Merge branch 'master' into less-compiler-warnings
This commit is contained in:
Axel Kohlmeyer
@ -43,6 +43,29 @@ function(validate_option name values)
|
||||
endif()
|
||||
endfunction(validate_option)
|
||||
|
||||
function(get_lammps_version version_header variable)
|
||||
file(READ ${version_header} line)
|
||||
set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
|
||||
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
|
||||
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
|
||||
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
|
||||
string(STRIP ${day} day)
|
||||
string(STRIP ${month} month)
|
||||
string(STRIP ${year} year)
|
||||
list(FIND MONTHS "${month}" month)
|
||||
string(LENGTH ${day} day_length)
|
||||
string(LENGTH ${month} month_length)
|
||||
if(day_length EQUAL 1)
|
||||
set(day "0${day}")
|
||||
endif()
|
||||
if(month_length EQUAL 1)
|
||||
set(month "0${month}")
|
||||
endif()
|
||||
set(${variable} "${year}${month}${day}" PARENT_SCOPE)
|
||||
endfunction()
|
||||
|
||||
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
|
||||
|
||||
# Cmake modules/macros are in a subdirectory to keep this file cleaner
|
||||
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
|
||||
|
||||
@ -121,10 +144,10 @@ if(BUILD_LIB)
|
||||
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
|
||||
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
|
||||
endif()
|
||||
set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
|
||||
mark_as_advanced(LIB_SUFFIX)
|
||||
if(LIB_SUFFIX)
|
||||
set(LIB_SUFFIX "_${LIB_SUFFIX}")
|
||||
set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
|
||||
mark_as_advanced(LAMMPS_LIB_SUFFIX)
|
||||
if(LAMMPS_LIB_SUFFIX)
|
||||
set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
|
||||
endif()
|
||||
endif()
|
||||
|
||||
@ -188,7 +211,7 @@ if(ENABLE_TESTING)
|
||||
endif(ENABLE_TESTING)
|
||||
|
||||
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
|
||||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
|
||||
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
|
||||
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
|
||||
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
|
||||
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
|
||||
@ -481,6 +504,39 @@ if(PKG_KIM)
|
||||
include_directories(${KIM_INCLUDE_DIRS})
|
||||
endif()
|
||||
|
||||
if(PKG_MESSAGE)
|
||||
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
|
||||
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
|
||||
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.cpp)
|
||||
|
||||
if(BUILD_SHARED_LIBS)
|
||||
add_library(cslib SHARED ${cslib_SOURCES})
|
||||
else()
|
||||
add_library(cslib STATIC ${cslib_SOURCES})
|
||||
endif()
|
||||
|
||||
if(BUILD_MPI)
|
||||
target_compile_definitions(cslib PRIVATE -DMPI_YES)
|
||||
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
|
||||
else()
|
||||
target_compile_definitions(cslib PRIVATE -DMPI_NO)
|
||||
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
|
||||
endif()
|
||||
|
||||
if(MESSAGE_ZMQ)
|
||||
target_compile_definitions(cslib PRIVATE -DZMQ_YES)
|
||||
find_package(ZMQ REQUIRED)
|
||||
target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
|
||||
target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
|
||||
else()
|
||||
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
|
||||
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
|
||||
endif()
|
||||
|
||||
list(APPEND LAMMPS_LINK_LIBS cslib)
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
|
||||
endif()
|
||||
|
||||
if(PKG_MSCG)
|
||||
find_package(GSL REQUIRED)
|
||||
option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
|
||||
@ -1040,14 +1096,14 @@ if(BUILD_LIB)
|
||||
if(LAMMPS_DEPS)
|
||||
add_dependencies(lammps ${LAMMPS_DEPS})
|
||||
endif()
|
||||
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX})
|
||||
if(BUILD_SHARED_LIBS)
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
|
||||
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
|
||||
endif()
|
||||
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
|
||||
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
|
||||
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
|
||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
|
||||
else()
|
||||
list(APPEND LMP_SOURCES ${LIB_SOURCES})
|
||||
endif()
|
||||
@ -1177,7 +1233,7 @@ endif()
|
||||
###############################################################################
|
||||
# Print package summary
|
||||
###############################################################################
|
||||
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
|
||||
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
|
||||
if(PKG_${PKG})
|
||||
message(STATUS "Building package: ${PKG}")
|
||||
endif()
|
||||
|
||||
48
cmake/FindLAMMPS.cmake.in
Normal file
48
cmake/FindLAMMPS.cmake.in
Normal file
@ -0,0 +1,48 @@
|
||||
# - Find liblammps
|
||||
# Find the native liblammps headers and libraries.
|
||||
#
|
||||
# The following variables will set:
|
||||
# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
|
||||
# LAMMPS_LIBRARIES - List of libraries when using lammps.
|
||||
# LAMMPS_API_DEFINES - lammps library api defines
|
||||
# LAMMPS_VERSION - lammps library version
|
||||
# LAMMPS_FOUND - True if liblammps found.
|
||||
#
|
||||
# In addition a LAMMPS::LAMMPS imported target is getting created.
|
||||
#
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
# certain rights in this software. This software is distributed under
|
||||
# the GNU General Public License.
|
||||
#
|
||||
# See the README file in the top-level LAMMPS directory.
|
||||
#
|
||||
|
||||
find_package(PkgConfig)
|
||||
|
||||
pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
|
||||
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
|
||||
|
||||
set(LAMMPS_VERSION @LAMMPS_VERSION@)
|
||||
set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
|
||||
|
||||
find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
|
||||
|
||||
set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
|
||||
set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
|
||||
|
||||
mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
|
||||
|
||||
if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
|
||||
add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
|
||||
set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
|
||||
endif()
|
||||
8
cmake/Modules/FindZMQ.cmake
Normal file
8
cmake/Modules/FindZMQ.cmake
Normal file
@ -0,0 +1,8 @@
|
||||
find_path(ZMQ_INCLUDE_DIR zmq.h)
|
||||
find_library(ZMQ_LIBRARY NAMES zmq)
|
||||
|
||||
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
|
||||
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
|
||||
@ -4,15 +4,15 @@
|
||||
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
|
||||
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
|
||||
|
||||
prefix=@CMAKE_INSTALL_FULL_PREFIX@
|
||||
prefix=@CMAKE_INSTALL_PREFIX@
|
||||
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
|
||||
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
|
||||
|
||||
Name: liblammps@LAMMPS_MACHINE@
|
||||
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
|
||||
URL: http://lammps.sandia.gov
|
||||
Version:
|
||||
Version: @LAMMPS_VERSION@
|
||||
Requires:
|
||||
Libs: -L${libdir} -llammps@LIB_SUFFIX@@
|
||||
Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
|
||||
Libs.private: -lm
|
||||
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
|
||||
|
||||
@ -31,6 +31,7 @@ This is the list of packages that may require additional steps.
