS build, use the dummy MPI library provided in
@@ -145,7 +145,7 @@ By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any "accelerator
packages"_Speed_packages.html you have included in the build.
-You can tell CMake to look for a specific compiler with these varaible
+You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the FLAGS variables if you want to
experiment with alternate optimization flags. You should specify all
3 compilers, so that the small number of LAMMPS source files written
@@ -216,8 +216,8 @@ LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the "Howto couple"_Howto_couple.html doc
page for more info on coupling LAMMPS to other codes. See the
-"Python"_Python doc page for more info on wrapping and running LAMMPS
-from Python via its library interface.
+"Python"_Python_head.html doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
[CMake variables]:
@@ -247,7 +247,7 @@ Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
-the lib/packages directroy, since they are always built as shared
+the lib/packages directory, since they are always built as shared
libraries using the -fPIC switch. However, if a library like MPI or
FFTW does not exist as a shared library, the shared library build will
generate an error. This means you will need to install a shared
@@ -299,7 +299,7 @@ Install LAMMPS after a build :h4,link(install)
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
-that you may need super-user priveleges (e.g. sudo) if the directory
+that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
[CMake variable]:
diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt
index c42bb21c7e129d2bca820515331f3c80f0bbbe5b..f8b52056fc1616e1ac84174ddeab7aafb27d91ee 100644
--- a/doc/src/Build_cmake.txt
+++ b/doc/src/Build_cmake.txt
@@ -13,12 +13,10 @@ This page is a short summary of how to use CMake to build LAMMPS.
Details on CMake variables that enable specific LAMMPS build options
are given on the pages linked to from the "Build"_Build.html doc page.
-Richard Berger (Temple U) has also written a more comprehensive guide
+Richard Berger (Temple U) has also written a "more comprehensive
+guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
for how to use CMake to build LAMMPS. If you are new to CMake it is a
-good place to start:
-
-"Bulding LAMMPS using
-CMake"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+good place to start.
:line
@@ -42,7 +40,7 @@ executable called "lmp" and a library called "liblammps.a" in the
If your machine has multiple CPU cores (most do these days), using a
command like "make -jN" (with N being the number of available local
CPU cores) can be much faster. If you plan to do development on
-LAMMPS or need to recompile LAMMPS repeatedly, installation of the
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
ccache (= Compiler Cache) software may speed up compilation even more.
After compilation, you can optionally copy the LAMMPS executable and
@@ -52,7 +50,7 @@ make install # optional, copy LAMMPS executable & library elsewhere :pre
:line
-There are 3 variants of CMake: a command-line verison (cmake), a text mode
+There are 3 variants of CMake: a command-line version (cmake), a text mode
UI version (ccmake), and a graphical GUI version (cmake-GUI). You can use
any of them interchangeably to configure and create the LAMMPS build
environment. On Linux all the versions produce a Makefile as their
@@ -81,8 +79,9 @@ directory to un-install all packages. The purge removes all the *.h
files auto-generated by make.
You must have CMake version 2.8 or later on your system to build
-LAMMPS. If you include the GPU or KOKKOS packages, CMake version 3.2
-or later is required. Installation instructions for CMake are below.
+LAMMPS. A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version. CMake will print a message telling you if a later
+version is required. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from
@@ -189,7 +188,7 @@ module list # is a cmake module already loaded?
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name :pre
-Most Linux distributions offer precompiled cmake packages through
+Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
"https://cmake.org/download/"_https://cmake.org/download/.
diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt
index 6bbf504496006b30daf8652f5275f419686e26ab..088ffd8972f3d8b5228ab73c454b03558fd7f9bd 100644
--- a/doc/src/Build_extras.txt
+++ b/doc/src/Build_extras.txt
@@ -48,7 +48,7 @@ This is the list of packages that may require additional steps.
"USER-QMMM"_#user-qmmm,
"USER-QUIP"_#user-quip,
"USER-SMD"_#user-smd,
-"USER-VTK"_#user-vtk :tb(c=6,ea=c)
+"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
:line
@@ -175,8 +175,15 @@ package?" page.
[CMake build]:
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path # path to KIM shared library (only needed if a custom location)
--D KIM_INCLUDE_DIR=path # path to KIM include directory (only needed if a custom location) :pre
+-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
+-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
+inside the CMake build directory. If the KIM library is already on
+your system (in a location CMake cannot find it), KIM_LIBRARY is the
+filename (plus path) of the KIM library file, not the directory the
+library file is in. KIM_INCLUDE_DIR is the directory the KIM include
+file is in.
[Traditional make]:
@@ -296,7 +303,13 @@ library.
[CMake build]:
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
--D LATTE_LIBRARY=path # path to LATTE shared library (only needed if a custom location) :pre
+-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) :pre
+
+If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and
+built inside the CMake build directory. If the LATTE library is
+already on your system (in a location CMake cannot find it),
+LATTE_LIBRARY is the filename (plus path) of the LATTE library file,
+not the directory the library file is in.
[Traditional make]:
@@ -327,7 +340,7 @@ NOTE: the use of the MEAM package is discouraged, as it has been
superseded by the USER-MEAMC package, which is a direct translation of
the Fortran code in the MEAM library to C++. The code in USER-MEAMC
should be functionally equivalent to the MEAM package, fully supports
-use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
+use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does
not), and has optimizations that make it significantly faster than the
MEAM package.
@@ -371,8 +384,15 @@ lib/mscg/README and MSCG/Install files for more details.
[CMake build]:
-D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes
--D MSCG_LIBRARY=path # path to MSCG shared library (only needed if a custom location)
--D MSCG_INCLUDE_DIR=path # path to MSCG include directory (only needed if a custom location) :pre
+-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location)
+-D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
+inside the CMake build directory. If the MSCG library is already on
+your system (in a location CMake cannot find it), MSCG_LIBRARY is the
+filename (plus path) of the MSCG library file, not the directory the
+library file is in. MSCG_INCLUDE_DIR is the directory the MSCG
+include file is in.
[Traditional make]:
@@ -450,7 +470,7 @@ lib/python/README for more details.
-D PYTHON_EXECUTABLE=path # path to Python executable to use :pre
-Without this setting, CMake will ues the default Python on your
+Without this setting, CMake will guess the default Python on your
system. To use a different Python version, you can either create a
virtualenv, activate it and then run cmake. Or you can set the
PYTHON_EXECUTABLE variable to specify which Python interpreter should
@@ -515,8 +535,15 @@ library"_voro_home.
[CMake build]:
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
--D VORO_LIBRARY=path # (only needed if at custom location) path to VORO shared library
--D VORO_INCLUDE_DIR=path # (only needed if at custom location) path to VORO include directory :pre
+-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
+-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
+built inside the CMake build directory. If the Voro++ library is
+already on your system (in a location CMake cannot find it),
+VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in. VORO_INCLUDE_DIR is the
+directory the Voro++ include file is in.
[Traditional make]:
@@ -660,7 +687,7 @@ the HDF5 library.
No additional settings are needed besides "-D PKG_USER-H5MD=yes".
-This should autodetect the H5MD library on your system. Several
+This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is
installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user
@@ -750,7 +777,7 @@ on your system.
No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
-This should autodetect the NETCDF library if it is installed on your
+This should auto-detect the NETCDF library if it is installed on your
system at standard locations. Several advanced CMake NETCDF options
exist if you need to specify where it was installed. Use the ccmake
(terminal window) or cmake-gui (graphical) tools to see these options
@@ -877,7 +904,10 @@ Eigen3 is a template library, so you do not need to build it.
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) :pre
-Set EIGEN3_INCLUDE_DIR if CMake cannot find the Eigen3 library.
+If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
+inside the CMake build directory. If the Eigen3 library is already on
+your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
+is the directory the Eigen3++ include file is in.
[Traditional make]:
@@ -906,7 +936,7 @@ your system.
No additional settings are needed besides "-D PKG_USER-VTK=yes".
-This should autodetect the VTK library if it is installed on your
+This should auto-detect the VTK library if it is installed on your
system at standard locations. Several advanced VTK options exist if
you need to specify where it was installed. Use the ccmake (terminal
window) or cmake-gui (graphical) tools to see these options and set
diff --git a/doc/src/Build_make.txt b/doc/src/Build_make.txt
index c00ce1f4208ba04a8517b98a9128cb63e886ef8b..ad18695e46245686444a8ae5d3e8ec7728a1d64b 100644
--- a/doc/src/Build_make.txt
+++ b/doc/src/Build_make.txt
@@ -35,16 +35,16 @@ This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
-do development on LAMMPS or need to recompile LAMMPS repeatedly, the
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
-uninstalling packages), you must recompile and relink the LAMMPS
+uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
-recompiled.
+re-compiled.
NOTE: When you build LAMMPS for the first time, a long list of *.d
files will be printed out rapidly. This is not an error; it is the
@@ -71,8 +71,8 @@ Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags
for optimized performance. Please note, however, that some of these
customized machine Makefile are contributed by users. Since both
-compilers, OS configs, and LAMMPS itself keep changing, their settings
-may become outdated:
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt
index 0c7d1917de3085452f3a933cef39967adca5c6ea..4f71e9eb18067d4ef3210aada08a8722e38e8687 100644
--- a/doc/src/Build_package.txt
+++ b/doc/src/Build_package.txt
@@ -59,7 +59,7 @@ packages:
"USER-QMMM"_Build_extras.html#user-qmmm,
"USER-QUIP"_Build_extras.html#user-quip,
"USER-SMD"_Build_extras.html#user-smd,
-"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c)
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
The mechanism for including packages is simple but different for CMake
versus make.
diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt
index 773217e3a0e205f4d818c349f7a96b09d7526eba..500130ecee81ba7622fe5e6851509e57ef98e56f 100644
--- a/doc/src/Build_settings.txt
+++ b/doc/src/Build_settings.txt
@@ -80,8 +80,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run using the "kspace_style
-pppm"_kspace_style.html command. The "Run output"_doc page gives more
-details.
+pppm"_kspace_style.html command. The "Run output"_Run_output.html
+doc page gives more details.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
@@ -101,7 +101,7 @@ Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
-4-byte floats. Double precesion means they are 8-byte doubles. Note
+4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the -DFFT_SINGLE
@@ -193,7 +193,7 @@ Output of JPG, PNG, and movie files :h4,link(graphics)
The "dump image"_dump_image.html command has options to output JPEG or
PNG image files. Likewise the "dump movie"_dump_image.html command
-ouputs movie files in MPEG format. Using these options requires the
+outputs movie files in MPEG format. Using these options requires the
following settings:
[CMake variables]:
@@ -206,7 +206,7 @@ following settings:
# default = yes if CMake can find ffmpeg, else no :pre
Usually these settings are all that is needed. If CMake cannot find
-the graphics header, library, executuable files, you can set these
+the graphics header, library, executable files, you can set these
variables:
-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file
diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0caad589fb4497938797092297e41dbc4fbc6ac2
--- /dev/null
+++ b/doc/src/Build_windows.txt
@@ -0,0 +1,97 @@
+"Higher level section"_Build.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
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines. The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers). If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin. If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows. There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers. We instead rely on the feedback of the users
+of these pre-compiled LAMMPS packages for Windows. We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.
diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt
index 13db1272b928e558ceda0853df22162945e6c6e5..aec5a9db8b726453d16a36211fd54eddf7b35754 100644
--- a/doc/src/Commands_all.txt
+++ b/doc/src/Commands_all.txt
@@ -19,7 +19,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
All commands :h3
-An alphabetic list of all LAMMPS commmands.
+An alphabetic list of all LAMMPS commands.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 48069d3120048e9d59ead6a3f2959be296d078de..0cf433d53a5bef331c65654a97d76eb2f7347796 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -95,7 +95,7 @@ OPT.
"helix (o)"_dihedral_helix.html,
"multi/harmonic (o)"_dihedral_multi_harmonic.html,
"nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.htm;,
+"opls (iko)"_dihedral_opls.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
"table (o)"_dihedral_table.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/Commands_parse.txt b/doc/src/Commands_parse.txt
index cbe2261986bb8f8f96089dac3dff3a03dc39dd42..1d7c754fa718a8a4b38e8a04c2cd657c7d704a90 100644
--- a/doc/src/Commands_parse.txt
+++ b/doc/src/Commands_parse.txt
@@ -14,7 +14,7 @@ LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
-Here are 6 rulse for how each line in the input script is parsed by
+Here are 6 rules for how each line in the input script is parsed by
LAMMPS:
(1) If the last printable character on the line is a "&" character,
@@ -71,7 +71,7 @@ floating-point value. The format string is used to output the result
of the variable expression evaluation. If a format string is not
specified a high-precision "%.20g" is used as the default.
-This can be useful for formatting print output to a desired precion:
+This can be useful for formatting print output to a desired precision:
print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
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/Errors_messages.txt b/doc/src/Errors_messages.txt
index d279b5e9758c0366169abb962e3d27b9fddaa56e..a74182967cc7f49987f0256c7427ded847dd5985 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -743,7 +743,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
-{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and recompile)} :dt
+{Cannot (yet) use single precision with MSM (remove -DFFT_SINGLE from Makefile and re-compile)} :dt
Single precision cannot be used with MSM. :dd
@@ -5078,7 +5078,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/point requires atom attribute q} :dt
@@ -5092,7 +5092,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/shielded requires atom attribute q} :dt
@@ -5110,7 +5110,7 @@ Self-explanatory. :dd
Occurs when number of neighbor atoms for an atom increased too much
during a run. Increase SAFE_ZONE and MIN_CAP in fix_qeq.h and
-recompile. :dd
+re-compile. :dd
{Fix qeq/slater requires atom attribute q} :dt
@@ -5541,7 +5541,7 @@ See the package gpu command. :dd
{GPUs are requested but Kokkos has not been compiled for CUDA} :dt
-Recompile Kokkos with CUDA support to use GPUs. :dd
+Re-compile Kokkos with CUDA support to use GPUs. :dd
{Ghost velocity forward comm not yet implemented with Kokkos} :dt
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index dd3402ba8641c487f1a6a4210fa27f1b6ae062ff..98b66f2aa569040bea2ea260b3cb37ddd84764f2 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -13,7 +13,7 @@ This is an alphabetic list of the WARNING messages LAMMPS prints out
and the reason why. If the explanation here is not sufficient, the
documentation for the offending command may help. Warning messages
also list the source file and line number where the warning was
-generated. For example, a message lile this:
+generated. For example, a message like this:
WARNING: Bond atom missing in box size check (domain.cpp:187) :pre
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index fc7329aad5846382382bf1e112bece67570c45d6..438ea561a10f9fa87f0e119aedd26bdbd13e89dd 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -8,27 +8,44 @@ Section"_Examples.html :c
:line
-How to discussions :h2
+Howto discussions :h2
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
"glossary"_http://lammps.sandia.gov website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.
-
-The example input scripts included in the examples dir of the LAMMPS
+terminology with links to corresponding LAMMPS manual pages. The
+example input scripts included in the examples dir of the LAMMPS
distribution and highlighted on the "Examples"_Examples.html doc page
also show how to setup and run various kinds of simulations.
+Tutorials howto :h3
+
<!-- RST
.. toctree::
+ :name: tutorials
:maxdepth: 1
Howto_github
Howto_pylammps
Howto_bash
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+General howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: general
:maxdepth: 1
Howto_restart
@@ -38,35 +55,86 @@ also show how to setup and run various kinds of simulations.
Howto_library
Howto_couple
-.. toctree::
- :maxdepth: 1
+END_RST -->
- Howto_output
- Howto_chunk
+<!-- HTML_ONLY -->
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"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)
+
+<!-- END_HTML_ONLY -->
+
+Settings howto :h3
+
+<!-- RST
.. toctree::
+ :name: settings
:maxdepth: 1
Howto_2d
Howto_triclinic
+ Howto_thermostat
+ Howto_barostat
Howto_walls
Howto_nemd
- Howto_granular
- Howto_spherical
Howto_dispersion
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+
+Analysis howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: analysis
:maxdepth: 1
+ Howto_output
+ Howto_chunk
Howto_temperature
- Howto_thermostat
- Howto_barostat
Howto_elastic
Howto_kappa
Howto_viscosity
Howto_diffusion
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+"Calculate temperature"_Howto_temperature.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Force fields howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: force
:maxdepth: 1
Howto_bioFF
@@ -74,9 +142,27 @@ also show how to setup and run various kinds of simulations.