|
||||
"KOKKOS"_#kokkos,
|
||||
"LATTE"_#latte,
|
||||
"MEAM"_#meam,
|
||||
"MESSAGE"_#message,
|
||||
"MSCG"_#mscg,
|
||||
"OPT"_#opt,
|
||||
"POEMS"_#poems,
|
||||
@ -361,6 +362,10 @@ make lib-meam args="-m mpi" # build with default Fortran compiler compatible
|
||||
make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
|
||||
make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
|
||||
|
||||
NOTE: You should test building the MEAM library with both the Intel
|
||||
and GNU compilers to see if a simulation runs faster with one versus
|
||||
the other on your system.
|
||||
|
||||
The build should produce two files: lib/meam/libmeam.a and
|
||||
lib/meam/Makefile.lammps. The latter is copied from an existing
|
||||
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
|
||||
@ -373,6 +378,35 @@ file.
|
||||
|
||||
:line
|
||||
|
||||
MESSAGE package :h4,link(message)
|
||||
|
||||
This package can optionally include support for messaging via sockets,
|
||||
using the open-source "ZeroMQ library"_http://zeromq.org, which must
|
||||
be installed on your system.
|
||||
|
||||
[CMake build]:
|
||||
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
Before building LAMMPS, you must build the CSlib library in
|
||||
lib/message. You can build the CSlib library manually if you prefer;
|
||||
follow the instructions in lib/message/README. You can also do it in
|
||||
one step from the lammps/src dir, using a command like these, which
|
||||
simply invoke the lib/message/Install.py script with the specified args:
|
||||
|
||||
make lib-message # print help message
|
||||
make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
|
||||
make lib-message args="-s" # build as serial lib with no ZMQ support
|
||||
|
||||
The build should produce two files: lib/message/cslib/src/libmessage.a
|
||||
and lib/message/Makefile.lammps. The latter is copied from an
|
||||
existing Makefile.lammps.* and has settings to link with the ZeroMQ
|
||||
library if requested in the build.
|
||||
|
||||
:line
|
||||
|
||||
MSCG package :h4,link(mscg)
|
||||
|
||||
To build with this package, you must download and build the MS-CG
|
||||
|
||||
@ -42,6 +42,7 @@ packages:
|
||||
"KOKKOS"_Build_extras.html#kokkos,
|
||||
"LATTE"_Build_extras.html#latte,
|
||||
"MEAM"_Build_extras.html#meam,
|
||||
"MESSAGE"_#Build_extras.html#message,
|
||||
"MSCG"_Build_extras.html#mscg,
|
||||
"OPT"_Build_extras.html#opt,
|
||||
"POEMS"_Build_extras.html#poems,
|
||||
|
||||
@ -71,6 +71,7 @@ An alphabetic list of all LAMMPS commands.
|
||||
"lattice"_lattice.html,
|
||||
"log"_log.html,
|
||||
"mass"_mass.html,
|
||||
"message"_message.html,
|
||||
"minimize"_minimize.html,
|
||||
"min_modify"_min_modify.html,
|
||||
"min_style"_min_style.html,
|
||||
@ -103,6 +104,7 @@ An alphabetic list of all LAMMPS commands.
|
||||
"restart"_restart.html,
|
||||
"run"_run.html,
|
||||
"run_style"_run_style.html,
|
||||
"server"_server.html,
|
||||
"set"_set.html,
|
||||
"shell"_shell.html,
|
||||
"special_bonds"_special_bonds.html,
|
||||
|
||||
@ -54,6 +54,7 @@ General howto :h3
|
||||
Howto_replica
|
||||
Howto_library
|
||||
Howto_couple
|
||||
Howto_client_server
|
||||
|
||||
END_RST -->
|
||||
|
||||
@ -64,7 +65,8 @@ END_RST -->
|
||||
"Run multiple simulations from one input script"_Howto_multiple.html
|
||||
"Multi-replica simulations"_Howto_replica.html
|
||||
"Library interface to LAMMPS"_Howto_library.html
|
||||
"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
|
||||
"Couple LAMMPS to other codes"_Howto_couple.html
|
||||
"Using LAMMPS in client/server mode"_Howto_client_server.html :all(b)
|
||||
|
||||
<!-- END_HTML_ONLY -->
|
||||
|
||||
|
||||
131
doc/src/Howto_client_server.txt
Normal file
131
doc/src/Howto_client_server.txt
Normal file
@ -0,0 +1,131 @@
|
||||
"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
|
||||
Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
Using LAMMPS in client/server mode
|
||||
|
||||
Client/server coupling of two codes is where one code is the "client"
|
||||
and sends request messages to a "server" code. The server responds to
|
||||
each request with a reply message. This enables the two codes to work
|
||||
in tandem to perform a simulation. LAMMPS can act as either a client
|
||||
or server code.
|
||||
|
||||
Some advantages of client/server coupling are that the two codes run
|
||||
as stand-alone executables; they are not linked together. Thus
|
||||
neither code needs to have a library interface. This often makes it
|
||||
easier to run the two codes on different numbers of processors. If a
|
||||
message protocol (format and content) is defined for a particular kind
|
||||
of simulation, then in principle any code that implements the
|
||||
client-side protocol can be used in tandem with any code that
|
||||
implements the server-side protocol, without the two codes needing to
|
||||
know anything more specific about each other.
|
||||
|
||||
A simple example of client/server coupling is where LAMMPS is the
|
||||
client code performing MD timestepping. Each timestep it sends a
|
||||
message to a server quantum code containing current coords of all the
|
||||
atoms. The quantum code computes energy and forces based on the
|
||||
coords. It returns them as a message to LAMMPS, which completes the
|
||||
timestep.
|
||||
|
||||
Alternate methods for code coupling with LAMMPS are described on
|
||||
the "Howto couple"_Howto_couple.html doc page.
|
||||
|
||||
LAMMPS support for client/server coupling is in its "MESSAGE
|
||||
package"_Packages_details.html#PKG-MESSAGE which implements several
|
||||
commands that enable LAMMPS to act as a client or server, as discussed
|
||||
below. The MESSAGE package also wraps a client/server library called
|
||||
CSlib which enables two codes to exchange messages in different ways,
|
||||
either via files, sockets, or MPI. The CSlib is provided with LAMMPS
|
||||
in the lib/message dir. The CSlib has its own
|
||||
"website"_http://cslib.sandia.gov with documentation and test
|
||||
programs.
|
||||
|
||||
NOTE: For client/server coupling to work between LAMMPS and another
|
||||
code, the other code also has to use the CSlib. This can sometimes be
|
||||
done without any modifications to the other code by simply wrapping it
|
||||
with a Python script that exchanges CSlib messages with LAMMPS and
|
||||
prepares input for or processes output from the other code. The other
|
||||
code also has to implement a matching protocol for the format and
|
||||
content of messages that LAMMPS exchanges with it.