Howto_tip4p
Howto_spc
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Packages howto :h3
+
+<!-- RST
+
.. toctree::
+ :name: packages
:maxdepth: 1
+ Howto_spherical
+ Howto_granular
Howto_body
Howto_polarizable
Howto_coreshell
@@ -87,43 +173,11 @@ also show how to setup and run various kinds of simulations.
END_RST -->
-<!-- HTML_ONLY -->
-
-"Using GitHub with LAMMPS"_Howto_github.html
-"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
-
-"Restart a simulation"_Howto_restart.html
-"Visualize LAMMPS snapshots"_Howto_viz.html
-"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)
-"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
-"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+<!-- HTML_ONLY -->
-"2d simulations"_Howto_2d.html
-"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
-"Walls"_Howto_walls.html
-"NEMD simulations"_Howto_nemd.html
-"Granular models"_Howto_granular.html
"Finite-size spherical and aspherical particles"_Howto_spherical.html
-"Long-range dispersion settings"_Howto_dispersion.html :all(b)
-
-"Calculate temperature"_Howto_temperature.html
-"Thermostats"_Howto_thermostat.html
-"Barostats"_Howto_barostat.html
-"Calculate elastic constants"_Howto_elastic.html
-"Calculate thermal conductivity"_Howto_kappa.html
-"Calculate viscosity"_Howto_viscosity.html
-"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
-
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
-"TIP3P water model"_Howto_tip3p.html
-"TIP4P water model"_Howto_tip4p.html
-"SPC water model"_Howto_spc.html :all(b)
-
+"Granular models"_Howto_granular.html
"Body style particles"_Howto_body.html
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt
index 7c3db891524379f49fe38134186764e07eeff959..33233346006d2d2d7b25d04baeb01311d77e5a30 100644
--- a/doc/src/Howto_barostat.txt
+++ b/doc/src/Howto_barostat.txt
@@ -64,11 +64,11 @@ Thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes pressure
values. As explained on the doc page for the
"thermo_style"_thermo_style.html command, the default pressure is
-setup by the thermo command itself. It is NOT the presure associated
+setup by the thermo command itself. It is NOT the pressure associated
with any barostatting fix you have defined or with any compute you
-have defined that calculates a presure. The doc pages for the
+have defined that calculates a pressure. The doc pages for the
barostatting fixes explain the ID of the pressure compute they create.
-Thus if you want to view these pressurse, you need to specify them
+Thus if you want to view these pressures, you need to specify them
explicitly via the "thermo_style custom"_thermo_style.html command.
Or you can use the "thermo_modify"_thermo_modify.html command to
re-define what pressure compute is used for default thermodynamic
diff --git a/doc/src/Howto_body.txt b/doc/src/Howto_body.txt
index 3535349b461589aa6ddafdf4e9a3d684a546c2e1..3e7db9bc8e4b735ad93014b8a86a8c7b2ffe3bc4 100644
--- a/doc/src/Howto_body.txt
+++ b/doc/src/Howto_body.txt
@@ -337,7 +337,7 @@ the sphere that surrounds each vertex. The diameter value can be
different for each body particle. These floating-point values can be
listed on as many lines as you wish; see the
"read_data"_read_data.html command for more details. Because the
-maxmimum vertices per face is hard-coded to be 4
+maximum number of vertices per face is hard-coded to be 4
(i.e. quadrilaterals), faces with more than 4 vertices need to be
split into triangles or quadrilaterals. For triangular faces, the
last vertex index should be set to -1.
diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt
index 401c1e359c05ee83ef37ecbae44073cdd4ecfacf..6c920c9bc3da9463589362805d5e46592996ffe4 100644
--- a/doc/src/Howto_diffusion.txt
+++ b/doc/src/Howto_diffusion.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Calculate a diffusion coefficient :h3
+Calculate diffusion coefficients :h3
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt
index 4ea286258e11a38aa07e6e93df4c3e22cb0aca0a..8a5953d84dbf692bddb7be8b58a86a2680aea526 100644
--- a/doc/src/Howto_dispersion.txt
+++ b/doc/src/Howto_dispersion.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Long-raage dispersion settings :h3
+Long-range dispersion settings :h3
The PPPM method computes interactions by splitting the pair potential
into two parts, one of which is computed in a normal pairwise fashion,
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index 741078e7eb7cb74a574c0e0bada4cca4414cce89..9a9656784ce7e81b5d82e0e74f029b605ac122bc 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -171,16 +171,16 @@ void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
+same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
-resulting vector is not ordered by atom ID. Atom IDs can be requetsed
+resulting vector is not ordered by atom ID. Atom IDs can be requested
by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt
index 8be4b66e78a511b404987929d247ce3836a40086..a12bf13f2e9ca2914012b1121cc0951b282bcbcc 100644
--- a/doc/src/Howto_pylammps.txt
+++ b/doc/src/Howto_pylammps.txt
@@ -73,7 +73,7 @@ that package into your current Python installation.
cd $LAMMPS_DIR/python
python install.py :pre
-NOTE: Recompiling the shared library requires reinstalling the Python package
+NOTE: Recompiling the shared library requires re-installing the Python package
Installation inside of a virtualenv :h5
diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt
index 1e737df655462c2fc0e1059ac7bc56ecdb120287..4dfe4e2f6c88eab104e813e0051138c25434b4ef 100644
--- a/doc/src/Howto_spherical.txt
+++ b/doc/src/Howto_spherical.txt
@@ -159,7 +159,7 @@ ellipsoidal particles:
The advantage of these fixes is that those which thermostat the
particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting. The "fix langevin"_fix_langevin
+calculation and thermostatting. The "fix langevin"_fix_langevin.html
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
ellipsoidal particles. Other thermostatting fixes only operate on the
diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt
index 1b9adb49a5701789dafc9f86cebc23a87623411c..b549f99be2f2e8d27c0d54eb251cd9ab31105e78 100644
--- a/doc/src/Howto_spins.txt
+++ b/doc/src/Howto_spins.txt
@@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Magnetic spins :h3
-The magnetic spin simualtions are enabled by the SPIN package, whose
+The magnetic spin simulations are enabled by the SPIN package, whose
implementation is detailed in "Tranchida"_#Tranchida7.
-The model representents the simulation of atomic magnetic spins coupled
+The model represents the simulation of atomic magnetic spins coupled
to lattice vibrations. The dynamics of those magnetic spins can be used
to simulate a broad range a phenomena related to magneto-elasticity, or
or to study the influence of defects on the magnetic properties of
@@ -43,7 +43,7 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
-All the computed magnetic properties can be outputed by two main
+All the computed magnetic properties can be output by two main
commands. The first one is "compute spin"_compute_spin.html, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
index 8a9e262da1b071abde5ab8b6957addba8444b718..896cc96a403a2555b9aceb1cb7da90793d9a909a 100644
--- a/doc/src/Howto_temperature.txt
+++ b/doc/src/Howto_temperature.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-Calcalate temperature :h3
+Calculate temperature :h3
Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
diff --git a/doc/src/Install_patch.txt b/doc/src/Install_patch.txt
index 3d0b27370e1285e293f247e02c7a4fac0c24c630..ff9b14c12c162dcd9112fde9298d18f5370e3220 100644
--- a/doc/src/Install_patch.txt
+++ b/doc/src/Install_patch.txt
@@ -17,10 +17,11 @@ how to stay current are on the "Install git"_Install_git.html and
If you prefer to download a tarball, as described on the "Install
git"_Install_tarball.html doc page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
-a patch file is posted on the "bug and feature page"_bug of the
-website, along with a list of changed files and details about what is
-in the new patch release. This page explains how to apply the patch
-file to your local LAMMPS directory.
+a patch file is posted on the "bug and feature
+page"_http://lammps.sandia.gov/bug.html of the LAMMPS website, along
+with a list of changed files and details about what is in the new patch
+release. This page explains how to apply the patch file to your local
+LAMMPS directory.
NOTE: You should not apply patch files to a local Git or SVN repo of
LAMMPS, only to an unpacked tarball. Use Git and SVN commands to
diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt
index 5d9efb30775e4d5d510a6e633a9f62a12adea409..b909265a3eebc70abdcbbb8a439fa319589a8346 100644
--- a/doc/src/Intro_authors.txt
+++ b/doc/src/Intro_authors.txt
@@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
:line
-LAMMPS authors :h3
+Authors of LAMMPS :h3
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
@@ -15,7 +15,8 @@ University:
"Steve Plimpton"_sjp, sjplimp at sandia.gov
Aidan Thompson, athomps at sandia.gov
Stan Moore, stamoor at sandia.gov
-Axel Kohlmeyer, akohlmey at gmail.com :ul
+Axel Kohlmeyer, akohlmey at gmail.com
+Richard Berger, richard.berger at temple.edu :ul
:link(sjp,http://www.cs.sandia.gov/~sjplimp)
@@ -24,26 +25,31 @@ and Ray Shan, now at Materials Design.
:line
-The following folks are responsible for significant contributions to
-the code, or other aspects of the LAMMPS development effort. Many of
-the packages they have written are somewhat unique to LAMMPS and the
-code would not be as general-purpose as it is without their expertise
-and efforts.
+The "Authors page"_http://lammps.sandia.gov/authors.html of the
+"LAMMPS website"_lws has a comprehensive list of all the individuals
+who have contributed code for a new feature or command or tool to
+LAMMPS.
-Richard Berger (Temple U), Python interface, GitHub site, Sphinx doc pages
+:line
+
+The following folks deserve special recognition. Many of the packages
+they have written are unique for an MD code and LAMMPS would not be as
+general-purpose as it is without their expertise and efforts.
+
+Metin Aktulga (MSU), USER-REAXC package for C version of ReaxFF
+Mike Brown (Intel), GPU and USER-INTEL packages
+Colin Denniston (U Western Ontario), USER-LB package
+Georg Ganzenmuller (EMI), USER-SMD and USER-SPH packages
+Andres Jaramillo-Botero (Caltech), USER-EFF package for electron force field
+Reese Jones (Sandia) and colleagues, USER-ATC package for atom/continuum coupling
+Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
+Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
+Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
+Mike Parks (Sandia), PERI package for Peridynamics
Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages
-Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
-Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
-Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
-Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
-Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
-Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
-Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
-Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
-Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
+Christian Trott (Sandia), USER-CUDA and KOKKOS packages
+Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD
+Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul
:line
@@ -58,322 +64,3 @@ Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
Steve Lustig (Dupont)
Jim Belak and Roy Pollock (LLNL) :ul
-:line
-
-Here is a timeline for when various individuals contributed to a new
-feature or command or tool added to LAMMPS:
-
-Aug18 : CMake build option for LAMMPS : Christoph Junghans (LANL), Richard Berger, and Axel Kohlmeyer (Temple U)
-Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U)
-Jun18 : SPIN package : Julien Tranchida (Sandia and CEA)
-Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland)
-May18 : fix bond/react : Jake Gissinger (CU Boulder)
-Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U)
-Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U)
-Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg)
-Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum)
-Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil)
-Dec17 : fix python/move : Richard Berger (Temple U)
-Nov17 : pair extep : Jaap Kroes (Radboud U)
-Oct17 : USER-UEF package : David Nicholson (MIT)
-Oct17 : fix rhok : Ulf Pederson (Roskilde U)
-Oct17 : bond gromos : Axel Kohlmeyer (Temple U)
-Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu
-Sep17 : fix latte : Christian Negre (LANL)
-Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU)
-Aug17 : USER-MESO package : Zhen Li (Brown University)
-Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U)
-Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University)
-Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U)
-Jun17 : pair vashishita/gpu : Anders Hafreager (UiO)
-Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U)
-Jun17 : compute cnp/atom : Paulo Branicio (USC)
-May17 : fix python and pair python : Richard Berger (Temple U)
-May17 : pair edip/multi : Chao Jiang (U Wisconsin)
-May17 : pair gw and gw/zbl : German Samolyuk (ORNL)
-Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U)
-Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU)
-Mar17 : fix filter/corotate : Lukas Fath (KIT)
-Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit)
-Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design)
-Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh)
-Jan17 : fix mscg : Lauren Abbott (Sandia)
-Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU)
-Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu
-Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University)
-Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano
-Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia)
-Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia)
-Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC)
-Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London)
-Sep16 : pair vashishta/table : Anders Hafreager (U Oslo)
-Sep16 : kspace pppm/kk : Stan Moore (Sandia)
-Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado)
-Aug16 : fix controller : Aidan Thompson (Sandia)
-Jul16 : dipole integration by DLM method : Iain Bethune (EPCC)
-Jul16 : dihedral spherical : Andrew Jewett
-Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia)
-Jun16 : fix orient/bcc : Tegar Wicaksono (UBC)
-Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge)
-Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC)
-May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : write_coeff : Axel Kohlmeyer (Temple U)
-Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U)
-Apr16 : bond write : Axel Kohlmeyer (Temple U)
-Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands)
-Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU)
-Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing)
-Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen
-Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL)
-Dec15 : fix qeq/fire : Ray Shan (Sandia)
-Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University)
-Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple)
-Nov15 : compute hexorder/atom : Aidan Thompson (Sandia)
-Oct15 : displace_atoms variable option : Reese Jones (Sandia)
-Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL)
-Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS)
-Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading)
-Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU)
-Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U)
-Aug15 : timer command : Axel Kohlmeyer (Temple U)
-Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven)
-Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U)
-Aug15 : USER-SMD package : Georg Gunzenmueller (EMI)
-Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU)
-Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton)
-Jul15 : pair_modify special : Axel Kohlmeyer (Temple U)
-Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia)
-Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS)
-Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U)
-Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL)
-Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U)
-Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich)
-Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge)
-Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia)
-Feb15 : fix tfmc : Kristof Bal (U of Antwerp)
-Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS)
-Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia)
-Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago)
-Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL)
-Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF)
-Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College)
-Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia)
-Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators
-Aug14 : USER-INTEL package : Mike Brown (Intel)
-May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia)
-May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand)
-Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL)
-Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U)
-Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM)
-Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U)
-Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA)
-Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM)
-Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario)
-Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley)
-Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida)
-Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U)
-Sep13 : xmgrace tool : Vikas Varshney
-Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia)
-Aug13 : pair nm and variants : Julien Devemy (ICCF)
-Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia)
-Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio)
-Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS)
-Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State)
-Jul13 : polybond tool : Zachary Kraus (Georgia Tech)
-Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia)
-Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia)
-Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia)
-Jun13 : fix tune/kspace : Paul Crozier (Sandia)
-Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF)
-May13 : compute msd/nongauss : Rob Hoy
-May13 : pair list : Axel Kohlmeyer (Temple U)
-May13 : triclinic support for long-range solvers : Stan Moore (Sandia)
-Apr13 : dump_modify nfile and fileper : Christopher Knight
-Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University)
-Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University)
-Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona)
-Feb13 : fix species : Ray Shan (Sandia)
-Jan13 : compute voronoi/atom : Daniel Schwen
-Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame)
-Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL)
-Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics)
-Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics)
-Oct12 : improper_style fourier : Loukas Peristeras (Scienomics)
-Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University)
-Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB)
-Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL)
-Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia)
-Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL)
-Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville)
-Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia)
-Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia)
-Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple)
-Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple)
-May12 : read_dump : Tim Sirk (ARL)
-May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens)
-May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology)
-Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU)
-Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU)
-Feb12 : minimize forcezero linesearch : Asad Hasan (CMU)
-Feb12 : pair_style beck : Jon Zimmerman (Sandia)
-Feb12 : pair_style meam/spline : Alex Stukowski (LLNL)
-Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn)
-Jan12 : dihedral_style table : Andrew Jewett (UCSB)
-Jan12 : angle_style dipole : Mario Orsi
-Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia)
-Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia)
-Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL)
-Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago)
-Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR)
-Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia)
-Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC)
-Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U)
-Sep11 : pair_style edip : Luca Ferraro (CASPUR)
-Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany)
-Aug11 : fix restrain : Craig Tenney (Sandia)
-Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau)
-Aug11 : pair_style lj/sf : Laurent Joly (U Lyon)
-Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg
-Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg
-Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg
-Aug11 : pair_style dipole/sf : Mario Orsi
-Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon)
-Aug11 : FFT support via FFTW3, MKL, ACML, KISS FFT libraries : \
- Axel Kohlmeyer (Temple U)
-Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \
- Chandra Veer Singh (Cornell)
-Jun11 : Windows build option via Microsoft Visual Studio : \
- Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia)
-Jun11 : dump image : Nathan Fabian (Sandia)
-May11 : pppm GPU single and double : Mike Brown (ORNL)
-May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA)
-2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL)
-- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech)
-- : fix adapt and compute ti for thermodynamic integration for \
- free energies : Sai Jayaraman (Sandia)
-- : pair_style born and gauss : Sai Jayaraman (Sandia)
-- : stochastic rotation dynamics (SRD) via fix srd : \
- Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF)
-- : ipp Perl script tool : Reese Jones (Sandia)
-- : eam_database and createatoms tools : Xiaowang Zhou (Sandia)
-- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech)
-- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia)
-- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida)
-- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \
- Paul Saxe (Materials Design) and Reese Jones (Sandia)
-- : pair_style peri/lps : Mike Parks (Sandia)
-- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford)
-- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U)
-- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan)
-- : public SVN & Git repositories for LAMMPS : \
- Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia)
-- : compute heat/flux : German Samolyuk (ORNL) and \
- Mario Pinto (Computational Research Lab, Pune, India)
-- : pair_style yukawa/colloid : Randy Schunk (Sandia)
-- : fix wall/colloid : Jeremy Lechman (Sandia)
-2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ)
-- : concentration-dependent EAM potential : \
- Alexander Stukowski (Technical University of Darmstadt)
-- : parallel replica dymamics (PRD) : Mike Brown (Sandia)
-- : min_style hftn : Todd Plantenga (Sandia)
-- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia)
-- : dump cfg : Liang Wan (Chinese Academy of Sciences)
-- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland)
-- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia)
-- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo
-- : fix langevin tally : Carolyn Phillips (U Michigan)
-- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \
- Philip Howell (Siemens), Vikas Varsney (AFRL)
-- : region cone : Pim Schravendijk
-- : pair_style born/coul/long : Ahmed Ismail (Sandia)
-- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
-- : fix box/relax : Aidan Thompson and David Olmsted (Sandia)
-- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
-- : compute cna/atom : Liang Wan (Chinese Academy of Sciences)
-2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U)
-- : peridynamics : Mike Parks (Sandia)
-- : fix smd for steered MD : Axel Kohlmeyer (U Penn)
-- : GROMACS pair potentials : Mark Stevens (Sandia)
-- : lmp2vmd tool : Axel Kohlmeyer (U Penn)
-- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn)
-- : cosine/delta angle potential : Axel Kohlmeyer (U Penn)
-- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain
-- : pair_style lubricate : Randy Schunk (Sandia)
-- : compute ackland/atom : Gerolf Ziegenhain
-- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \
- Pieter in 't Veld (Sandia)
-- : AI-REBO bond-order potential : Ase Henry (MIT)
-- : making LAMMPS a true "object" that can be instantiated \
- multiple times, e.g. as a library : Ben FrantzDale (RPI)
-- : pymol_asphere viz tool : Mike Brown (Sandia)
-2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia)
-- : tensile and shear deformations : Pieter in 't Veld (Sandia)
-- : GayBerne potential : Mike Brown (Sandia)
-- : ellipsoidal particles : Mike Brown (Sandia)
-- : colloid potentials : Pieter in 't Veld (Sandia)
-- : fix heat : Paul Crozier and Ed Webb (Sandia)
-- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia)
-- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue)
-- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia)
-- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB)
-- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia)
-- : MEAM potential : Greg Wagner (Sandia)
-- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \
- James Fischer (High Performance Technologies), \
- David Richie and Vincent Natoli (Stone Ridge Technologies)
-2006 : fix wall/lj126 : Mark Stevens (Sandia)
-- : Stillinger-Weber and Tersoff potentials : \
- Aidan Thompson and Xiaowang Zhou (Sandia)
-- : region prism : Pieter in 't Veld (Sandia)
-- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : OPLS dihedral potential: Mark Stevens (Sandia)
-- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI)
-- : faster pair hybrid potential: James Fischer \
- (High Performance Technologies, Inc), Vincent Natoli and \
- David Richie (Stone Ridge Technology)
-- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia)
-- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U)
-- : grain boundary orientation fix : Koenraad Janssens and \
- David Olmsted (Sandia)
-- : pair_style lj/smooth potential : Craig Maloney (UCSB)
-- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \
- (Johns Hopkins U) and Paul Crozier (Sandia)
-- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea)
-- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U)
-- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \
- Mark Stevens (Sandia)
-- : Finnis/Sinclair EAM: Tim Lau (MIT)
-- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \
- Frank van Swol (Sandia)
-- : TIP4P potential (4-site water): Ahmed Ismail and \
- Amalie Frischknecht (Sandia)
-2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute)
-- : compressed dump files: Erik Luijten (U Illinois)
-- : cylindrical indenter fix: Ravi Agrawal (Northwestern U)
-- : electric field fix: Christina Payne (Vanderbilt U)
-- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \
- Vikas Varshney (U Akron)
-- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia)
-- : Morse bond potential: Jeff Greathouse (Sandia)
-- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
-- : force tables for long-range Coulombics: Paul Crozier (Sandia)
-2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
- Christian Burisch (Bochum University, Germany)
-- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
-- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
- Andrey Kalinichev (Sandia)
-- : parallel tempering: Mark Sears (Sandia)
-earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
-- : multi-harmonic dihedral potential: Mathias Putz (Sandia)
-- : embedded atom method (EAM) potential: Stephen Foiles (Sandia)
-- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray)
-- : HTFN energy minimizer: Todd Plantenga (Sandia)
-- : class 2 force fields: Eric Simon (Cray)
-- : NVT/NPT integrators: Mark Stevens (Sandia)
-- : rRESPA: Mark Stevens & Paul Crozier (Sandia)
-- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c)
diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt
index 49c14bc5f06d463037d294d28873b43fdf6c7f14..cd822c778f29db10193966d27b7f7f0cada6392d 100644
--- a/doc/src/Intro_overview.txt
+++ b/doc/src/Intro_overview.txt
@@ -17,7 +17,7 @@ variety of interatomic potentials (force fields) and boundary
conditions. It can model 2d or 3d systems with only a few particles
up to millions or billions.
-LAMMPS can be built and run on a laptop or destop machine, but is
+LAMMPS can be built and run on a laptop or desktop machine, but is
designed for parallel computers. It will run on any parallel machine
that supports the "MPI"_mpi message-passing library. This includes
shared-memory boxes and distributed-memory clusters and
@@ -45,7 +45,7 @@ nature; some long-range models are included as well.
LAMMPS uses neighbor lists to keep track of nearby particles. The
lists are optimized for systems with particles that are repulsive at
short distances, so that the local density of particles never becomes
-too large. This is in contrast to methods used for modeling plasmas
+too large. This is in contrast to methods used for modeling plasma
or gravitational bodies (e.g. galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques to
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 30e186410657b0770183fd160d2769b44be58d5c..ad3e66a4b27b93645e0f7ed4b2ec628e160597b9 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="16 Aug 2018 version">
+<META NAME="docnumber" CONTENT="22 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
-16 Aug 2018 version :c,h2
+22 Aug 2018 version :c,h2
"What is a LAMMPS version?"_Manual_version.html
@@ -66,7 +66,7 @@ every LAMMPS command.
.. toctree::
:maxdepth: 2
- :numbered:
+ :numbered: 3
:caption: User Documentation
:name: userdoc
:includehidden:
diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt
index 747a55a7296d0ab206c0119ecb7a85dd5e8e7a36..ac12dd7b2ed3da973c726b6d4ded6a68745fb34e 100644
--- a/doc/src/Manual_build.txt
+++ b/doc/src/Manual_build.txt
@@ -10,15 +10,16 @@ Section"_Manual.html :c
Building the LAMMPS manual :h2
-Depending on how you obtained LAMMPS, the doc directory has
-2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
+Depending on how you obtained LAMMPS, the doc directory has 2 or 3
+sub-directories and optionally 2 PDF files and 2 e-book format files:
src # content files for LAMMPS documentation
html # HTML version of the LAMMPS manual (see html/Manual.html)
tools # tools and settings for building the documentation
Manual.pdf # large PDF version of entire manual
Developer.pdf # small PDF with info about how LAMMPS is structured
-LAMMPS.epub # Manual in ePUB format :pre
+LAMMPS.epub # Manual in ePUB e-book format
+LAMMPS.mobi # Manual in MOBI e-book format :pre
If you downloaded LAMMPS as a tarball from the web site, all these
directories and files should be included.
@@ -40,7 +41,7 @@ HTML files already exist. This requires various tools including
Sphinx, which the build process will attempt to download and install
on your system, if not already available. See more details below.
-(c) You can genererate an older, simpler, less-fancy style of HTML
+(c) You can generate an older, simpler, less-fancy style of HTML
documentation by typing "make old". This will create an "old"
directory. This can be useful if (b) does not work on your box for
some reason, or you want to quickly view the HTML version of a doc
@@ -61,6 +62,7 @@ make old # generate old-style HTML pages in old dir via txt2html
make fetch # fetch HTML doc pages and 2 PDF files from web site
# as a tarball and unpack into html dir and 2 PDFs
make epub # generate LAMMPS.epub in ePUB format using Sphinx
+make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data :pre
@@ -68,7 +70,7 @@ make clean-all # remove entire build folder and any cached data :pre
Installing prerequisites for HTML build :h3
-To run the HTML documention build toolchain, Python 3 and virtualenv
+To run the HTML documentation build toolchain, Python 3 and virtualenv
have to be installed. Here are instructions for common setups:
Ubuntu :h4
@@ -81,7 +83,7 @@ sudo yum install python3-virtualenv :pre
Fedora (since version 22) :h4
-sudo dnf install python3-virtualenv pre
+sudo dnf install python3-virtualenv :pre
MacOS X :h4
@@ -115,10 +117,8 @@ ePUB :h4
Same as for HTML. This uses the same tools and configuration
files as the HTML tree.
-For converting the generated ePUB file to a mobi format file
+For converting the generated ePUB file to a MOBI format file
(for e-book readers like Kindle, that cannot read ePUB), you
also need to have the 'ebook-convert' tool from the "calibre"
software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
-You first create the ePUB file with 'make epub' and then do:
-
-ebook-convert LAMMPS.epub LAMMPS.mobi :pre
+You first create the ePUB file and then convert it with 'make mobi'
diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt
index cf94b40281417805515700d697dc84cbd476fc38..4ab1eddf218786a6dca4c2b4f77bcda26fa3d57f 100644
--- a/doc/src/Modify_overview.txt
+++ b/doc/src/Modify_overview.txt
@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Overview :h3
The best way to add a new feature to LAMMPS is to find a similar
-featureand look at the corresponding source and header files to figure
+feature and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the hi-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 5ab85a80c842c8a0a1672af8140e27e0be33d0e8..381dc2e99589f5702dfd4ebf3f5ec615c2dd307b 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -297,7 +297,7 @@ lib/gpu/README
"Section 2.6 -sf gpu"_Run_options.html
"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
-"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
+"Commands all"_lc pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -382,6 +382,11 @@ switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
+KOKKOS makes extensive use of advanced C++ features, which can
+expose compiler bugs, especially when compiling for maximum
+performance at high optimization levels. Please see the file
+lib/kokkos/README for a list of compilers and their respective
+platforms, that are known to work.
[Authors:] The KOKKOS package was created primarily by Christian Trott
and Stan Moore (Sandia), with contributions from other folks as well.
@@ -407,7 +412,7 @@ lib/kokkos/README
"Section 2.6 -sf kk"_Run_options.html
"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -846,7 +851,7 @@ multi-replica simulations in LAMMPS. Methods in the package include
nudged elastic band (NEB), parallel replica dynamics (PRD),
temperature accelerated dynamics (TAD), parallel tempering, and a
verlet/split algorithm for performing long-range Coulombics on one set
-of processors, and the remainder of the force field calcalation on
+of processors, and the remainder of the force field calculation on
another set.
[Supporting info:]
@@ -869,7 +874,7 @@ RIGID package :link(PKG-RIGID),h4
[Contents:]
Fixes which enforce rigid constraints on collections of atoms or
-particles. This includes SHAKE and RATTLE, as well as varous
+particles. This includes SHAKE and RATTLE, as well as various
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
@@ -1365,7 +1370,7 @@ which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
-supported, performance will be suboptimal.
+supported, performance will be sub-optimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
@@ -1387,7 +1392,7 @@ src/USER-INTEL/README
"Section 2.6 -sf intel"_Run_options.html
"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -1577,8 +1582,6 @@ molecular visualization and analysis program, to enable LAMMPS to dump
snapshots in formats compatible with various molecular simulation
tools.
-:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
-
To use this package you must have the desired VMD plugins available on
your system.
@@ -1588,7 +1591,7 @@ plugin via the "dump molfile"_dump_molfile.html command. Plugins can
be obtained from a VMD installation which has to match the platform
that you are using to compile LAMMPS for. By adding plugins to VMD,
support for new file formats can be added to LAMMPS (or VMD or other
-programs that use them) without having to recompile the application
+programs that use them) without having to re-compile the application
itself. More information about the VMD molfile plugins can be found
at
"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
@@ -1630,6 +1633,7 @@ tools:
"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
:link(ovito,http://www.ovito.org)
+:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
:link(atomeye,http://www.libatoms.org)
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@@ -1693,7 +1697,7 @@ src/USER-OMP/README
"Section 2.6 -sf omp"_Run_options.html
"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
:line
@@ -1993,3 +1997,5 @@ src/USER-VTK: filenames -> commands
src/USER-VTK/README
lib/vtk/README
"dump vtk"_dump_vtk.html :ul
+
+
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index a79caae141c68a4a0f5bcd6383658e20c3a307a9..2feb4e142d32f63c3008ffa3bc582dc2a2257062 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -25,42 +25,42 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
-dash = no library
+no = no library
sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
-"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
-"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
-"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
-"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
-"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
-"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
-"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, no
+"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, no
+"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, n/a, no
+"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, no
+"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, n/a, sys
+"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, no
+"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, no
"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
-"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
+"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, no
"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, no
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
-"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
-"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
+"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
-"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, -
-"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
-"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
+"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
"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
+"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, no
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
-"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
+"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
-"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
-"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
-"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
-"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
+"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
+"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
+"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
+"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, no
+"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, no
+"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, no
+"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, n/a, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 7157ebead0ffaef0ec03508272f4a58b698719da..7db2fa895ceaa020552d6e05502b67bc174ca54b 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -32,7 +32,7 @@ refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
-dash = no library
+no = no library
sys = system library: you likely have it on your machine
int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
@@ -40,35 +40,35 @@ ext = external library: you will need to download and install it on your machine
Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
-"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
-"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
-"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
+"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
+"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no
+"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no
"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
-"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
-"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
-"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
-"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
-"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
-"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
-"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
-"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
-"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
-"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
-"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
-"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
-"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
+"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, no
+"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, no
+"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, no
+"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no
+"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no
+"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext
+"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
+"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
+"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
+"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
+"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
+"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
+"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
+"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
+"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
-"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
+"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
-"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
+"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
-"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
-"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
-"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
+"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
+"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
+"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
+"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt
index 029c8f831cc537da73f898ac5ba3172036a54faf..3c382de1ba2b6661aceada829de918721d4f2673 100644
--- a/doc/src/Python_call.txt
+++ b/doc/src/Python_call.txt
@@ -59,9 +59,9 @@ and callbacks to LAMMPS.
The "fix python/invoke"_fix_python_invoke.html command can execute
Python code at selected timesteps during a simulation run.
-The "pair_style python"_pair_python command allows you to define
+The "pair_style python"_pair_python.html command allows you to define
pairwise potentials as python code which encodes a single pairwise
-interaction. This is useful for rapid-developement and debugging of a
+interaction. This is useful for rapid development and debugging of a
new potential.
To use any of these commands, you only need to build LAMMPS with the
diff --git a/doc/src/Python_head.txt b/doc/src/Python_head.txt
index 1f0236842993a5a7492f3e805b32939a3c2fdff0..54f995c565b741456fcfc02cee75b4072c52b361 100644
--- a/doc/src/Python_head.txt
+++ b/doc/src/Python_head.txt
@@ -62,11 +62,11 @@ library interface provided in src/library.h and src/library.h. That
interface is exposed to Python either when calling LAMMPS from Python
or when calling Python from a LAMMPS input script and then calling
back to LAMMPS from Python code. The library interface is designed to
-be easy to add funcionality to. Thus the Python interface to LAMMPS
+be easy to add functionality to. Thus the Python interface to LAMMPS
is also easy to extend as well.