|
||||
|
||||
These are the commands currently in the MESSAGE package for two
|
||||
protocols, MD and MC (Monte Carlo). New protocols can easily be
|
||||
defined and added to this directory, where LAMMPS acts as either the
|
||||
client or server.
|
||||
|
||||
"message"_message.html
|
||||
"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
|
||||
"server md"_server_md.html = LAMMPS is a server for computing MD forces
|
||||
"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy
|
||||
|
||||
The server doc files give details of the message protocols
|
||||
for data that is exchanged bewteen the client and server.
|
||||
|
||||
These example directories illustrate how to use LAMMPS as either a
|
||||
client or server code:
|
||||
|
||||
examples/message
|
||||
examples/COUPLE/README
|
||||
examples/COUPLE/lammps_mc
|
||||
examples/COUPLE/lammps_vasp :ul
|
||||
|
||||
The examples/message dir couples a client instance of LAMMPS to a
|
||||
server instance of LAMMPS.
|
||||
|
||||
The lammps_mc dir shows how to couple LAMMPS as a server to a simple
|
||||
Monte Carlo client code as the driver.
|
||||
|
||||
The lammps_vasp dir shows how to couple LAMMPS as a client code
|
||||
running MD timestepping to VASP acting as a server providing quantum
|
||||
DFT forces, thru a Python wrapper script on VASP.
|
||||
|
||||
Here is how to launch a client and server code together for any of the
|
||||
4 modes of message exchange that the "message"_message.html command
|
||||
and the CSlib support. Here LAMMPS is used as both the client and
|
||||
server code. Another code could be subsitituted for either.
|
||||
|
||||
The examples below show launching both codes from the same window (or
|
||||
batch script), using the "&" character to launch the first code in the
|
||||
background. For all modes except {mpi/one}, you could also launch the
|
||||
codes in separate windows on your desktop machine. It does not
|
||||
matter whether you launch the client or server first.
|
||||
|
||||
In these examples either code can be run on one or more processors.
|
||||
If running in a non-MPI mode (file or zmq) you can launch a code on a
|
||||
single processor without using mpirun.
|
||||
|
||||
IMPORTANT: If you run in mpi/two mode, you must launch both codes via
|
||||
mpirun, even if one or both of them runs on a single processor. This
|
||||
is so that MPI can figure out how to connect both MPI processes
|
||||
together to exchange MPI messages between them.
|
||||
|
||||
For message exchange in {file}, {zmq}, or {mpi/two} modes:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
|
||||
|
||||
% mpirun -np 4 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
|
||||
|
||||
% mpirun -np 2 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
|
||||
|
||||
For message exchange in {mpi/one} mode:
|
||||
|
||||
Launch both codes in a single mpirun command:
|
||||
|
||||
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
|
||||
|
||||
The two -np values determine how many procs the client and the server
|
||||
run on.
|
||||
|
||||
A LAMMPS executable run in this manner must use the -mpicolor color
|
||||
command-line option as their its option, where color is an integer
|
||||
label that will be used to distinguish one executable from another in
|
||||
the multiple executables that the mpirun command launches. In this
|
||||
example the client was colored with a 0, and the server with a 1.
|
||||
@ -16,10 +16,12 @@ atoms and pass those forces to LAMMPS. Or a continuum finite element
|
||||
nodal points, compute a FE solution, and return interpolated forces on
|
||||
MD atoms.
|
||||
|
||||
LAMMPS can be coupled to other codes in at least 3 ways. Each has
|
||||
LAMMPS can be coupled to other codes in at least 4 ways. Each has
|
||||
advantages and disadvantages, which you'll have to think about in the
|
||||
context of your application.
|
||||
|
||||
:line
|
||||
|
||||
(1) Define a new "fix"_fix.html command that calls the other code. In
|
||||
this scenario, LAMMPS is the driver code. During its timestepping,
|
||||
the fix is invoked, and can make library calls to the other code,
|
||||
@ -32,6 +34,8 @@ LAMMPS.
|
||||
|
||||
:link(poems,http://www.rpi.edu/~anderk5/lab)
|
||||
|
||||
:line
|
||||
|
||||
(2) Define a new LAMMPS command that calls the other code. This is
|
||||
conceptually similar to method (1), but in this case LAMMPS and the
|
||||
other code are on a more equal footing. Note that now the other code
|
||||
@ -52,6 +56,8 @@ command writes and reads.
|
||||
See the "Modify command"_Modify_command.html doc page for info on how
|
||||
to add a new command to LAMMPS.
|
||||
|
||||
:line
|
||||
|
||||
(3) Use LAMMPS as a library called by another code. In this case the
|
||||
other code is the driver and calls LAMMPS as needed. Or a wrapper
|
||||
code could link and call both LAMMPS and another code as libraries.
|
||||
@ -102,3 +108,9 @@ on all the processors. Or it might allocate half the processors to
|
||||
LAMMPS and half to the other code and run both codes simultaneously
|
||||
before syncing them up periodically. Or it might instantiate multiple
|
||||
instances of LAMMPS to perform different calculations.
|
||||
|
||||
:line
|
||||
|
||||
(4) Couple LAMMPS with another code in a client/server mode. This is
|
||||
described on the "Howto client/server"_Howto_client_server.html doc
|
||||
page.
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="22 Aug 2018 version">
|
||||
<META NAME="docnumber" CONTENT="31 Aug 2018 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
@ -21,7 +21,7 @@
|
||||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
22 Aug 2018 version :c,h2
|
||||
31 Aug 2018 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
||||
@ -549,10 +549,6 @@ This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
NOTE: You should test building the MEAM library with both the Intel
|
||||
and GNU compilers to see if a simulation runs faster with one versus
|
||||
the other on your system.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MEAM: filenames -> commands
|
||||
@ -563,6 +559,31 @@ examples/meam :ul
|
||||
|
||||
:line
|
||||
|
||||
MESSAGE package :link(PKG-MESSAGE),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
Commands to use LAMMPS as either a client or server and couple it to
|
||||
another application.