If you create interesting Python scripts that run LAMMPS or
interesting Python functions that can be called from a LAMMPS input
-script, that you think would be genearlly useful, please post them as
+script, that you think would be generally useful, please post them as
a pull request to our "GitHub site"_https://github.com/lammps/lammps,
and they can be added to the LAMMPS distribution or webpage.
diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt
index 9a3ea93fc30ee932cbc1a85e374f37fb41bddee9..e76af83962336cb267a738f4cfee4ad84c41f9dc 100644
--- a/doc/src/Python_library.txt
+++ b/doc/src/Python_library.txt
@@ -186,20 +186,20 @@ keyword as a float.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
-The set_variable() methosd sets an existing string-style variable to a
+The set_variable() method sets an existing string-style variable to a
new string value, so that subsequent LAMMPS commands can access the
variable.
-The reset_box() emthods resets the size and shape of the simulation
+The reset_box() method resets the size and shape of the simulation
box, e.g. as part of restoring a previously extracted and saved state
of a simulation.
The gather methods collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
-same vector of values to each callling processor. The scatter
+same vector of values to each calling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
-passed by all calling processors, to invididual atoms, which may be
-owned by different processos.
+passed by all calling processors, to individual atoms, which may be
+owned by different processors.
Note that the data returned by the gather methods,
e.g. gather_atoms("x"), is different from the data structure returned
diff --git a/doc/src/Run_basics.txt b/doc/src/Run_basics.txt
index 02139a8c69ad9f7ddb37b7fa8e24e7b080de5d37..1b7387b46ba672c1cb92cfe1f49f7d98d2593166 100644
--- a/doc/src/Run_basics.txt
+++ b/doc/src/Run_basics.txt
@@ -75,7 +75,7 @@ setenv OMP_NUM_THREADS 2 # csh or tcsh :pre
This can also be done via the "package"_package.html command or via
the "-pk command-line switch"_Run_options.html which invokes the
package command. See the "package"_package.html command or
-"Speed"_Speed.html doc pages for more details about which accerlarator
+"Speed"_Speed.html doc pages for more details about which accelerator
packages and which commands support multi-threading.
:line
diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt
index 2b93cc7d4944f4a3e61a826d9967986fb5d32516..85c9a6550d637036815cd58f53326dfe3c930363 100644
--- a/doc/src/Run_windows.txt
+++ b/doc/src/Run_windows.txt
@@ -33,8 +33,8 @@ in parallel, follow these steps.
Download and install a compatible MPI library binary package:
-for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
-for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
+for 32-bit Windows: "mpich2-1.4.1p1-win-ia32.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+for 64-bit Windows: "mpich2-1.4.1p1-win-x86-64.msi"_http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi :ul
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the
diff --git a/doc/src/Speed_bench.txt b/doc/src/Speed_bench.txt
index 8e407d14ea6bdb7428bff3818a670a9a84244f63..a3d0bf4f46f95c07f04c304449d4399a6c79c95f 100644
--- a/doc/src/Speed_bench.txt
+++ b/doc/src/Speed_bench.txt
@@ -11,7 +11,7 @@ Benchmarks :h3
Current LAMMPS performance is discussed on the "Benchmarks
page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
-where timings and parallel efficiencies are listed. The page has
+where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
@@ -77,8 +77,8 @@ style, force field, cutoff, etc) can then be estimated.
Performance on a parallel machine can also be predicted from one-core
or one-node timings if the parallel efficiency can be estimated. The
communication bandwidth and latency of a particular parallel machine
-affects the efficiency. On most machines LAMMPS will give parallel
-efficiencies on these benchmarks above 50% so long as the number of
+affects the efficiency. On most machines LAMMPS will give a parallel
+efficiency on these benchmarks above 50% so long as the number of
atoms/core is a few 100 or greater, and closer to 100% for large
numbers of atoms/core. This is for all-MPI mode with one MPI task per
core. For nodes with accelerator options or hardware (OpenMP, GPU,
diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt
index 1a17b39c79b672e43062770253ae5e82fc1f998d..c93407515e5cebe6b8e278c62ea36b731c2b121b 100644
--- a/doc/src/Speed_compare.txt
+++ b/doc/src/Speed_compare.txt
@@ -9,65 +9,108 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Comparison of various accelerator packages :h3
-NOTE: this section still needs to be re-worked with additional KOKKOS
-and USER-INTEL information.
-
The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
-run on GPUs, and run on Intel Xeon Phi coprocessors.
+run on GPUs, optimize for vector units on CPUs and run on Intel
+Xeon Phi (co-)processors.
-All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
-hardware, but they do it in different ways.
+All of these packages can accelerate a LAMMPS calculation taking
+advantage of hardware features, but they do it in different ways
+and acceleration is not always guaranteed.
As a consequence, for a particular simulation on specific hardware,
-one package may be faster than the other. We give guidelines below,
-but the best way to determine which package is faster for your input
-script is to try both of them on your machine. See the benchmarking
+one package may be faster than the other. We give some guidelines
+below, but the best way to determine which package is faster for your
+input script is to try multiple of them on your machine and experiment
+with available performance tuning settings. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
-The GPU package allows you to assign multiple CPUs (cores) to a single
-GPU (a common configuration for "hybrid" nodes that contain multicore
-CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
-
-The GPU package moves per-atom data (coordinates, forces)
-back-and-forth between the CPU and GPU every timestep. The
-KOKKOS/CUDA package only does this on timesteps when a CPU calculation
-is required (e.g. to invoke a fix or compute that is non-GPU-ized).
-Hence, if you can formulate your input script to only use GPU-ized
-fixes and computes, and avoid doing I/O too often (thermo output, dump
-file snapshots, restart files), then the data transfer cost of the
-KOKKOS/CUDA package can be very low, causing it to run faster than the
-GPU package. :l
-
-The GPU package is often faster than the KOKKOS/CUDA package, if the
-number of atoms per GPU is smaller. The crossover point, in terms of
-atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
-strongly on the pair style. For example, for a simple Lennard Jones
+Both, the GPU and the KOKKOS package allows you to assign multiple
+MPI ranks (= CPU cores) to the same GPU. For the GPU package, this
+can lead to a speedup through better utilization of the GPU (by
+overlapping computation and data transfer) and more efficient
+computation of the non-GPU accelerated parts of LAMMPS through MPI
+parallelization, as all system data is maintained and updated on
+the host. For KOKKOS, there is less to no benefit from this, due
+to its different memory management model, which tries to retain
+data on the GPU.
+ :ulb,l
+
+The GPU package moves per-atom data (coordinates, forces, and
+(optionally) neighbor list data, if not computed on the GPU) between
+the CPU and GPU at every timestep. The KOKKOS/CUDA package only does
+this on timesteps when a CPU calculation is required (e.g. to invoke
+a fix or compute that is non-GPU-ized). Hence, if you can formulate
+your input script to only use GPU-ized fixes and computes, and avoid
+doing I/O too often (thermo output, dump file snapshots, restart files),
+then the data transfer cost of the KOKKOS/CUDA package can be very low,
+causing it to run faster than the GPU package. :l
+
+The GPU package is often faster than the KOKKOS/CUDA package, when the
+number of atoms per GPU is on the smaller side. The crossover point,
+in terms of atoms/GPU at which the KOKKOS/CUDA package becomes faster
+depends strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
-Both packages compute bonded interactions (bonds, angles, etc) on the
-CPU. If the GPU package is running with several MPI processes
+Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
+etc) on the CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
-spread across more CPUs and hence the GPU package can run faster. :l
-
-When using the GPU package with multiple CPUs assigned to one GPU, its
-performance depends to some extent on high bandwidth between the CPUs
-and the GPU. Hence its performance is affected if full 16 PCIe lanes
-are not available for each GPU. In HPC environments this can be the
-case if S2050/70 servers are used, where two devices generally share
-one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l
+spread across more CPUs and hence the GPU package can run faster in these
+cases. :l
+
+When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
+performance depends to some extent on the available bandwidth between
+the CPUs and the GPU. This can differ significantly based on the
+available bus technology, capability of the host CPU and mainboard,
+the wiring of the buses and whether switches are used to increase the
+number of available bus slots, or if GPUs are housed in an external
+enclosure. This can become quite complex. :l
+
+To achieve significant acceleration through GPUs, both KOKKOS and GPU
+package require capable GPUs with fast on-device memory and efficient
+data transfer rates. This requests capable upper mid-level to high-end
+(desktop) GPUs. Using lower performance GPUs (e.g. on laptops) may
+result in a slowdown instead. :l
+
+For the GPU package, specifically when running in parallel with MPI,
+if it often more efficient to exclude the PPPM kspace style from GPU
+acceleration and instead run it - concurrently with a GPU accelerated
+pair style - on the CPU. This can often be easily achieved with placing
+a {suffix off} command before and a {suffix on} command after the
+{kspace_style pppm} command. :l
+
+The KOKKOS/OpenMP and USER-OMP package have different thread management
+strategies, which should result in USER-OMP being more efficient for a
+small number of threads with increasing overhead as the number of threads
+per MPI rank grows. The KOKKOS/OpenMP kernels have less overhead in that
+case, but have lower performance with few threads. :l
+
+The USER-INTEL package contains many options and settings for achieving
+additional performance on Intel hardware (CPU and accelerator cards), but
+to unlock this potential, an Intel compiler is required. The package code
+will compile with GNU gcc, but it will not be as efficient. :l
:ule
-[Differences between the two packages:]
+[Differences between the GPU and KOKKOS packages:]
-The GPU package accelerates only pair force, neighbor list, and PPPM
-calculations. :ulb,l
+The GPU package accelerates only pair force, neighbor list, and (parts
+of) PPPM calculations. The KOKKOS package attempts to run most of the
+calculation on the GPU, but can transparently support non-accelerated
+code (with a performance penalty due to having data transfers between
+host and GPU). :ulb,l
The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+
+The GPU package can be compiled for CUDA or OpenCL and thus supports
+both, Nvidia and AMD GPUs well. On Nvidia hardware, using CUDA is typically
+resulting in equal or better performance over OpenCL. :l
+
+OpenCL in the GPU package does theoretically also support Intel CPUs or
+Intel Xeon Phi, but the native support for those in KOKKOS (or USER-INTEL)
+is superior. :l
:ule
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index 3ae4639dc2391b492410a450c8f9b3ad56402684..bddefc50314d6d73879337bf84bb1a79238888bf 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -9,17 +9,17 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
GPU package :h3
-The GPU package was developed by Mike Brown at ORNL and his
-collaborators, particularly Trung Nguyen (ORNL). It provides GPU
-versions of many pair styles, including the 3-body Stillinger-Weber
-pair style, and for "kspace_style pppm"_kspace_style.html for
-long-range Coulombics. It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL
+and his collaborators, particularly Trung Nguyen (now at Northwestern).
+It provides GPU versions of many pair styles and for parts of the
+"kspace_style pppm"_kspace_style.html for long-range Coulombics.
+It has the following general features:
It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
e.g. within a node of a parallel machine. :ulb,l
-Atom-based data (e.g. coordinates, forces) moves back-and-forth
+Atom-based data (e.g. coordinates, forces) are moved back-and-forth
between the CPU(s) and GPU every timestep. :l
Neighbor lists can be built on the CPU or on the GPU :l
@@ -28,8 +28,8 @@ The charge assignment and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l
-Asynchronous force computations can be performed simultaneously on the
-CPU(s) and GPU. :l
+Force computations of different style (pair vs. bond/angle/dihedral/improper)
+can be performed concurrently on the GPU and CPU(s), respectively. :l
It allows for GPU computations to be performed in single or double
precision, or in mixed-mode precision, where pairwise forces are
@@ -39,21 +39,32 @@ force vectors. :l
LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
-same functionality can eventually be supported on a variety of GPU
-hardware. :l
+same functionality is supported on a variety of hardware. :l
:ule
[Required hardware/software:]
-To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA CUDA software on your system:
-
-Check if you have an NVIDIA GPU: cat
-/proc/driver/nvidia/gpus/0/information Go to
-http://www.nvidia.com/object/cuda_get.html Install a driver and
-toolkit appropriate for your system (SDK is not necessary) Run
-lammps/lib/gpu/nvc_get_devices (after building the GPU library, see
-below) to list supported devices and properties :ul
+To compile and use this package in CUDA mode, you currently need
+to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
+toolkit software on your system (this is primarily tested on Linux
+and completely unsupported on Windows):
+
+Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/*/information :ulb,l
+Go to http://www.nvidia.com/object/cuda_get.html :l
+Install a driver and toolkit appropriate for your system (SDK is not necessary) :l
+Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
+list supported devices and properties :ule,l
+
+To compile and use this package in OpenCL mode, you currently need
+to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
+In OpenCL mode, the acceleration depends on having an "OpenCL Installable Client
+Driver (ICD)"_https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader
+installed. There can be multiple of them for the same or different hardware
+(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
+as 'platforms'. The GPU library will select the [first] suitable platform,
+but this can be overridden using the device option of the "package"_package.html
+command. run lammps/lib/gpu/ocl_get_devices to get a list of available
+platforms and devices with a suitable ICD available.
[Building LAMMPS with the GPU package:]
@@ -120,7 +131,10 @@ GPUs/node to use, as well as other options.
The performance of a GPU versus a multi-core CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
-precision used on the GPU (double, single, mixed).
+precision used on the GPU (double, single, mixed). Using the GPU package
+in OpenCL mode on CPUs (which uses vectorization and multithreading) is
+usually resulting in inferior performance compared to using LAMMPS' native
+threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the GPU package on various
@@ -146,7 +160,7 @@ The "package gpu"_package.html command has several options for tuning
performance. Neighbor lists can be built on the GPU or CPU. Force
calculations can be dynamically balanced across the CPU cores and
GPUs. GPU-specific settings can be made which can be optimized
-for different hardware. See the "packakge"_package.html command
+for different hardware. See the "package"_package.html command
doc page for details. :l
As described by the "package gpu"_package.html command, GPU
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index ef876a7d42108a3ae8aad4f6c2f65670f65e0223..bf078fb57652b747c99b17d12d4f441618e58d24 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -68,7 +68,7 @@ In most molecular dynamics software, parallelization parameters
to changing the order of operations with finite-precision
calculations. The USER-INTEL package is deterministic. This means
that the results should be reproducible from run to run with the
-{same} parallel configurations and when using determinstic
+{same} parallel configurations and when using deterministic
libraries or library settings (MPI, OpenMP, FFT). However, there
are differences in the USER-INTEL package that can change the
order of operations compared to LAMMPS without acceleration:
@@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to
styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
-grid numa"_processors.html" to the beginning of the input script for
+grid numa"_processors.html to the beginning of the input script for
better scalability.
When running on many nodes, performance might be better when using
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index eb787df5d6ac8a1e97136453a8eda62f754bdc0b..04cf53691be0c7379bd031b8feefe46119627748 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -93,12 +93,12 @@ The "t Nt" option specifies how many OpenMP threads per MPI task to
use with a node. The default is Nt = 1, which is MPI-only mode. Note
that the product of MPI tasks * OpenMP threads/task should not exceed
the physical number of cores (on a node), otherwise performance will
-suffer. If hyperthreading is enabled, then the product of MPI tasks *
-OpenMP threads/task should not exceed the physical number of cores *
-hardware threads. The "-k on" switch also issues a "package kokkos"
-command (with no additional arguments) which sets various KOKKOS
-options to default values, as discussed on the "package"_package.html
-command doc page.
+suffer. If Hyper-Threading (HT) is enabled, then the product of MPI
+tasks * OpenMP threads/task should not exceed the physical number of
+cores * hardware threads. The "-k on" switch also issues a
+"package kokkos" command (with no additional arguments) which sets
+various KOKKOS options to default values, as discussed on the
+"package"_package.html command doc page.
The "-sf kk" "command-line switch"_Run_options.html will automatically
append the "/kk" suffix to styles that support it. In this manner no
@@ -149,7 +149,7 @@ Intel Knight's Landing (KNL) Xeon Phi:
KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are
reserved for the OS, and only 64 or 66 cores are used. Each core has 4
-hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
+Hyper-Threads,so there are effectively N = 256 (4*64) or N = 264 (4*66)
cores to run on. The product of MPI tasks * OpenMP threads/task should
not exceed this limit, otherwise performance will suffer. Note that
with the KOKKOS package you do not need to specify how many KNLs there
@@ -228,7 +228,7 @@ for details and default settings. Experimenting with its options can
provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
-mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
NOTE: For good performance of the KOKKOS package on GPUs, you must
have Kepler generation GPUs (or later). The Kokkos library exploits
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 647ff71e36593f9a642c22360e74c36752e43e7d..dd12685dc547a4115229d68409ba0d6c544fd323 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -50,6 +50,6 @@ inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
+uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
LAMMPS, to obtain synchronized timings.
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index 0abf54430ef042de4e04080cd741332cf5a7b85f..238909d1b47c1711562687b79f6f402a618c23e5 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -29,7 +29,7 @@ instructions.
[Run with the USER-OMP package from the command line:]
-These example asume one or more 16-core nodes.
+These examples assume one or more 16-core nodes.
env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script # 1 MPI task, 16 threads according to OMP_NUM_THREADS
lmp_mpi -sf omp -in in.script # 1 MPI task, no threads, optimized kernels
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index 6c837885cd4dd5272e9b7925d84aa01ee8f9ab79..4c87091e7e20c675413c605738ec776813b52b9b 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available for a particular
-style, find the style name in the "Commands_all"_Commands_all.html
+style, find the style name in the "Commands_all"_lc
style pages (fix,compute,pair,etc) and see what suffixes are listed
(g,i,k,o,t) with it. The doc pages for individual commands
(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list
diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt
index 8b4e779cbe869ca7eda71988c841b41ea116f0a3..a9ad5032cec07de0048ba0288733267caaf18f8e 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -43,40 +43,55 @@ to edit for your platform) which will build several of the tools which
reside in that directory. Most of them are larger packages in their
own sub-directories with their own Makefiles and/or README files.
-"amber2lmp"_#amber
-"binary2txt"_#binary
-"ch2lmp"_#charmm
-"chain"_#chain
-"colvars"_#colvars
-"createatoms"_#createatoms
-"doxygen"_#doxygen
-"drude"_#drude
-"eam database"_#eamdb
-"eam generate"_#eamgn
-"eff"_#eff
-"emacs"_#emacs
-"fep"_#fep
-"i-pi"_#ipi
-"ipp"_#ipp
-"kate"_#kate
-"lmp2arc"_#arc
-"lmp2cfg"_#cfg
-"matlab"_#matlab
-"micelle2d"_#micelle
-"moltemplate"_#moltemplate
-"msi2lmp"_#msi
-"phonon"_#phonon
-"polybond"_#polybond
-"pymol_asphere"_#pymol
-"python"_#pythontools
-"reax"_#reax_tool
-"smd"_#smd
-"vim"_#vim
-"xmgrace"_#xmgrace :ul
-
-:line
-
-amber2lmp tool :h3,link(amber)
+:line
+
+Pre-processing tools :h3
+
+"amber2lmp"_#amber,
+"ch2lmp"_#charmm,
+"chain"_#chain,
+"createatoms"_#createatoms,
+"drude"_#drude,
+"eam database"_#eamdb,
+"eam generate"_#eamgn,
+"eff"_#eff,
+"ipp"_#ipp,
+"micelle2d"_#micelle,
+"moltemplate"_#moltemplate,
+"msi2lmp"_#msi,
+"polybond"_#polybond :tb(c=6,ea=c,a=l)
+
+Post-processing tools :h3
+
+"amber2lmp"_#amber,
+"binary2txt"_#binary,
+"ch2lmp"_#charmm,
+"colvars"_#colvars,
+"eff"_#eff,
+"fep"_#fep,
+"lmp2arc"_#arc,
+"lmp2cfg"_#cfg,
+"matlab"_#matlab,
+"phonon"_#phonon,
+"pymol_asphere"_#pymol,
+"python"_#pythontools,
+"reax"_#reax_tool,
+"smd"_#smd,
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+
+Miscellaneous tools :h3
+
+"doxygen"_#doxygen,
+"emacs"_#emacs,
+"i-pi"_#ipi,
+"kate"_#kate,
+"vim"_#vim :tb(c=5,ea=c,a=l)
+
+:line
+
+Tool descriptions :h3
+
+amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@@ -91,7 +106,7 @@ necessary modifications yourself.
:line
-binary2txt tool :h3,link(binary)
+binary2txt tool :h4,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@@ -104,7 +119,7 @@ since binary files are not compatible across all platforms.
:line
-ch2lmp tool :h3,link(charmm)
+ch2lmp tool :h4,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@@ -129,7 +144,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
-chain tool :h3,link(chain)
+chain tool :h4,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@@ -146,7 +161,7 @@ for the "chain benchmark"_Speed_bench.html.
:line
-colvars tools :h3,link(colvars)
+colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@@ -168,7 +183,7 @@ gmail.com) at ICTP, Italy.
:line
-createatoms tool :h3,link(createatoms)
+createatoms tool :h4,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@@ -181,7 +196,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
-doxygen tool :h3,link(doxygen)
+doxygen tool :h4,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@@ -193,7 +208,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
-drude tool :h3,link(drude)
+drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@@ -206,7 +221,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
-eam database tool :h3,link(eamdb)
+eam database tool :h4,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@@ -222,7 +237,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
-eam generate tool :h3,link(eamgn)
+eam generate tool :h4,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@@ -235,7 +250,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
-eff tool :h3,link(eff)
+eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@@ -246,7 +261,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
-emacs tool :h3,link(emacs)
+emacs tool :h4,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -257,7 +272,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
-fep tool :h3,link(fep)
+fep tool :h4,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@@ -270,7 +285,7 @@ See README file in the tools/fep directory.
:line
-i-pi tool :h3,link(ipi)
+i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@@ -287,7 +302,7 @@ calculations with LAMMPS.
:line
-ipp tool :h3,link(ipp)
+ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@@ -301,7 +316,7 @@ tools/createatoms tool's input file.
:line
-kate tool :h3,link(kate)
+kate tool :h4,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -312,7 +327,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
-lmp2arc tool :h3,link(arc)
+lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@@ -328,7 +343,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
-lmp2cfg tool :h3,link(cfg)
+lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@@ -339,7 +354,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
-matlab tool :h3,link(matlab)
+matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@@ -357,7 +372,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
-micelle2d tool :h3,link(micelle)
+micelle2d tool :h4,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@@ -374,7 +389,7 @@ definition file. This tool was used to create the system for the
:line
-moltemplate tool :h3,link(moltemplate)
+moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@@ -388,7 +403,7 @@ supports it. It has its own WWW page at
:line
-msi2lmp tool :h3,link(msi)
+msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -405,7 +420,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
-phonon tool :h3,link(phonon)
+phonon tool :h4,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -420,7 +435,7 @@ University.
:line
-polybond tool :h3,link(polybond)
+polybond tool :h4,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@@ -434,7 +449,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
-pymol_asphere tool :h3,link(pymol)
+pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@@ -452,7 +467,7 @@ This tool was written by Mike Brown at Sandia.
:line
-python tool :h3,link(pythontools)
+python tool :h4,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@@ -468,7 +483,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
-reax tool :h3,link(reax_tool)
+reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -479,7 +494,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
-smd tool :h3,link(smd)
+smd tool :h4,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@@ -495,7 +510,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
-vim tool :h3,link(vim)
+vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@@ -506,7 +521,7 @@ ziegenhain.com)
:line
-xmgrace tool :h3,link(xmgrace)
+xmgrace tool :h4,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
diff --git a/doc/src/USER/atc/man_add_molecule.html b/doc/src/USER/atc/man_add_molecule.html
index 8d9625e1bd0e926742f0283c5229880681f89431..4e7810aa615c202f1c94158517552a8ec47d7aa5 100644
--- a/doc/src/USER/atc/man_add_molecule.html
+++ b/doc/src/USER/atc/man_add_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_add_species.html b/doc/src/USER/atc/man_add_species.html
index 9beded1b164d22c57f5800d62d258bf0867e9999..a990ab626fbc62322b0c63cf346066298de3cf98 100644
--- a/doc/src/USER/atc/man_add_species.html
+++ b/doc/src/USER/atc/man_add_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_element_map.html b/doc/src/USER/atc/man_atom_element_map.html
index 6725170928a49b0887e1e09e3fc1634b94666773..a5707d280e831c83ab93de07a2b9e2476cba1894 100644
--- a/doc/src/USER/atc/man_atom_element_map.html
+++ b/doc/src/USER/atc/man_atom_element_map.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atom_weight.html b/doc/src/USER/atc/man_atom_weight.html
index 28bc90fa01c053c99983a594100b086ddd6b08a5..350ab13b92ad1e47baa672fed6448cfa9e4c55f6 100644
--- a/doc/src/USER/atc/man_atom_weight.html
+++ b/doc/src/USER/atc/man_atom_weight.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_atomic_charge.html b/doc/src/USER/atc/man_atomic_charge.html
index ef787f53acc2632e066aaf14766b5df0ac350706..17e854a37f5e0472632918537b766ef5ae796be5 100644
--- a/doc/src/USER/atc/man_atomic_charge.html
+++ b/doc/src/USER/atc/man_atomic_charge.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary.html b/doc/src/USER/atc/man_boundary.html
index 61596d3b31899ea0a65cdd4332753b61b3436eeb..8dcf328dd3ba8df57c87b5c258314bc681da6980 100644
--- a/doc/src/USER/atc/man_boundary.html
+++ b/doc/src/USER/atc/man_boundary.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_dynamics.html b/doc/src/USER/atc/man_boundary_dynamics.html
index 40b82f3f6113ba5b21416776a4927fc2f05de3de..335ff2d20957f62def15c506845d9601e0035548 100644
--- a/doc/src/USER/atc/man_boundary_dynamics.html
+++ b/doc/src/USER/atc/man_boundary_dynamics.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_faceset.html b/doc/src/USER/atc/man_boundary_faceset.html
index 7eb950f78e54c7dfd17f4f7121332a592265f236..6c2fb8494028f4934a9af203c6f98806cd385c8a 100644
--- a/doc/src/USER/atc/man_boundary_faceset.html
+++ b/doc/src/USER/atc/man_boundary_faceset.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_boundary_integral.html b/doc/src/USER/atc/man_boundary_integral.html
index 0663dba176e57066ea8b878f5bf3b7b2e1280889..c4b0d4865e75e5b518c0f42285378f568de4a8e1 100644
--- a/doc/src/USER/atc/man_boundary_integral.html
+++ b/doc/src/USER/atc/man_boundary_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html
index a731b09116dd2a9e7fb677b5fcc12b433023bdfa..baa306a1c80afc280f2aa8d31551de329726fb8e 100644
--- a/doc/src/USER/atc/man_consistent_fe_initialization.html
+++ b/doc/src/USER/atc/man_consistent_fe_initialization.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_contour_integral.html b/doc/src/USER/atc/man_contour_integral.html
index 690f0fcc986e9670071c54d30c5cdc70a1756601..16f6d9abadbb15176737ff7d6950ae7d8f0e81fa 100644
--- a/doc/src/USER/atc/man_contour_integral.html
+++ b/doc/src/USER/atc/man_contour_integral.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control.html b/doc/src/USER/atc/man_control.html
index 900952ba0b39735f31d74d8a44b6c6fd80067667..e94a9a52ef84db97b7c5598182f97e249eb30379 100644
--- a/doc/src/USER/atc/man_control.html
+++ b/doc/src/USER/atc/man_control.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_momentum.html b/doc/src/USER/atc/man_control_momentum.html
index 8f4f48659561834285e915632ec4dd8802cb1f1a..e3074eae8f14acf35018fe1f357d42995ecf1066 100644
--- a/doc/src/USER/atc/man_control_momentum.html
+++ b/doc/src/USER/atc/man_control_momentum.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_thermal.html b/doc/src/USER/atc/man_control_thermal.html
index eab186f71502d82b1667487b8b6e9c621e887e57..8d32f1c4f9aa78d407540e3872405fd724d9b73e 100644
--- a/doc/src/USER/atc/man_control_thermal.html
+++ b/doc/src/USER/atc/man_control_thermal.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
index a337a495e0e3eaf2cedb69441267654cdb68316a..d28ec334f5ac84e08570760ddf0bc87896cb4691 100644
--- a/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
+++ b/doc/src/USER/atc/man_control_thermal_correction_max_iterations.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_decomposition.html b/doc/src/USER/atc/man_decomposition.html
index d54a2010342e783243cc0ab90f8010515c23a892..98eedafa6cfc7295ae980e6a8e11268ec75c7a3d 100644
--- a/doc/src/USER/atc/man_decomposition.html
+++ b/doc/src/USER/atc/man_decomposition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_electron_integration.html b/doc/src/USER/atc/man_electron_integration.html
index ab454c16d271fa0e9ed02e186601f9c2cdc0259e..7cf40f6813e318e57df6fca20dfffc3669839994 100644
--- a/doc/src/USER/atc/man_electron_integration.html
+++ b/doc/src/USER/atc/man_electron_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_equilibrium_start.html b/doc/src/USER/atc/man_equilibrium_start.html
index d01253c4b3e574981cc3d2e32159a4639bd7bcd3..8c81ce5925c0bbb504a9399ef5680f0e78220141 100644
--- a/doc/src/USER/atc/man_equilibrium_start.html
+++ b/doc/src/USER/atc/man_equilibrium_start.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_extrinsic_exchange.html b/doc/src/USER/atc/man_extrinsic_exchange.html
index 4f1f5962d9f3956bd1be3bf7a41c6a028769b07e..f4d1b01e880cb17a8ee9174090c68b029156dc5d 100644
--- a/doc/src/USER/atc/man_extrinsic_exchange.html
+++ b/doc/src/USER/atc/man_extrinsic_exchange.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fe_md_boundary.html b/doc/src/USER/atc/man_fe_md_boundary.html
index e517dd4855d86a90fe95517bf3bb07a0c99425f1..e39ddd3cec063f57b0e80476dc18b66daadff2b3 100644
--- a/doc/src/USER/atc/man_fe_md_boundary.html
+++ b/doc/src/USER/atc/man_fe_md_boundary.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fem_mesh.html b/doc/src/USER/atc/man_fem_mesh.html
index b8ba584816bc2b2fce453df4f12f2a3589378feb..485b8c95a0f24f91fa5c44bc69cfbe9c1676a940 100644
--- a/doc/src/USER/atc/man_fem_mesh.html
+++ b/doc/src/USER/atc/man_fem_mesh.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_filter_scale.html b/doc/src/USER/atc/man_filter_scale.html
index 7a871f5c8141c7c8122919f0c2ea8b5abdfa27ca..e2190dea21b38aad2feca6dedd6f684117025a3d 100644
--- a/doc/src/USER/atc/man_filter_scale.html
+++ b/doc/src/USER/atc/man_filter_scale.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_filter_type.html b/doc/src/USER/atc/man_filter_type.html
index 2711d128e9f945be4e7c65ad8e18be43b2b78d08..0928139d7dabdd499826726274ce6a5f8a556d91 100644
--- a/doc/src/USER/atc/man_filter_type.html
+++ b/doc/src/USER/atc/man_filter_type.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_atc.html b/doc/src/USER/atc/man_fix_atc.html
index 7cc6cfea5bad5089cfbddab53036c75ed2fedd0f..f6f7b43a38b7c45d48fb7748e8e46d499ba81119 100644
--- a/doc/src/USER/atc/man_fix_atc.html
+++ b/doc/src/USER/atc/man_fix_atc.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_flux.html b/doc/src/USER/atc/man_fix_flux.html
index 42815def6bca896ee183505fb869a327908b5853..31bd5619a37ba7aa7db08768f4810a3924cd6524 100644
--- a/doc/src/USER/atc/man_fix_flux.html
+++ b/doc/src/USER/atc/man_fix_flux.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_fix_nodes.html b/doc/src/USER/atc/man_fix_nodes.html
index 03cf86eb9220720940f1fae44257a3df93addd12..2245e32607ceb217c23e4cf35642844be2a5aec0 100644
--- a/doc/src/USER/atc/man_fix_nodes.html
+++ b/doc/src/USER/atc/man_fix_nodes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_computes.html b/doc/src/USER/atc/man_hardy_computes.html
index b45b7dfb0101a117ca58cc7faf78b1eec80a3a06..ec2dc3ccb915f280b1370e49b862d0e5988dbecc 100644
--- a/doc/src/USER/atc/man_hardy_computes.html
+++ b/doc/src/USER/atc/man_hardy_computes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_fields.html b/doc/src/USER/atc/man_hardy_fields.html
index 17903aabd0d913d0d0bb78b9998c7c4105df4fba..483e5be6bdf560fb2dfdbc1a28c7069a3b76eda8 100644
--- a/doc/src/USER/atc/man_hardy_fields.html
+++ b/doc/src/USER/atc/man_hardy_fields.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_hardy_gradients.html b/doc/src/USER/atc/man_hardy_gradients.html
index 00935f0ae25968b2c633a068899e03917241edaf..1874ad152e030bbc26afce4f96198bcb26697d98 100644
--- a/doc/src/USER/atc/man_hardy_gradients.html
+++ b/doc/src/USER/atc/man_hardy_gradients.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
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<hr>
diff --git a/doc/src/USER/atc/man_poisson_solver.html b/doc/src/USER/atc/man_poisson_solver.html