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#message on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MESSAGE: filenames -> commands
|
||||
lib/message/README
|
||||
"message"_message.html
|
||||
"fix client/md"_fix_client_md.html
|
||||
"server md"_server_md.html
|
||||
"server mc"_server_mc.html
|
||||
examples/message :ul
|
||||
|
||||
:line
|
||||
|
||||
MISC package :link(PKG-MISC),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
@ -47,6 +47,7 @@ Package, Description, Doc page, Example, Library
|
||||
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
|
||||
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
|
||||
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
|
||||
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
|
||||
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
|
||||
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
|
||||
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, n/a, no
|
||||
|
||||
@ -18,6 +18,7 @@ letter abbreviation can be used:
|
||||
"-i or -in"_#file
|
||||
"-k or -kokkos"_#run-kokkos
|
||||
"-l or -log"_#log
|
||||
"-m or -mpicolor"_#mpicolor
|
||||
"-nc or -nocite"_#nocite
|
||||
"-pk or -package"_#package
|
||||
"-p or -partition"_#partition
|
||||
@ -175,6 +176,30 @@ Option -plog will override the name of the partition log files file.N.
|
||||
|
||||
:line
|
||||
|
||||
[-mpicolor] color :link(mpi)
|
||||
|
||||
If used, this must be the first command-line argument after the LAMMPS
|
||||
executable name. It is only used when LAMMPS is launched by an mpirun
|
||||
command which also launches another executable(s) at the same time.
|
||||
(The other executable could be LAMMPS as well.) The color is an
|
||||
integer value which should be different for each executable (another
|
||||
application may set this value in a different way). LAMMPS and the
|
||||
other executable(s) perform an MPI_Comm_split() with their own colors
|
||||
to shrink the MPI_COMM_WORLD communication to be the subset of
|
||||
processors they are actually running on.
|
||||
|
||||
Currently, this is only used in LAMMPS to perform client/server
|
||||
messaging with another application. LAMMPS can act as either a client
|
||||
or server (or both). More details are given on the "Howto
|
||||
client/server"_Howto_client_server.html doc page.
|
||||
|
||||
Specifically, this refers to the "mpi/one" mode of messaging provided
|
||||
by the "message"_message.html command and the CSlib library LAMMPS
|
||||
links with from the lib/message directory. See the
|
||||
"message"_message.html command for more details.
|
||||
|
||||
:line
|
||||
|
||||
[-nocite] :link(nocite)
|
||||
|
||||
Disable writing the log.cite file which is normally written to list
|
||||
|
||||
@ -56,6 +56,7 @@ Commands :h1
|
||||
lattice
|
||||
log
|
||||
mass
|
||||
message
|
||||
min_modify
|
||||
min_style
|
||||
minimize
|
||||
@ -87,6 +88,7 @@ Commands :h1
|
||||
restart
|
||||
run
|
||||
run_style
|
||||
server
|
||||
set
|
||||
shell
|
||||
special_bonds
|
||||
|
||||
106
doc/src/fix_client_md.txt
Normal file
106
doc/src/fix_client_md.txt
Normal file
@ -0,0 +1,106 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix client/md command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID client/md :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
client/md = style name of this fix command :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all client/md :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix style enables LAMMPS to run as a "client" code and
|
||||
communicate each timestep with a separate "server" code to perform an
|
||||
MD simulation together.
|
||||
|
||||
The "Howto client/server"_Howto_client_server.html doc page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When using this fix, LAMMPS (as the client code) passes the current
|
||||
coordinates of all particles to the server code each timestep, which
|
||||
computes their interaction, and returns the energy, forces, and virial
|
||||
for the interacting particles to LAMMPS, so it can complete the
|
||||
timestep.
|
||||
|
||||
The server code could be a quantum code, or another classical MD code
|
||||
which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
|
||||
does not have. In the quantum case, this fix is a mechanism for
|
||||
running {ab initio} MD with quantum forces.
|
||||
|
||||
The group associated with this fix is ignored.
|
||||
|
||||
The protocol and "units"_units.html for message format and content
|
||||
that LAMMPS exchanges with the server code is defined on the "server
|
||||
md"_server_md.html doc page.
|
||||
|
||||
Note that when using LAMMPS as an MD client, your LAMMPS input script
|
||||
should not normally contain force field commands, like a
|
||||
"pair_style"_doc/pair_style.html, "bond_style"_doc/bond_style.html, or
|
||||
"kspace_style"_kspace_style.html commmand. However it is possible for
|
||||
a server code to only compute a portion of the full force-field, while
|
||||
LAMMPS computes the remaining part. Your LAMMPS script can also
|
||||
specify boundary conditions or force constraints in the usual way,
|
||||
which will be added to the per-atom forces returned by the server
|
||||
code.
|
||||
|
||||
See the examples/message dir for example scripts where LAMMPS is both
|
||||
the "client" and/or "server" code for this kind of client/server MD
|
||||
simulation. The examples/message/README file explains how to launch
|
||||
LAMMPS and another code in tandem to perform a coupled simulation.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {energy} option is supported by this
|
||||
fix to add the potential energy computed by the server application to
|
||||
the system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the server application's contribution to the system's
|
||||
virial as part of "thermodynamic output"_thermo_style.html. The
|
||||
default is {virial yes}
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Howto_output.html. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the MESSAGE package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
"message"_message.html command to setup the messaging protocol with
|
||||
the other server code.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"message"_message.html, "server"_server.html
|
||||
|
||||
[Default:] none
|
||||
@ -167,6 +167,7 @@ label.html
|
||||
lattice.html
|
||||
log.html
|
||||
mass.html
|
||||
message.html
|
||||
min_modify.html
|
||||
min_style.html
|
||||
minimize.html
|
||||
@ -194,6 +195,9 @@ reset_timestep.html
|
||||
restart.html
|
||||
run.html
|
||||
run_style.html
|
||||
server.html
|
||||
server_mc.html
|
||||
server_md.html
|
||||
set.html
|
||||
shell.html
|
||||
special_bonds.html
|
||||
@ -241,6 +245,7 @@ fix_bond_create.html
|
||||
fix_bond_react.html
|
||||
fix_bond_swap.html
|
||||
fix_box_relax.html
|
||||
fix_client_md.html
|
||||
fix_cmap.html
|
||||
fix_colvars.html
|
||||
fix_controller.html
|
||||
|
||||
162
doc/src/message.txt
Normal file
162
doc/src/message.txt
Normal file
@ -0,0 +1,162 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Command_all.html)
|
||||
|
||||
:line
|
||||
|
||||
message command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
message which protocol mode arg :pre
|
||||
|
||||
which = {client} or {server} :ulb,l
|
||||
protocol = {md} or {mc} :l
|
||||
mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
|
||||
{file} arg = filename
|
||||
filename = file used for message exchanges
|
||||
{zmq} arg = socket-ID
|
||||
socket-ID for client = localhost:5555, see description below
|
||||
socket-ID for server = *:5555, see description below
|
||||
{mpi/one} arg = none
|
||||
{mpi/two} arg = filename
|
||||
filename = file used to establish communication bewteen 2 MPI jobs :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
message client md file tmp.couple
|
||||
message server md file tmp.couple :pre
|
||||
|
||||
message client md zmq localhost:5555
|
||||
message server md zmq *:5555 :pre
|
||||
|
||||
message client md mpi/one
|
||||
message server md mpi/one :pre
|
||||
|
||||
message client md mpi/two tmp.couple
|
||||
message server md mpi/two tmp.couple :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Establish a messaging protocol between LAMMPS and another code for the
|
||||
purpose of client/server coupling.