index b6fabbb27c1613cf8cda041d04560d9c4458b1b3..3e22a51f3e9e4eada56e1fe337018dec72e863d5 100644
--- a/doc/src/USER/atc/man_poisson_solver.html
+++ b/doc/src/USER/atc/man_poisson_solver.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_read_restart.html b/doc/src/USER/atc/man_read_restart.html
index 5fc21282f68860c6726887df2e9916c9b8bfcfff..d13151a12ed3c01ed2d2504f53e2fbd219173a49 100644
--- a/doc/src/USER/atc/man_read_restart.html
+++ b/doc/src/USER/atc/man_read_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_molecule.html b/doc/src/USER/atc/man_remove_molecule.html
index e6ad418de6871e7b4dab85dc02eede170bbf048d..54e4e3419fbcf126d22287759c25d45cdb523443 100644
--- a/doc/src/USER/atc/man_remove_molecule.html
+++ b/doc/src/USER/atc/man_remove_molecule.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_source.html b/doc/src/USER/atc/man_remove_source.html
index acea7a56074df6c0ed151296fcd1d1048abc1426..c15e0ca46ddcbdb4192d709990f0e3979572e712 100644
--- a/doc/src/USER/atc/man_remove_source.html
+++ b/doc/src/USER/atc/man_remove_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_remove_species.html b/doc/src/USER/atc/man_remove_species.html
index 561364518fe2033590626709f6fd1ac72b512c77..ee063ce57f524120279df2f36071986b33b3a813 100644
--- a/doc/src/USER/atc/man_remove_species.html
+++ b/doc/src/USER/atc/man_remove_species.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_reset_atomic_reference_positions.html b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
index 88e6748001c44716880a1b8a71b072d343e33d60..3c438610540faeb48a021a943e1d93628cac7358 100644
--- a/doc/src/USER/atc/man_reset_atomic_reference_positions.html
+++ b/doc/src/USER/atc/man_reset_atomic_reference_positions.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_reset_time.html b/doc/src/USER/atc/man_reset_time.html
index a6429bf6d6c8b040f9171787f779ef49a9333768..9607848e1a490c18addf77da883cb5568f65abae 100644
--- a/doc/src/USER/atc/man_reset_time.html
+++ b/doc/src/USER/atc/man_reset_time.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_sample_frequency.html b/doc/src/USER/atc/man_sample_frequency.html
index 4e48c4bb299c854bb86f26adcb83d1a771725a3e..9a9a8e3a02fbeb8d2cbee68a2b057d759f30ff8a 100644
--- a/doc/src/USER/atc/man_sample_frequency.html
+++ b/doc/src/USER/atc/man_sample_frequency.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_set.html b/doc/src/USER/atc/man_set.html
index cf775c9b36d4e9a43abab0d2716c0a6d7c70a29d..55ad8d952b8ae5fb679ba08c0bd83550be7870df 100644
--- a/doc/src/USER/atc/man_set.html
+++ b/doc/src/USER/atc/man_set.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source.html b/doc/src/USER/atc/man_source.html
index c7239f2c412db0ac97ec56462ce96c93d1726c7e..78fb1652ebc05a9a3296c6faee275c74b3230c3a 100644
--- a/doc/src/USER/atc/man_source.html
+++ b/doc/src/USER/atc/man_source.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_source_integration.html b/doc/src/USER/atc/man_source_integration.html
index 3f43340af827c5c61162078843dd7b6af7116ff9..3b261b781014715c1346623fb5d6cef6c0b86dee 100644
--- a/doc/src/USER/atc/man_source_integration.html
+++ b/doc/src/USER/atc/man_source_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_temperature_definition.html b/doc/src/USER/atc/man_temperature_definition.html
index a07ba29cab6f1780d61dfbc22bd0f5f50f3973b8..c317c06c00cf0aca03cd5eefaf212505cf34a616 100644
--- a/doc/src/USER/atc/man_temperature_definition.html
+++ b/doc/src/USER/atc/man_temperature_definition.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_thermal_time_integration.html b/doc/src/USER/atc/man_thermal_time_integration.html
index fe293138be2a7206963a5c2339be637da3542e6e..830591921e7dbd63cc73d1dc5f4ebb17c65c2d95 100644
--- a/doc/src/USER/atc/man_thermal_time_integration.html
+++ b/doc/src/USER/atc/man_thermal_time_integration.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_time_filter.html b/doc/src/USER/atc/man_time_filter.html
index 732eaa3a36114c766118a0ab5aadd541e6284ab5..5000fb079d2a0dc5f7ed1a474a8f516d03a3b5f0 100644
--- a/doc/src/USER/atc/man_time_filter.html
+++ b/doc/src/USER/atc/man_time_filter.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_track_displacement.html b/doc/src/USER/atc/man_track_displacement.html
index f5410816d75a779a6c6ec38c2e8bad1f64ac262f..2c7cf2615018eaf3a4be95be6ee15d0884c1bfd5 100644
--- a/doc/src/USER/atc/man_track_displacement.html
+++ b/doc/src/USER/atc/man_track_displacement.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_flux.html b/doc/src/USER/atc/man_unfix_flux.html
index 95e1f4be5a85ea44cb7db7b434a0eb053262b9b4..551896431a06dac1dedb2c7b35a2d03351a36fd4 100644
--- a/doc/src/USER/atc/man_unfix_flux.html
+++ b/doc/src/USER/atc/man_unfix_flux.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_unfix_nodes.html b/doc/src/USER/atc/man_unfix_nodes.html
index 78495c928a4751e188868ade7b93cbfb6496b04b..4dfd9b3cfc4c8755eeecfb1b2bffb24868564aae 100644
--- a/doc/src/USER/atc/man_unfix_nodes.html
+++ b/doc/src/USER/atc/man_unfix_nodes.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_atom_weights.html b/doc/src/USER/atc/man_write_atom_weights.html
index 8a0e5b62a81bb9488e6bf5e9e6f61dbfc929fef3..1722d74f67fa82dbabc61ea535f98553e4adcef8 100644
--- a/doc/src/USER/atc/man_write_atom_weights.html
+++ b/doc/src/USER/atc/man_write_atom_weights.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/USER/atc/man_write_restart.html b/doc/src/USER/atc/man_write_restart.html
index 6dca57673bbdabe393ad0fa2512f8c566a1f4374..74c6e2d289feac47f5f83f5a8448ee08115a7ad1 100644
--- a/doc/src/USER/atc/man_write_restart.html
+++ b/doc/src/USER/atc/man_write_restart.html
@@ -11,7 +11,7 @@
<a href="http://lammps.sandia.gov">LAMMPS Website</a>
<a href="../../Manual.html">LAMMPS Manual</a>
<a href="../../fix_atc.html">USER-AtC Manual</a>
- <a href="../../Section_commands.html#comm">Commands</a>
+ <a href="../../Commands_all.html">Commands</a>
</center>
<hr>
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index 4b4ac3862d102b54ed08cb0b2d8b63f84ec32f89..0f0b241b766c1e5b19b37aedb652b85be57ebbd7 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -67,7 +67,7 @@ when required. An example are the bond (angle, etc) methods which
need to find the local index of an atom with a specific global ID
which is a bond (angle, etc) partner. LAMMPS performs this operation
efficiently by creating a "map", which is either an {array} or {hash}
-table, as descibed below.
+table, as described below.
When the {map} keyword is not specified in your input script, LAMMPS
only creates a map for "atom_styles"_atom_style.html for molecular
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index 7d9e443e7da7455de147ca1531daab58887e65f8..8facb4de63ebfb527e11108ba02e381db6a1425f 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -173,7 +173,7 @@ There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands
compute"_Commands_compute.html doc page are followed by one or more of
-(g,i,k,o,t) to indicate which accerlerated styles exist.
+(g,i,k,o,t) to indicate which accelerated styles exist.
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
"angle/local"_compute_bond_local.html - theta and energy of each angle
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index cda4a36b34d01c83a4977440adc94e747ea090df..46db81eb9e3d366592e3a1a9e254fb3d3f04170a 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -32,7 +32,7 @@ according to the formulation given in "(Ackland)"_#Ackland.
Historically, LAMMPS had two, slightly different implementations of
the algorithm from the paper. With the {legacy} keyword, it is
possible to switch between the pre-2015 ({legacy yes}) and post-2015
-implemention ({legacy no}). The post-2015 variant is the default.
+implementation ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt
index 66eecd195da4fb19851d5d84349c72391e51add6..ddc4cc82d30483aa2e5352ed034da9a48bfdb87b 100644
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@@ -67,7 +67,7 @@ identify crystal-like atoms in a system, as discussed in "ten
Wolde"_#tenWolde1.
The ID of the previously specified "compute
-orientorder/atom"_compute_orientorder/atom command is specified as
+orientorder/atom"_compute_orientorder_atom.html command is specified as
{orientorderID}. The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
described in its documentation. Note that orientorder/atom compute
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 669ab9f7ca3ea74e4a3a8a0b5537c0b09cbd814d..7cea62c7b3a4e824de53b234bba0176130447941 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -85,7 +85,7 @@ dump 1 all custom 100 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
refresh c_dsp delay 100 :pre
-The "dump_modify thresh"_dump_modify.html command will only ouptut
+The "dump_modify thresh"_dump_modify.html command will only output
atoms that have displaced more than 0.6 Angstroms on each snapshot
(assuming metal units). The dump_modify {refresh} option triggers a
call to this compute at the end of every dump.
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index b3891841b8ce04185b3f0705e877b8c34f87b34f..04f0fd0b82df8a98ac3a11311ba95fe4a7882479 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -14,7 +14,7 @@ compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
ID, group-ID are documented in "compute"_compute.html command :l
entropy/atom = style name of this compute command :l
-sigma = width of gaussians used in the g(r) smoothening :l
+sigma = width of gaussians used in the g(r) smoothing :l
cutoff = cutoff for the g(r) calculation :l
one or more keyword/value pairs may be appended :l
keyword = {avg} or {local}
@@ -49,14 +49,14 @@ This parameter for atom i is computed using the following formula from
where r is a distance, g(r) is the radial distribution function of atom
i and rho is the density of the system. The g(r) computed for each
-atom i can be noisy and therefore it is smoothened using:
+atom i can be noisy and therefore it is smoothed using:
:c,image(Eqs/pair_entropy2.jpg)
where the sum in j goes through the neighbors of atom i, and sigma is a
-parameter to control the smoothening.
+parameter to control the smoothing.
-The input parameters are {sigma} the smoothening parameter, and the
+The input parameters are {sigma} the smoothing parameter, and the
{cutoff} for the calculation of g(r).
If the keyword {avg} has the setting {yes}, then this compute also
@@ -82,7 +82,7 @@ If the {local yes} option is used, the g(r) is normalized by the
local density around each atom, that is to say the density around each
atom is the number of neighbors within the neighbor list cutoff divided
by the corresponding volume. This option can be useful when dealing with
-inhomogeneus systems such as those that have surfaces.
+inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
constant 4.05 Angstroms),
diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt
index 192ea0bc9ec96d6c7691214f78f7cf2c080f4ddd..5ba2100fbaa0bb51ab8f2bc112cb22248d745639 100644
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
N = # of extra degrees of freedom to subtract
{extra} syntax is identical to {extra/dof}, will be disabled at some point
{dynamic/dof} value = {yes} or {no}
- yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
:ule
diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt
index a2c25fcc8dc0dbe737e3efb76fd1ef57197dd765..b309019e30fd7927b1c3226612e4f065f397efad 100644
--- a/doc/src/compute_pair.txt
+++ b/doc/src/compute_pair.txt
@@ -27,7 +27,9 @@ compute 1 all pair reax :pre
Define a computation that extracts additional values calculated by a
pair style, and makes them accessible for output or further processing
-by other commands. The group specified for this command is ignored.
+by other commands.
+
+NOTE: The group specified for this command is [ignored].
The specified {pstyle} must be a pair style used in your simulation
either by itself or as a sub-style in a "pair_style hybrid or
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index c4c0fc405ff563273c1d9b1ff72c51a638eedf02..72ed0ba5c4003af0a1ca3881baf190a93f6db58d 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -27,8 +27,8 @@ compute 2 all pressure/uef my_temp_uef virial :pre
This command is used to compute the pressure tensor in
the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or
-"fix npt/uef"_fix_nh_uef.html" is used.
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html is used.
It is not necessary to use this command to compute the scalar
value of the pressure. A "compute pressure"_compute_pressure.html
may be used for that purpose.
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index 512009093c0e052e8e7b43f44455d1f61d7e6fb8..bc1e3049fadc20b8f98018bcf2cf1fe69426e85f 100644
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@@ -158,7 +158,7 @@ corresponding attribute is in, e.g. velocity units for vx, charge
units for q, etc.
For the spin quantities, sp is in the units of the Bohr magneton, spx,
-spy, and spz are adimentional quantities, and fmx, fmy and fmz are
+spy, and spz are adimensional quantities, and fmx, fmy and fmz are
given in rad.THz.
[Restrictions:] none
diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt
index 04b38682cc4957ac67459b18652249b1dfb75f14..d11ae9e3bf0ba508a42e46e4cdb8023e33ef21f1 100644
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@@ -182,7 +182,7 @@ change from zero to one at the location of the spike in g(r).
NOTE: compute rdf can handle dynamic groups and systems where atoms
are added or removed, but this causes that certain normalization
-parameters need to be recomputed in every step and include collective
+parameters need to be re-computed in every step and include collective
communication operations. This will reduce performance and limit
parallel efficiency and scaling. For systems, where only the type
of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html),
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 9b829a70fcb82a1de7defbafbce6b949ca833f20..67c6209bdf302e471ce2847a1400f4b8ccc799c5 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -92,7 +92,7 @@ dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\
This section explains the rigid body attributes that can be specified.
-The {id} attribute is the atomID of the atom which owns the rigid body, which is
+The {id} attribute is the atom-ID of the atom which owns the rigid body, which is
assigned by the "fix rigid/small"_fix_rigid.html command.
The {mol} attribute is the molecule ID of the rigid body. It should
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index 92f5923de05f735931aae9908844b197ad127fe3..e9ff2e739b111a8b733fd7aa01f31262834ed45f 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -25,7 +25,7 @@ Define a computation that outputs the CFL-stable time increment per
particle. This time increment is essentially given by the speed of
sound, divided by the SPH smoothing length. Because both the speed of
sound and the smoothing length typically change during the course of a
-simulation, the stable time increment needs to be recomputed every
+simulation, the stable time increment needs to be re-computed every
time step. This calculation is performed automatically in the
relevant SPH pair styles and this compute only serves to make the
stable time increment accessible for output purposes.
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 787ff8cdcfa822ba37c896d464e6c9655d5e543a..e6185a2dd8f88ca2c5c4196f4621e067bb684a8c 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -48,7 +48,7 @@ variable temp_mag equal c_out_mag\[6\] :pre
thermo 10
thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre
-This serie of commands evaluates the total magnetization along z, the norm of
+This series of commands evaluates the total magnetization along z, the norm of
the total magnetization, and the magnetic temperature. Three variables are
assigned to those quantities. The thermo and thermo_style commands print them
every 10 timesteps.
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index 9a509da4503db6cb3a9e03b0314de6300e28d36b..97e1d6e1ae87ff94166dd20f67518c5dc1d29d92 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -24,8 +24,8 @@ compute 2 sel temp/uef :pre
This command is used to compute the kinetic energy tensor in
the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or
-"fix npt/uef"_fix_nh_uef.html" is used.
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html is used.