|
||||
|
||||
The "Howto client/server"_Howto_client_server.html doc page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
:line
|
||||
|
||||
The {which} argument defines LAMMPS to be the client or the server.
|
||||
|
||||
:line
|
||||
|
||||
The {protocol} argument defines the format and content of messages
|
||||
that will be exchanged between the two codes. The current options
|
||||
are:
|
||||
|
||||
md = run dynamics with another code
|
||||
mc = perform Monte Carlo moves with another code :ul
|
||||
|
||||
For protocol {md}, LAMMPS can be either a client or server. See the
|
||||
"server md"_server_md.html doc page for details on the protocol.
|
||||
|
||||
For protocol {mc}, LAMMPS can be the server. See the "server
|
||||
mc"_server_mc.html doc page for details on the protocol.
|
||||
|
||||
:line
|
||||
|
||||
The {mode} argument specifies how messages are exchanged between the
|
||||
client and server codes. Both codes must use the same mode and use
|
||||
consistent parameters.
|
||||
|
||||
For mode {file}, the 2 codes communicate via binary files. They must
|
||||
use the same filename, which is actually a file prefix. Several files
|
||||
with that prefix will be created and deleted as a simulation runs.
|
||||
The filename can include a path. Both codes must be able to access
|
||||
the path/file in a common filesystem.
|
||||
|
||||
For mode {zmq}, the 2 codes communicate via a socket on the server
|
||||
code's machine. Support for socket messaging is provided by the
|
||||
open-source "ZeroMQ library"_http://zeromq.org, which must be
|
||||
installed on your system. The client specifies an IP address (IPv4
|
||||
format) or the DNS name of the machine the server code is running on,
|
||||
followed by a 4-digit port ID for the socket, separated by a colon.
|
||||
E.g.
|
||||
|
||||
localhost:5555 # client and server running on same machine
|
||||
192.168.1.1:5555 # server is 192.168.1.1
|
||||
deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre
|
||||
|
||||
The server specifes "*:5555" where "*" represents all available
|
||||
interfaces on the server's machine, and the port ID must match
|
||||
what the client specifies.
|
||||
|
||||
NOTE: What are allowed port IDs?
|
||||
|
||||
NOTE: Additional explanation is needed here about how to use the {zmq}
|
||||
mode on a parallel machine, e.g. a cluster with many nodes.
|
||||
|
||||
For mode {mpi/one}, the 2 codes communicate via MPI and are launched
|
||||
by the same mpirun command, e.g. with this syntax for OpenMPI:
|
||||
|
||||
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
|
||||
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server :pre
|
||||
|
||||
Note the use of the "-mpicolor color" command-line argument with
|
||||
LAMMPS. See the "command-line args"_Run_options.html doc page for
|
||||
further explanation.
|
||||
|
||||
For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
|
||||
be 2 separate mpirun commands. The specified {filename} argument is a
|
||||
file the 2 MPI processes will use to exchange info so that an MPI
|
||||
inter-communicator can be established to enable the 2 codes to send
|
||||
MPI messages to each other. Both codes must be able to access the
|
||||
path/file in a common filesystem.
|
||||
|
||||
:line
|
||||
|
||||
Normally, the message command should be used at the top of a LAMMPS
|
||||
input script. It performs an initial handshake with the other code to
|
||||
setup messaging and to verify that both codes are using the same
|
||||
message protocol and mode. Assuming both codes are launched at
|
||||
(nearly) the same time, the other code should perform the same kind of
|
||||
initialization.
|
||||
|
||||
If LAMMPS is the client code, it will begin sending messages when a
|
||||
LAMMPS client command begins its operation. E.g. for the "fix
|
||||
client/md"_fix_client_md.html command, it is when a "run"_run.html
|
||||
command is executed.
|
||||
|
||||
If LAMMPS is the server code, it will begin receiving messages when
|
||||
the "server"_server.html command is invoked.
|
||||
|
||||
A fix client command will terminate its messaging with the server when
|
||||
LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The
|
||||
server command will terminate its messaging with the client when the
|
||||
client signals it. Then the remainder of the LAMMPS input script will
|
||||
be processed.
|
||||
|
||||
If both codes do something similar, this means a new round of
|
||||
client/server messaging can be initiated after termination by re-using
|
||||
a 2nd message command in your LAMMPS input script, followed by a new
|
||||
fix client or server command.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"server"_server.html, "fix client/md"_fix_client_md.html
|
||||
|
||||
[Default:] none
|
||||
71
doc/src/server.txt
Normal file
71
doc/src/server.txt
Normal file
@ -0,0 +1,71 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
server command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
server protocol :pre
|
||||
|
||||
protocol = {md} or {mc} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
server md :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it receives
|
||||
messages from a separate "client" code and responds by sending a reply
|
||||
message back to the client. The specified {protocol} determines the
|
||||
format and content of messages LAMMPS expects to receive and how it
|
||||
responds.
|
||||
|
||||
The "Howto client/server"_Howto_client_server.html doc page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS script will be
|
||||
processed.
|
||||
|
||||
The {protocol} argument defines the format and content of messages
|
||||
that will be exchanged between the two codes. The current options
|
||||
are:
|
||||
|
||||
"md"_server_md.html = run dynamics with another code
|
||||
"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
|
||||
|
||||
For protocol {md}, LAMMPS can be either a client (via the "fix
|
||||
client/md"_fix_client_md.html command) or server. See the "server
|
||||
md"_server_md.html doc page for details on the protocol.
|
||||
|
||||
For protocol {mc}, LAMMPS can be the server. See the "server
|
||||
mc"_server_mc.html doc page for details on the protocol.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
"message"_message.html command to setup the messaging protocol with
|
||||
the other client code.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"message"_message.html, "fix client/md"_fix_client_md.html
|
||||
|
||||
[Default:] none
|
||||
116
doc/src/server_mc.txt
Normal file
116
doc/src/server_mc.txt
Normal file
@ -0,0 +1,116 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
server mc command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
server mc :pre
|
||||
|
||||
mc = the protocol argument to the "server"_server.html command
|
||||
|
||||
[Examples:]
|
||||
|
||||
server mc :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it will
|
||||
expect messages from a separate "client" code that match the {mc}
|
||||
protocol for format and content explained below. For each message
|
||||
LAMMPS receives it will send a message back to the client.
|
||||
|
||||
The "Howto client/server"_Howto_client_server.html doc page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS script will be
|
||||
processed.
|
||||
|
||||
The "server"_server.html doc page gives other options for using LAMMPS
|
||||
See an example of how this command is used in
|
||||
examples/COUPLE/lammps_mc/in.server.
|
||||
|
||||
:line
|
||||
|
||||
When using this command, LAMMPS (as the server code) receives
|
||||
instructions from a Monte Carlo (MC) driver to displace random atoms,
|
||||
compute the energy before and after displacement, and run dynamics to
|
||||
equilibrate the system.
|
||||
|
||||
The MC driver performs the random displacements on random atoms,
|
||||
accepts or rejects the move in an MC sense, and orchestrates the MD
|
||||
runs.
|
||||
|
||||
The format and content of the exchanged messages are explained here in
|
||||
a conceptual sense. Python-style pseudo code for the library calls to
|
||||
the CSlib is shown, which performs the actual message exchange between
|
||||
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
|
||||
pages for more details on the actual library syntax. The "cs" object
|
||||
in this pseudo code is a pointer to an instance of the CSlib.
|
||||
|
||||
See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
|
||||
these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an
|
||||
example of how an MC driver code can use these messages.
|
||||
|
||||
Let NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
|
||||
|
||||
[Client sends one of these kinds of message]:
|
||||
|
||||
cs->send(NATOMS,0) # msgID = 1 with no fields :pre
|
||||
|
||||
cs->send(EINIT,0) # msgID = 2 with no fields :pre
|
||||
|
||||
cs->send(DISPLACE,2) # msgID = 3 with 2 fields
|
||||
cs->pack_int(1,ID) # 1st field = ID of atom to displace
|
||||
cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom :pre
|
||||
|
||||
cs->send(ACCEPT,1) # msgID = 4 with 1 field
|
||||
cs->pack_int(1,flag) # 1st field = accept/reject flag :pre
|
||||
|
||||
cs->send(RUN,1) # msgID = 5 with 1 field
|
||||
cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre
|
||||
|
||||
[Server replies]:
|
||||
|
||||
cs->send(NATOMS,1) # msgID = 1 with 1 field
|
||||
cs->pack_int(1,natoms) # 1st field = number of atoms :pre
|
||||
|
||||
cs->send(EINIT,2) # msgID = 2 with 2 fields
|
||||
cs->pack_double(1,poteng) # 1st field = potential energy of system
|
||||
cs->pack(2,3*natoms,x) # 2nd field = 3N coords of Natoms :pre
|
||||
|
||||
cs->send(DISPLACE,1) # msgID = 3 with 1 field
|
||||
cs->pack_double(1,poteng) # 1st field = new potential energy of system :pre
|
||||
|
||||
cs->send(ACCEPT,0) # msgID = 4 with no fields
|
||||
|
||||
cs->send(RUN,0) # msgID = 5 with no fields
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
"message"_message.html command to setup the messaging protocol with
|
||||
the other client code.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"message"_message.html
|
||||
|
||||
[Default:] none
|
||||
147
doc/src/server_md.txt
Normal file
147
doc/src/server_md.txt
Normal file
@ -0,0 +1,147 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
server md command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
server md :pre
|
||||
|
||||
md = the protocol argument to the "server"_server.html command
|
||||
|
||||
[Examples:]
|
||||
|
||||
server md :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it will
|
||||
expect messages from a separate "client" code that match the {md}
|
||||
protocol for format and content explained below. For each message
|
||||
LAMMPS receives it will send a message back to the client.
|
||||
|
||||
The "Howto client/server"_Howto_client_server.html doc page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS script will be
|
||||
processed.
|
||||
|
||||
The "server"_server.html doc page gives other options for using LAMMPS
|
||||
in server mode. See an example of how this command is used in
|
||||
examples/message/in.message.server.
|
||||
|
||||
:line
|
||||
|
||||
When using this command, LAMMPS (as the server code) receives the
|
||||
current coordinates of all particles from the client code each
|
||||
timestep, computes their interaction, and returns the energy, forces,
|
||||
and pressure for the interacting particles to the client code, so it
|
||||
can complete the timestep. This command could also be used with a
|
||||
client code that performs energy minimization, using the server to
|
||||
compute forces and energy each iteration of its minimizer.
|
||||
|
||||
When using the "fix client/md" command, LAMMPS (as the client code)
|
||||
does the timestepping and receives needed energy, forces, and pressure
|
||||
values from the server code.
|
||||
|
||||
The format and content of the exchanged messages are explained here in
|
||||
a conceptual sense. Python-style pseudo code for the library calls to
|
||||
the CSlib is shown, which performs the actual message exchange between
|
||||
the two codes. See the "CSlib website"_http://cslib.sandia.gov doc
|
||||
pages for more details on the actual library syntax. The "cs" object
|
||||
in this pseudo code is a pointer to an instance of the CSlib.
|
||||
|
||||
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
|
||||
files for details on how LAMMPS uses these messages. See the
|
||||
examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
|
||||
a quantum code (VASP) can use use these messages.
|
||||
|
||||
The following pseudo-code uses these values, defined as enums.
|
||||
|
||||
enum{SETUP=1,STEP};
|
||||
enum{DIM=1,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE};
|
||||
enum{FORCES=1,ENERGY,PRESSURE,ERROR}; :pre
|
||||
|
||||
[Client sends 2 kinds of messages]:
|
||||
|
||||
# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
|
||||
# optional fields: UNITS, CHARGE :pre
|
||||
|
||||
cs->send(SETUP,nfields) # msgID with nfields :pre
|
||||
|
||||
cs->pack_int(DIM,dim) # dimension (2,3) of simulation
|
||||
cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
|
||||
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
|
||||
cs->pack(BOX,9,box) # 3 edge vectors of simulation box
|
||||
cs->pack_int(NATOMS,natoms) # total number of atoms
|
||||
cs->pack_int(NTYPES,ntypes) # number of atom types
|
||||
cs->pack(TYPES,natoms,type) # vector of per-atom types
|
||||
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
|
||||
cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
|
||||
cs->pack(CHARGE,natoms,q) # vector of per-atom charge :pre
|
||||
|
||||
# required fields: COORDS
|
||||
# optional fields: ORIGIN, BOX :pre
|
||||
|
||||
cs->send(STEP,nfields) # msgID with nfields :pre
|
||||
|
||||
cs->pack(COORDS,3*natoms,x) # vector of 3N atom coords
|
||||
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
|
||||
cs->pack(BOX,9,box) # 3 edge vectors of simulation box
|
||||
|
||||
[Server replies to either kind of message]:
|
||||
|
||||
# required fields: FORCES, ENERGY, PRESSURE
|
||||
# optional fields: ERROR :pre
|
||||
|
||||
cs->send(msgID,nfields) # msgID with nfields
|
||||
cs->pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
|
||||
cs->pack(ENERGY,1,poteng) # total potential energy of system
|
||||
cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
|
||||
cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence) :pre
|
||||
|
||||
:line
|
||||
|
||||
The units for various quantities that are sent and received iva
|
||||
messages are defined for atomic-scale simulations in the table below.
|
||||
The client and server codes (including LAMMPS) can use internal units
|
||||
different than these (e.g. "real units"_units.html in LAMMPS), so long
|
||||
as they convert to these units for meesaging.