It is not necessary to use this command to compute the scalar
value of the temperature. A "compute temp"_compute_temp.html
may be used for that purpose.
diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt
index 57faf97ad1bf1d213135707989985a1f866a8f8d..a55288e1dbad05e79f32d047355bafd3d65d3caa 100644
--- a/doc/src/delete_atoms.txt
+++ b/doc/src/delete_atoms.txt
@@ -84,7 +84,7 @@ connectivity that has already been assigned. However, the
"reset_ids"_reset_ids.html command can be used after this command to
accomplish the same thing.
-Note that the re-assignement of IDs is not really a compression, where
+Note that the re-assignment of IDs is not really a compression, where
gaps in atom IDs are removed by decrementing atom IDs that are larger.
Instead the IDs for all atoms are erased, and new IDs are assigned so
that the atoms owned by individual processors have consecutive IDs, as
diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt
index b29fa82f2d0d16c9b1a252073080aba43332605c..4e336046968ca3b0dc3c7f32db3a341ece4d9c9b 100644
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@@ -140,7 +140,7 @@ enough for a processor to acquire the ghost atoms its needs to compute
bond, angle, etc interactions.
If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
-weighting list is not recomputed, this can cause a later "fix
+weighting list is not re-computed, this can cause a later "fix
shake"_fix_shake.html command to fail due to an atom's bonds being
inconsistent with the weighting list. This should only happen if the
group used in the fix command includes both atoms in the bond, in
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 98bcbc5e551e85216732c74afebbc6c6b361a663..72f493591677e0e01eefde4f7044898f46966da1 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -914,7 +914,7 @@ flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
-maxifiles = -1
+maxfiles = -1
nfile = 1
pad = 0
pbc = no
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index dd2b212f0baafc6efd4200c42eb4439e1d6715e3..b5f157cf292cba47d11fc6258b0fdea4ca34cf54 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -99,7 +99,7 @@ USER-MOLFILE package only provides the interface code, not the plugins.
These can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD
-or other programs that use them) without having to recompile the
+or other programs that use them) without having to re-compile the
application itself. The plugins are installed in the directory:
<VMDHOME>/plugins/<VMDARCH>/molfile
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 9c3a1d0349fd097eb9f5572b943872bce1254a4e..ee0d006fe8396fc265a9493a27af86f156b58aea 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -30,7 +30,7 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a
timestepping or minimization. Examples include updating of atom
positions and velocities due to time integration, controlling
temperature, applying constraint forces to atoms, enforcing boundary
-conditions, computing diagnostics, etc. There are hundredes of fixes
+conditions, computing diagnostics, etc. There are hundreds of fixes
defined in LAMMPS and new ones can be added; see the
"Modify"_Modify.html doc page for details.
@@ -164,7 +164,7 @@ There are also additional accelerated fix styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands fix"_Commands_fix.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
-accerlerated styles exist.
+accelerated styles exist.
"adapt"_fix_adapt.html - change a simulation parameter over time
"addforce"_fix_addforce.html - add a force to each atom
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index 7acc22d702e4b7cfd496df2865fdbdc0844bd276..b7d4e7badfc5496c884c92ae7307d92550007893 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -56,7 +56,7 @@ value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
-should all be in atomspheres. Furthermore, the table should start/end at a
+should all be in atmospheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 7317dd26bb3b9d4b563b0266364490fafc39d37c..8e7cb1bdaef8b565a4138bcd5a68cd0d4343a277 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -34,7 +34,7 @@ react = mandatory argument indicating new reaction specification :l
Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
- map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
+ map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l
individual_keyword = {prob} or {stabilize_steps} :l
{prob} values = fraction seed
@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
nearest bonding partners, these two atoms are identified as the
bonding atom pair of the reaction site. Once this unique bonding atom
pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
[Default:]
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
:line
diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt
index be4fbd255b58983cd52ac8a9fbb1e4144b5a2f6c..0c5a4493ae7d7a2507770720bd025c44f157e5bd 100644
--- a/doc/src/fix_dt_reset.txt
+++ b/doc/src/fix_dt_reset.txt
@@ -14,7 +14,7 @@ fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command
dt/reset = style name of this fix command
-N = recompute dt every N timesteps
+N = re-compute dt every N timesteps
Tmin = minimum dt allowed which can be NULL (time units)
Tmax = maximum dt allowed which can be NULL (time units)
Xmax = maximum distance for an atom to move in one timestep (distance units)
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index b30966c2f941de518e42f4c90463f543a21fdad5..4868761d4207675072fc00c1f6fd66c1c7a06629 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -47,7 +47,7 @@ this can significantly accelerate the simulation.
The filter computes a cluster decomposition of the molecular structure
following the criteria indicated by the options a, b, t and m. This
process is similar to the approach in "fix shake"_fix_shake.html,
-however, the clusters are not kept contrained. Instead, the position
+however, the clusters are not kept constrained. Instead, the position
is slightly modified only for the computation of long-range forces. A
good cluster decomposition constitutes in building clusters which
contain the fastest covalent bonds inside clusters.
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index b115aba7dfa38d5a85a0aee82000d2e8bf568fcd..64486a9cc7922efb7a689c09aaba3b98d652671a 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -63,7 +63,7 @@ electrostatics, or that contain parameters that depend on box size:
all of these options will be initialized based on the cell size in the
LAMMPS-side initial configuration and kept constant during the run.
This is required to e.g. obtain reproducible and conserved forces.
-If the cell varies too wildly, it may be advisable to reinitialize
+If the cell varies too wildly, it may be advisable to re-initialize
these interactions at each call. This behavior can be requested by
setting the {reset} switch.
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 7bb25e0a687af2c0af3f14a1ccd9d0c9a73e7257..d4836706e2a8577cc3c27b70d9f630aaec1ede51 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -34,7 +34,7 @@ the following stochastic differential equation:
:c,image(Eqs/fix_langevin_spin_sLLG.jpg)
-with lambda the transverse damping, and eta a random verctor.
+with lambda the transverse damping, and eta a random vector.
This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG)
equation.
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index bd61e29dcb66f9c19772345cbe3c19161143474e..c97095bcfc98c015f59c271dc9aa70249351c587 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -44,7 +44,7 @@ Once LAMMPS is built with the LATTE package, you can run the example
input scripts for molecular dynamics or energy minimization that are
found in examples/latte.
-A step-by-step tutorial can be follwed at: "LAMMPS-LATTE
+A step-by-step tutorial can be followed at: "LAMMPS-LATTE
tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
The {peID} argument is not yet supported by fix latte, so it must be
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 1a5239782268f34870cd3ec3faac1b560f7c451a..d9012d8cb396371d3fd4568cbba35b19c5d6e275 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -187,7 +187,7 @@ NOTE: Care must be taken when choosing both a value for dx, and a
simulation domain size. This fix uses the same subdivision of the
simulation domain among processors as the main LAMMPS program. In
order to uniformly cover the simulation domain with lattice sites, the
-lengths of the individual LAMMPS subdomains must all be evenly
+lengths of the individual LAMMPS sub-domains must all be evenly
divisible by dx. If the simulation domain size is cubic, with equal
lengths in all dimensions, and the default value for dx is used, this
will automatically be satisfied.
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index ddb5f9a4cd4346e6f0d3195a101445c15eaedfde..f50747948a91152948fa1c31e4037ef735d2035a 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -21,7 +21,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof}
{virial} value = {yes} or {no}
{respa} value = {1} to {max respa level} or {0} (for outermost level)
{dynamic/dof} value = {yes} or {no}
- yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ yes/no = do or do not re-compute the number of degrees of freedom (DOF) contributing to the temperature
{bodyforces} value = {early} or {late}
early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index d331d9ad75fbf7c2a203bfe68bb1035abcfd410a..521dfff12b2fe03b0b8c5aa221e1a63abb596676 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -168,7 +168,7 @@ The difference between these two {estyle} options is as follows. When
{estyle} is specified as {last/efirst}, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
-intermediate repilica may relax "faster" and reach a lower energy than
+intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying {estyle} as {last/efirst/middle} which will alter the
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index ae403cafd1d8ff7c5ee8f6e7fcc0589dd9437cb6..dc05948de338c24441d5d1849c6f347dc2a8e311 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -174,7 +174,7 @@ This fix can be used with the "fix_modify"_fix_modify.html {temp} and
{press} options. The temperature and pressure computes used must be of
type {temp/uef} and {pressure/uef}.
-This fix computes the same global scalar and vecor quantities as "fix
+This fix computes the same global scalar and vector quantities as "fix
npt"_fix_nh.html.
The fix is not invoked during "energy minimization"_minimize.html.
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index a3d1ab702ebd6b28c55215a80d40d548017cc863..f013ebfae1ca4e28fe6b0335237f31fa78d568b4 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -11,7 +11,7 @@ fix rhok command :h3
fix ID group-ID rhok nx ny nz K a :pre
ID, group-ID are documented in "fix"_fix.html command
-nx, ny, nz = k-vektor of collective density field
+nx, ny, nz = k-vector of collective density field
K = spring constant of bias potential
a = anchor point of bias potential :ul
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index d489762e8022bdfe7f4d82af51a7642fe8fbd286..5d65856735d4125a6b0e62cebfb5b6980914622c 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -442,11 +442,11 @@ couple none :pre
The keyword/value option pairs are used in the following ways.
The {reinit} keyword determines, whether the rigid body properties
-are reinitialized between run commands. With the option {yes} (the
+are re-initialized between run commands. With the option {yes} (the
default) this is done, with the option {no} this is not done. Turning
-off the reinitialization can be helpful to protect rigid bodies against
+off the re-initialization can be helpful to protect rigid bodies against
unphysical manipulations between runs or when properties cannot be
-easily recomputed (e.g. when read from a file). When using the {infile}
+easily re-computed (e.g. when read from a file). When using the {infile}
keyword, the {reinit} option is automatically set to {no}.
The {langevin} and {temp} and {tparam} keywords perform thermostatting
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index 644c04eadb9efe7e64d6f51f68893e8d9e59a1e7..774842c7cfe83a47faa17aea140313a81e124fdb 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -77,7 +77,7 @@ normalized. But since it represents the {absolute} displacement of
group-ID2 relative to the fix group, (1,1,0) is a different spring
than (-1,-1,0). For each vector component, the displacement can be
described with the {auto} parameter. In this case the direction is
-recomputed in every step, which can be useful for steering a local
+re-computed in every step, which can be useful for steering a local
process where the whole object undergoes some other change. When the
relative positions and distance between the two groups are not in
equilibrium, the same spring force described above is applied to atoms
diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt
index ade64d2056e0e23e58e3e762620077d6ada3f1f1..2ee045141a70897ff5bb277f60d19e6bd00afb59 100644
--- a/doc/src/fix_surface_global.txt
+++ b/doc/src/fix_surface_global.txt
@@ -6,7 +6,7 @@
:line
-fix wall/surface/globale command :h3
+fix wall/surface/global command :h3
[Description:]
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index f1ff39d80b0c0806e1e3e4b6928f95b96abeef27..c296ff4039e0827464ba616081d6bb9630943056 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -25,6 +25,7 @@ Build_basics.html
Build_settings.html
Build_package.html
Build_extras.html
+Build_windows.html
Run_head.html
Run_basics.html
Run_options.html
@@ -523,6 +524,7 @@ 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/neb.txt b/doc/src/neb.txt
index 57e122fdcd53cec635f42746fd23c475f8fca7fc..75d199e0b4cd91e20e1e5e677ac09da52423c7dc 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -338,9 +338,9 @@ energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i.
-When a NEB calculation does not converge properly, the suplementary
+When a NEB calculation does not converge properly, the supplementary
information can help understanding what is going wrong. For instance
-when the path angle becomes accute the definition of tangent used in
+when the path angle becomes accute, the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2.
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 8b0581929ff10cffd2661b5268761e61a276e418..65117ba3c3c15d4ec4e4e2dfd5a27a9fe7115c61 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -363,7 +363,7 @@ specified with the OMP_NUM_THREADS environment variable or the {omp}
keyword). The extra thread is dedicated for performing part of the
"PPPM solver"_kspace_style.html computations and communications. This
can improve parallel performance on processors supporting
-Simultaneous Multithreading (SMT) such as Hyperthreading on Intel
+Simultaneous Multithreading (SMT) such as Hyper-Threading (HT) on Intel
processors. In this mode, one additional thread is generated per MPI
process. LAMMPS will generate a warning in the case that more threads
are used than available in SMT hardware on a node. If the PPPM solver
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_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 4c43978fe5a44eae7d15fc21aecf5e2d2c8f780c..d9780e03200bc41976535cc77de8d7edfbc348e5 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -52,18 +52,18 @@ The latter corrects for artifacts occurring at short distances which
become an issue for soft vdW potentials.
The {buck6d} styles include a smoothing function which is invoked
-according to the global smooting parameter within the specified
+according to the global smoothing parameter within the specified
cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing
within 90% of the cutoff. No smoothing is applied at a value
of 1.0. For the {gauss/dsf} style this smoothing is only applicable
for the dispersion damped Buckingham potential. For the {gauss/long}
styles the smoothing function can also be invoked for the real
-space coulomb interactions which enforce continous energies and
+space coulomb interactions which enforce continuous energies and
forces at the cutoff.
Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long}
evaluate a Coulomb potential using spherical Gaussian type charge
-distributions which effectively dampen electrostatic ineractions
+distributions which effectively dampen electrostatic interactions
for high charges at close distances. The electrostatic potential
is thus evaluated as:
diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt
index 63f85f23d5e480a77ccc5f0c673cdde81d5a2d16..88f95b5b2cb6f62fc2b2ea903093c21509e46c45 100644
--- a/doc/src/pair_coeff.txt
+++ b/doc/src/pair_coeff.txt
@@ -128,7 +128,7 @@ There are also additional accelerated pair styles (not listed on the
distribution for faster performance on CPUs, GPUs, and KNLs. The
individual style names on the "Commands pair"_Commands_pair.html doc
page are followed by one or more of (g,i,k,o,t) to indicate which
-accerlerated styles exist.
+accelerated styles exist.
:line
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index adaeeb8390e07f080259009962109f909857f56b..8b1ceab85857a0621b8ac6f9ad8b9cbdf8c33e88 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -16,7 +16,7 @@ max_cell_size = global maximum cell size for DSMC interactions (distance units)
seed = random # seed (positive integer)
weighting = macroparticle weighting
Tref = reference temperature (temperature units)
-Nrecompute = recompute v*sigma_max every this many timesteps (timesteps)
+Nrecompute = re-compute v*sigma_max every this many timesteps (timesteps)
Nsample = sample this many times in recomputing v*sigma_max :ul
[Examples:]
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 02d0db7af25e6c86f6ece52e56623bf71825173a..c74028faa91fe9ff80ef42560c13d1bf74b3c685 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -39,7 +39,7 @@ in "(Kolmogorov)"_#Kolmogorov2.
Where Tap(r_ij) is the taper function which provides a continuous
cutoff (up to third derivative) for interatomic separations larger than
-r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
+r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
It is important to include all the pairs to build the neighbor list for
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index f557e6c731db499de0820bbb39ef9aab1aa0f46a..912fca165750f7f9a63288ef34c8015f23a37a29 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -30,7 +30,7 @@ which is to take all normals along the z-axis.
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
-It is important to have a suffiently large cutoff to ensure smooth forces.
+It is important to have a sufficiently large cutoff to ensure smooth forces.
Energies are shifted so that they go continously to zero at the cutoff assuming
that the exponential part of {Vij} (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for {Vij} above.
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 23da86fc495a6daabdee6048cc4d8dcb72525b6b..e8baf14d2eefb694ff107609d65afad5d8f9b3f4 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -29,7 +29,7 @@ The {python} pair style provides a way to define pairwise additive
potential functions as python script code that is loaded into LAMMPS
from a python file which must contain specific python class definitions.
This allows to rapidly evaluate different potential functions without
-having to modify and recompile LAMMPS. Due to python being an
+having to modify and re-compile LAMMPS. Due to python being an
interpreted language, however, the performance of this pair style is
going to be significantly slower (often between 20x and 100x) than
corresponding compiled code. This penalty can be significantly reduced
@@ -98,7 +98,7 @@ verify, that the potential definition in the python class and in the
LAMMPS input match.
Here is an example for a single type Lennard-Jones potential class
-{LJCutMelt} in reducted units, which defines an atom type {lj} for
+{LJCutMelt} in reduced units, which defines an atom type {lj} for
which the parameters epsilon and sigma are both 1.0:
class LJCutMelt(LAMMPSPairPotential):
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index b33897c5aa506cd6be92ef275194ec2ceb83ce44..9dfead300ea5cda19aec67f9073a1bc44b1da51d 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -93,7 +93,7 @@ There are also additional accelerated pair styles (not listed here)
included in the LAMMPS distribution for faster performance on CPUs,
GPUs, and KNLs. The individual style names on the "Commands
pair"_Commands_pair.html doc page are followed by one or more of
-(g,i,k,o,t) to indicate which accerlerated styles exist.
+(g,i,k,o,t) to indicate which accelerated styles exist.
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
@@ -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/read_data.txt b/doc/src/read_data.txt
index ef899a15b44b153621cc194d317c3a313bd9afac..6aa30d9e634c30f4e0831a431c5e636f5c176bc2 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -124,14 +124,14 @@ bond atoms or bad dynamics.
The three choices for the {add} argument affect how the atom IDs and
molecule IDs of atoms in the data file are treated. If {append} is
specified, atoms in the data file are added to the current system,
-with their atom IDs reset so that an atomID = M in the data file
-becomes atomID = N+M, where N is the largest atom ID in the current
+with their atom IDs reset so that an atom-ID = M in the data file
+becomes atom-ID = N+M, where N is the largest atom ID in the current
system. This rule is applied to all occurrences of atom IDs in the
data file, e.g. in the Velocity or Bonds section. This is also done
for molecule IDs, if the atom style does support molecule IDs or
they are enabled via fix property/atom. If {IDoffset} is specified,
then {IDoffset} is a numeric value is given, e.g. 1000, so that an
-atomID = M in the data file becomes atomID = 1000+M. For systems
+atom-ID = M in the data file becomes atom-ID = 1000+M. For systems
with enabled molecule IDs, another numerical argument {MOLoffset}
is required representing the equivalent offset for molecule IDs.
If {merge} is specified, the data file atoms
@@ -139,7 +139,7 @@ are added to the current system without changing their IDs. They are
assumed to merge (without duplication) with the currently defined
atoms. It is up to you to insure there are no multiply defined atom
IDs, as LAMMPS only performs an incomplete check that this is the case
-by insuring the resulting max atomID >= the number of atoms. For
+by insuring the resulting max atom-ID >= the number of atoms. For
molecule IDs, there is no check done at all.
The {offset} and {shift} keywords can only be used if the {add}
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 0195dce9114f4a3d0bf30a805a1c0f0e31a70be7..79a481746ec8843b20d567a67b1c71a2a234e797 100644
--- a/doc/src/replicate.txt
+++ b/doc/src/replicate.txt
@@ -14,7 +14,7 @@ replicate nx ny nz {keyword} :pre
nx,ny,nz = replication factors in each dimension :ulb
optional {keyword} = {bbox} :l
- {bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
+ {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
[Examples:]
@@ -46,7 +46,7 @@ image flags that differ by 1. This will allow the bond to be
unwrapped appropriately.
The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's subdomain when assigning
+in replicas that overlap with a processor's sub-domain when assigning
atoms to processors, and thus can result in substantial speedups for
calculations using a large number of processors. It does require
temporarily using more memory.
diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt
index 391b51fde99e167d813bef98b3a62f96786ed1de..8b217c7b1cc5f60a566ca858354f9c1fdb84ec56 100644
--- a/doc/src/reset_ids.txt
+++ b/doc/src/reset_ids.txt
@@ -23,7 +23,7 @@ for bond, angle, dihedral, improper topology data. This will
create a set of IDs that are numbered contiguously from 1 to N
for a N atoms system.
-This can be useful to do after perfoming a "delete_atoms" command for
+This can be useful to do after performing a "delete_atoms" command for
a molecular system. The delete_atoms compress yes option will not
perform this operation due to the existence of bond topology. It can
also be useful to do after any simulation which has lost atoms,
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 7c034f36e0c6d002739c35362afca8440f9358a5..e0fae3909dc771ca15459230886ee5667a1715f2 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -49,7 +49,7 @@ as it writes successive restart files.
Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you,
for example, to write out archival restart files every 100000 steps
-using a single filenname, and more frequent temporary restart files
+using a single filename, and more frequent temporary restart files
every 1000 steps, using two filenames. Using restart 0 will turn off
both modes of output.
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 6dd9b56908960bbbe820bcd7f2667a3faf158a73..9defd1314ea9d404ff24aee6e106c2153af9c0dd 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -318,7 +318,7 @@ bond forces = level 1 (innermost loop)
angle forces = same level as bond forces
dihedral forces = same level as angle forces
improper forces = same level as dihedral forces
-pair forces = leven N (outermost level)
+pair forces = level N (outermost level)
kspace forces = same level as pair forces
inner, middle, outer forces = no default :ul
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index a57b61664d56e76b28d3aad9f2059bdbb24a9c31..283aad6c2d326b77111ffc94fc01d9bfde888249 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -64,7 +64,7 @@ e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a manybody potential will alter the
-neigborlist and thus can render the computation of those interactions
+neighbor list and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
@@ -110,7 +110,7 @@ simulation.
The two exceptions to this rule are (a) if the {angle} or {dihedral}
keywords are set to {yes} (see below), or (b) if the
"delete_bonds"_delete_bonds.html command is used with the {special}
-option that recomputes the 1-2,1-3,1-4 topologies after bonds are
+option that re-computes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the "delete_bonds"_delete_bonds.html command for more
details.
diff --git a/doc/utils/converters/lammpsdoc/lammps_filters.py b/doc/utils/converters/lammpsdoc/lammps_filters.py
index 11460185db56eed8d1b71e71f3b5ec4442c07f09..7b1481ceb9b75da66bbf388fab4d80560b995019 100644
--- a/doc/utils/converters/lammpsdoc/lammps_filters.py
+++ b/doc/utils/converters/lammpsdoc/lammps_filters.py
@@ -64,7 +64,7 @@ def filter_file_header_until_first_horizontal_line(content):
common_links = "\n.. _lws: http://lammps.sandia.gov\n" \
".. _ld: Manual.html\n" \
- ".. _lc: Section_commands.html#comm\n"
+ ".. _lc: Commands_all.html\n"
if first_hr >= 0:
return content[first_hr+len(hr):].lstrip() + common_links
diff --git a/doc/utils/converters/tests/test_lammps_filters.py b/doc/utils/converters/tests/test_lammps_filters.py
index 6c25c23a793828857f2e41ade334f1af9a75d12b..8d2fa2e57760257a2890fc3be91e49b93c70aa66 100644
--- a/doc/utils/converters/tests/test_lammps_filters.py
+++ b/doc/utils/converters/tests/test_lammps_filters.py
@@ -47,7 +47,7 @@ class TestStructuralFilters(unittest.TestCase):
self.assertEqual("Title\n\n"
"\n.. _lws: http://lammps.sandia.gov\n"
".. _ld: Manual.html\n"
- ".. _lc: Section_commands.html#comm\n", s)
+ ".. _lc: Commands_all.html\n", s)
def test_filter_multiple_horizontal_rules(self):
s = self.txt2rst.convert(":hline\n"
diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
index 39ee684a0b078edf4f771d3f52e975bbbf047d20..1eb53c70a29b5becf7c6abd236e3d2312bc00b4e 100644
--- a/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
+++ b/doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
@@ -18,7 +18,7 @@
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
{% endif %}
<a href="http://lammps.sandia.gov">Website</a>
- <a href="Section_commands.html#comm">Commands</a>
+ <a href="Commands_all.html">Commands</a>
{% endif %}
</li>
</ul>
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index fb08e4e97e5b19ad0713819f173a78555d0ff42d..febd5c20a02d74a4d588e697cde72da12e7be840 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -260,6 +260,8 @@ Caro
cartesian
Cates
cbecker
+ccache
+ccmake
CCu
cd
cdeam
@@ -286,6 +288,9 @@ cgs
Chalopin
Champaign
charmm
+charmmfsw
+charmmfsh
+charmm
CHARMM
checkmark
checkqeq
@@ -308,6 +313,8 @@ Clebsch
Clermont
clo
Clovertown
+cmake
+CMake
cmap
Cmax
cmdlist
@@ -410,6 +417,7 @@ Cval
cvar
cvff
cwiggle
+cygwin
Cygwin
Cyrot
cyrstals
@@ -585,6 +593,7 @@ ehanced
ehex
eHEX
Ei
+Eigen
Eigensolve
Eike
eim
@@ -713,7 +722,10 @@ fhg
Fi
figshare
Fij
-filenname
+filename
+filenames
+Filename
+Filenames
fileper
Fincham
Finchham
@@ -1385,6 +1397,7 @@ Mikami
Militzer
Minary
mincap
+mingw
minima
minimizations
minimizer
@@ -1456,6 +1469,7 @@ Mtotal
Muccioli
Mukherjee
Mulders
+multi
multibody
Multibody
multicenter
@@ -2489,6 +2503,7 @@ velocites
Verlag
verlet
Verlet
+versa
ves
vhi
vibrational
@@ -2566,6 +2581,7 @@ whitespace
Wi
Wicaksono
wih
+wildcard
Wirnsberger
wirtes
witin
diff --git a/examples/README b/examples/README
index a8dfe63d923f211598141b76a5ec892ea4e48d60..d6c946725f1beaacb7f19278e232bf5da035a533 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
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/lib/latte/Makefile.lammps.ifort b/lib/latte/Makefile.lammps.ifort
index 0491bdd8a5f41065df995def3b3c0105600fdf28..90010210af583dfd2a38823a82f64222ea0c460a 100644
--- a/lib/latte/Makefile.lammps.ifort
+++ b/lib/latte/Makefile.lammps.ifort
@@ -4,9 +4,9 @@
latte_SYSINC =
latte_SYSLIB = ../../lib/latte/filelink.o \
- -llatte -lifcore -lsvml -lompstub -limf -lmkl_intel_lp64 \
- -lmkl_intel_thread -lmkl_core -lmkl_intel_thread -lpthread \
- -openmp -O0
+ -llatte -lifport -lifcore -lsvml -lompstub -limf \
+ -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core \
+ -lmkl_intel_thread -lpthread -openmp
latte_SYSPATH = -openmp -L${MKLROOT}/lib/intel64 -lmkl_lapack95_lp64 \
-L/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64
diff --git a/python/lammps.py b/python/lammps.py
index 2f4ffb642ef084fbbd1b7567bfc363220288dafc..598e4c506f1bf64d451432305d8c15ae8bd82fdb 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -173,6 +173,9 @@ class lammps(object):
self.lib.lammps_open(narg,cargs,comm_val,byref(self.lmp))
else:
+ if lammps.has_mpi4py:
+ from mpi4py import MPI
+ self.comm = MPI.COMM_WORLD
self.opened = 1
if cmdargs:
cmdargs.insert(0,"lammps.py")
@@ -862,6 +865,10 @@ class PyLammps(object):
def run(self, *args, **kwargs):
output = self.__getattr__('run')(*args, **kwargs)
+
+ if(lammps.has_mpi4py):
+ output = self.lmp.comm.bcast(output, root=0)
+
self.runs += get_thermo_data(output)
return output
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/msm.cpp b/src/KSPACE/msm.cpp
index 9f3221449bb2329923cfa9ed987beb6f26e58e3f..efa2c87296dbd1a78ec7ffba150adb583e39acb2 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -177,7 +177,7 @@ void MSM::init()
if (sizeof(FFT_SCALAR) != 8)
error->all(FLERR,"Cannot (yet) use single precision with MSM "
- "(remove -DFFT_SINGLE from Makefile and recompile)");
+ "(remove -DFFT_SINGLE from Makefile and re-compile)");
// extract short-range Coulombic cutoff from pair style
@@ -419,7 +419,7 @@ void MSM::setup()
boxlo = domain->boxlo_lamda;
// ghost grid points depend on direct sum interaction limits,
- // so need to recompute local grid
+ // so need to re-compute local grid
set_grid_local();
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/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/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-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h
index 509eca5de35892b3094cf5749b7d6d088d7b0d18..3029ba9db541e095af265657d5f940998cce224f 100644
--- a/src/USER-COLVARS/fix_colvars.h
+++ b/src/USER-COLVARS/fix_colvars.h
@@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars)
#define LMP_FIX_COLVARS_H
#include "fix.h"
-#include <vector>
// forward declaration
class colvarproxy_lammps;
@@ -77,13 +76,6 @@ class FixColvars : public Fix {
int num_coords; // total number of atoms controlled by this fix
tagint *taglist; // list of all atom IDs referenced by colvars.
- // TODO get rid of these
- // std::vector<cvm::atom_pos> *coords; // coordinates of colvar atoms
- // std::vector<cvm::rvector> *forces; // received forces of colvar atoms
- // std::vector<cvm::rvector> *oforce; // old total forces of colvar atoms
- // std::vector<cvm::real> *masses;
- // std::vector<cvm::real> *charges;
-
int nmax; // size of atom communication buffer.
int size_one; // bytes per atom in communication buffer.
struct commdata *comm_buf; // communication buffer
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 c72a1b027bafa28c9e219f1348111c4ec4016f97..ceac93178d1c617a6b0f976f8be607c1f704532e 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;
}
@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
hang_catch++;
// let's go ahead and catch the simplest of hangs
//if (hang_catch > onemol->natoms*4)
- if (hang_catch > atom->nlocal*3) {
- error->all(FLERR,"Excessive iteration of superimpose algorithm");
+ if (hang_catch > atom->nlocal*30) {
+ error->one(FLERR,"Excessive iteration of superimpose algorithm");
}
}
}
@@ -1554,6 +1554,39 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
error->one(FLERR,"Atom affected by reaction too close to template edge");
}
+ // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+ // 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) {
+ 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) {
+ int onemol_atomi = equivalences[i][1][myrxn];
+ int onemol_batom;
+ for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+ if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ if (newton_bond) {
+ int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+ for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+ onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+ if (onemol_batom == equivalences[i][1][myrxn]) {
+ if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+ error->one(FLERR,"Bond type affected by reaction too close to template edge");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
for (int i = 0; i < twomol->natoms; i++) {
@@ -1828,13 +1861,13 @@ void FixBondReact::glove_ghostcheck()
// noteworthy: it's only relevant for parallel
// here we add glove to either local_mega_glove or ghostly_mega_glove
- int ghostly = 0;
- for (int i = 0; i < onemol->natoms; i++) {
- if (atom->map(glove[i][1]) >= atom->nlocal) {
- ghostly = 1;
- break;
- }
- }
+ int ghostly = 1;
+ //for (int i = 0; i < onemol->natoms; i++) {
+ // if (atom->map(glove[i][1]) >= atom->nlocal) {
+ // ghostly = 1;
+ // break;
+ // }
+ //}
if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
@@ -2067,7 +2100,7 @@ void FixBondReact::update_everything()
nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
}
- for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+ for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
}
special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];
@@ -2587,7 +2620,7 @@ 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();
}
@@ -2595,7 +2628,7 @@ 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 11bf2ae01ed2790cc65b62afe79c7bb2f392ee44..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");
}
@@ -394,7 +394,7 @@ void PairAGNI::read_file(char *file)
if (nwords == 0) continue;
if (nwords > MAXWORD)
- error->all(FLERR,"Increase MAXWORD and recompile");
+ error->all(FLERR,"Increase MAXWORD and re-compile");
// words = ptrs to all words in line
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..eb2f357890acb170e0772bb1d36a4a8b804570b1 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");
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 3aa6d7748ce96b2c095857ed5e9f6c2acbc9314d..49c9db172f585f3be93eddd9b46fe82ef5c863c2 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -88,7 +88,7 @@ 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");
@@ -457,7 +457,7 @@ 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..1eb848fe06ae254766f8cfb4c54b760974392524 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -1618,7 +1618,7 @@ 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/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..ea448bd17874355dd51334cb3f113a3fb14c3c7d 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];
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/library.cpp b/src/library.cpp
index 13e07568667d6319bd52b2c9fe6166decf292953..245ae7ba84fe645720e43aa227eed2ef6fd8f701 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 +1515,7 @@ 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 " %lld",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 db73df1ad124b44dd86c4e3f314a9bdcb162255a..2192b25d9147aef94706956d2c16eea09c51e2b9 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "16 Aug 2018"
+#define LAMMPS_VERSION "22 Aug 2018"