|
||||
|
||||
COORDS, ORIGIN, BOX = Angstroms
|
||||
CHARGE = multiple of electron charge (1.0 is a proton)
|
||||
ENERGY = eV
|
||||
FORCES = eV/Angstrom
|
||||
PRESSURE = bars :ul
|
||||
|
||||
Note that these are "metal units"_units.html in LAMMPS.
|
||||
|
||||
If you wish to run LAMMPS in another its non-atomic units, e.g. "lj
|
||||
units"_units.html, then the client and server should exchange a UNITS
|
||||
message as indicated above, and both the client and server should
|
||||
agree on the units for the data they exchange.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"message"_message.html, "fix client/md"_fix_client_md.html
|
||||
|
||||
[Default:] none
|
||||
@ -10,6 +10,7 @@ See these sections of the LAMMPS manaul for details:
|
||||
|
||||
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
|
||||
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
|
||||
6.29 Using LAMMPS in client/server mode (doc/Section_howto.html#howto_29)
|
||||
|
||||
In all of the examples included here, LAMMPS must first be built as a
|
||||
library. Basically, in the src dir you type one of
|
||||
@ -33,9 +34,13 @@ These are the sub-directories included in this directory:
|
||||
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
lammps_mc client/server coupling of Monte Carlo client
|
||||
with LAMMPS server for energy evaluation
|
||||
lammps_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
lammps_vasp client/server coupling of LAMMPS client with
|
||||
VASP quantum DFT as server for quantum forces
|
||||
library collection of useful inter-code communication routines
|
||||
fortran a simple wrapper on the LAMMPS library API that
|
||||
can be called from Fortran
|
||||
|
||||
33
examples/COUPLE/lammps_mc/Makefile
Normal file
33
examples/COUPLE/lammps_mc/Makefile
Normal file
@ -0,0 +1,33 @@
|
||||
# Makefile for MC
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
SRC = mc.cpp random_park.cpp
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# change this line for your machine to path for CSlib src dir
|
||||
|
||||
CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
|
||||
|
||||
# compiler/linker settings
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O3 -I$(CSLIB)
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O -L$(CSLIB)
|
||||
|
||||
# targets
|
||||
|
||||
mc: $(OBJ)
|
||||
# first line if built the CSlib within lib/message with ZMQ support
|
||||
# second line if built the CSlib without ZMQ support
|
||||
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
|
||||
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
|
||||
|
||||
clean:
|
||||
@rm -f *.o mc
|
||||
|
||||
# rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) -c $<
|
||||
128
examples/COUPLE/lammps_mc/README
Normal file
128
examples/COUPLE/lammps_mc/README
Normal file
@ -0,0 +1,128 @@
|
||||
Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
|
||||
|
||||
See the MESSAGE package (doc/Section_messages.html#MESSAGE)
|
||||
and Section_howto.html#howto10 for more details on how
|
||||
client/server coupling works in LAMMPS.
|
||||
|
||||
In this dir, the mc.cpp/h files are a standalone "client" MC code. It
|
||||
should be run on a single processor, though it could become a parallel
|
||||
program at some point. LAMMPS is also run as a standalone executable
|
||||
as a "server" on as many processors as desired using its "server mc"
|
||||
command; see it's doc page for details.
|
||||
|
||||
Messages are exchanged between MC and LAMMPS via a client/server
|
||||
library (CSlib), which is included in the LAMMPS distribution in
|
||||
lib/message. As explained below you can choose to exchange data
|
||||
between the two programs either via files or sockets (ZMQ). If the MC
|
||||
program became parallel, data could also be exchanged via MPI.
|
||||
|
||||
The MC code makes simple MC moves, by displacing a single random atom
|
||||
by a small random amount. It uses LAMMPS to calculate the energy
|
||||
change, and to run dynamics between MC moves.
|
||||
|
||||
----------------
|
||||
|
||||
Build LAMMPS with its MESSAGE package installed:
|
||||
|
||||
See the Build extras doc page and its MESSAGE package
|
||||
section for details.
|
||||
|
||||
CMake:
|
||||
|
||||
-D PKG_MESSAGE=yes # include the MESSAGE package
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
Traditional make:
|
||||
|
||||
% cd lammps/lib/message
|
||||
% python Install.py -m -z # build CSlib with MPI and ZMQ support
|
||||
% cd lammps/src
|
||||
% make yes-message
|
||||
% make mpi
|
||||
|
||||
You can leave off the -z if you do not have ZMQ on your system.
|
||||
|
||||
----------------
|
||||
|
||||
Build the MC client code
|
||||
|
||||
The source files for the MC code are in this dir. It links with the
|
||||
CSlib library in lib/message/cslib.
|
||||
|
||||
You must first build the CSlib in serial mode, e.g.
|
||||
|
||||
% cd lammps/lib/message/cslib/src
|
||||
% make lib # build serial and parallel lib with ZMQ support
|
||||
% make lib zmq=no # build serial and parallel lib without ZMQ support
|
||||
|
||||
Then edit the Makefile in this dir. The CSLIB variable should be the
|
||||
path to where the LAMMPS lib/message/cslib/src dir is on your system.
|
||||
If you built the CSlib without ZMQ support you will also need to
|
||||
comment/uncomment one line. Then you can just type
|
||||
|
||||
% make
|
||||
|
||||
and you should get an "mc" executable.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
Both the client (MC) and server (LAMMPS) must use the same messaging
|
||||
mode, namely file or zmq. This is an argument to the MC code; it can
|
||||
be selected by setting the "mode" variable when you run LAMMPS. The
|
||||
default mode = file.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means either of
|
||||
the messaging modes can be used and LAMMPS can be run in serial or
|
||||
parallel. The MC code is always run in serial.
|
||||
|
||||
When you run, the server should print out thermodynamic info
|
||||
for every MD run it performs (between MC moves). The client
|
||||
will print nothing until the simulation ends, then it will
|
||||
print stats about the accepted MC moves.
|
||||
|
||||
The examples below are commands you should use in two different
|
||||
terminal windows. The order of the two commands (client or server
|
||||
launch) does not matter. You can run them both in the same window if
|
||||
you append a "&" character to the first one to run it in the
|
||||
background.
|
||||
|
||||
--------------
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
|
||||
|
||||
--------------
|
||||
|
||||
The input script for the MC program is in.mc. You can edit it to run
|
||||
longer simulations.
|
||||
|
||||
500 nsteps = total # of steps of MD
|
||||
100 ndynamics = # of MD steps between MC moves
|
||||
0.1 delta = displacement size of MC move
|
||||
1.0 temperature = used in MC Boltzman factor
|
||||
12345 seed = random number seed
|
||||
|
||||
--------------
|
||||
|
||||
The problem size that LAMMPS is computing the MC energy for and
|
||||
running dynamics on is set by the x,y,z variables in the LAMMPS
|
||||
in.mc.server script. The default size is 500 particles. You can
|
||||
adjust the size as follows:
|
||||
|
||||
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
|
||||
7
examples/COUPLE/lammps_mc/in.mc
Normal file
7
examples/COUPLE/lammps_mc/in.mc
Normal file
@ -0,0 +1,7 @@
|
||||
# MC params
|
||||
|
||||
500 nsteps
|
||||
100 ndynamics
|
||||
0.1 delta
|
||||
1.0 temperature
|
||||
12345 seed
|
||||
36
examples/COUPLE/lammps_mc/in.mc.server
Normal file
36
examples/COUPLE/lammps_mc/in.mc.server
Normal file
@ -0,0 +1,36 @@
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server mc file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server mc zmq *:5555" &
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
254
examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
Normal file
254
examples/COUPLE/lammps_mc/log.28Aug18.file.g++.1
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc file tmp.couple
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000649929 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
93.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
93.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19501 ave 19501 max 19501 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
157.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1939 ave 1939 max 1939 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18757 ave 18757 max 18757 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18757
|
||||
Ave neighs/atom = 37.514
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18699 ave 18699 max 18699 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
|
||||
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1903 ave 1903 max 1903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18715 ave 18715 max 18715 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18715
|
||||
Ave neighs/atom = 37.43
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
157.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18683 ave 18683 max 18683 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18683
|
||||
Ave neighs/atom = 37.366
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
|
||||
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
|
||||
Total wall time: 0:00:02
|
||||
254
examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
Normal file
254
examples/COUPLE/lammps_mc/log.28Aug18.file.g++.4
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc file tmp.couple
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000592947 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
59.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.815e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875 ave 4875 max 4875 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
106.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.04e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875.25 ave 4885 max 4866 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
|
||||
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
113.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.755e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 124 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 1085.25 ave 1089 max 1079 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 4690.25 ave 4996 max 4401 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18761
|
||||
Ave neighs/atom = 37.522
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
|
||||
Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
117.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.563e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 123 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 1068.5 ave 1076 max 1063 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 4674.75 ave 4938 max 4419 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
|
||||
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
93.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.994e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1069 ave 1080 max 1055 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4672 ave 4803 max 4600 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18688
|
||||
Ave neighs/atom = 37.376
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
|
||||
Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
111.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.576e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 132 max 118 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 1057.5 ave 1068 max 1049 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 4685.75 ave 5045 max 4229 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 18743
|
||||
Ave neighs/atom = 37.486
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
|
||||
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
|
||||
Total wall time: 0:00:02
|
||||
254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
Normal file
254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.1
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc zmq *:5555
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000741005 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
52.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
52.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19501 ave 19501 max 19501 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
83.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1939 ave 1939 max 1939 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18757 ave 18757 max 18757 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18757
|
||||
Ave neighs/atom = 37.514
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
209.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18699 ave 18699 max 18699 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
|
||||
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
104.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1903 ave 1903 max 1903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18715 ave 18715 max 18715 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18715
|
||||
Ave neighs/atom = 37.43
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
209.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18683 ave 18683 max 18683 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18683
|
||||
Ave neighs/atom = 37.366
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
|
||||
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
|
||||
Total wall time: 0:00:00
|
||||
254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
Normal file
254
examples/COUPLE/lammps_mc/log.28Aug18.zmq.g++.4
Normal file
@ -0,0 +1,254 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc zmq *:5555
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000576019 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
89.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 4.768e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875 ave 4875 max 4875 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
94.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.457e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875.25 ave 4885 max 4866 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
|
||||
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
115.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.04e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 124 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 1085.25 ave 1089 max 1079 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 4690.25 ave 4996 max 4401 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18761
|
||||
Ave neighs/atom = 37.522
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
|
||||
Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
125.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.384e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 123 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 1068.5 ave 1076 max 1063 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 4674.75 ave 4938 max 4419 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
|
||||
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
112.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.444e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1069 ave 1080 max 1055 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4672 ave 4803 max 4600 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18688
|
||||
Ave neighs/atom = 37.376
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
|
||||
Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 132 max 118 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 1057.5 ave 1068 max 1049 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 4685.75 ave 5045 max 4229 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 18743
|
||||
Ave neighs/atom = 37.486
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
|
||||
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
|
||||
Total wall time: 0:00:00
|
||||
263
examples/COUPLE/lammps_mc/mc.cpp
Normal file
263
examples/COUPLE/lammps_mc/mc.cpp
Normal file
@ -0,0 +1,263 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// MC code used with LAMMPS in client/server mode
|
||||
// MC is the client, LAMMPS is the server
|
||||
|
||||
// Syntax: mc infile mode modearg
|
||||
// mode = file, zmq
|
||||
// modearg = filename for file, localhost:5555 for zmq
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "mc.h"
|
||||
#include "random_park.h"
|
||||
|
||||
#include "cslib.h"
|
||||
using namespace CSLIB_NS;
|
||||
|
||||
void error(const char *);
|
||||
CSlib *cs_create(char *, char *);
|
||||
|
||||
#define MAXLINE 256
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
// main program
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) {
|
||||
error("Syntax: mc infile mode modearg");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// initialize CSlib
|
||||
|
||||
CSlib *cs = cs_create(arg[2],arg[3]);
|
||||
|
||||
// create MC class and perform run
|
||||
|
||||
MC *mc = new MC(arg[1],cs);
|
||||
mc->run();
|
||||
|
||||
// final MC stats
|
||||
|
||||
int naccept = mc->naccept;
|
||||
int nattempt = mc->nattempt;
|
||||
|
||||
printf("------ MC stats ------\n");
|
||||
printf("MC attempts = %d\n",nattempt);
|
||||
printf("MC accepts = %d\n",naccept);
|
||||
printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
|
||||
|
||||
// clean up
|
||||
|
||||
delete cs;
|
||||
delete mc;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void error(const char *str)
|
||||
{
|
||||
printf("ERROR: %s\n",str);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
CSlib *cs_create(char *mode, char *arg)
|
||||
{
|
||||
CSlib *cs = new CSlib(0,mode,arg,NULL);
|
||||
|
||||
// initial handshake to agree on protocol
|
||||
|
||||
cs->send(0,1);
|
||||
cs->pack_string(1,(char *) "mc");
|
||||
|
||||
int msgID,nfield;
|
||||
int *fieldID,*fieldtype,*fieldlen;
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
|
||||
return cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// MC class
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
MC::MC(char *mcfile, void *cs_caller)
|
||||
//MC::MC(char *mcfile, CSlib *cs_caller)
|
||||
{
|
||||
cs_void = cs_caller;
|
||||
|
||||
// setup MC params
|
||||
|
||||
options(mcfile);
|
||||
|
||||
// random # generator
|
||||
|
||||
random = new RanPark(seed);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MC::~MC()
|
||||
{
|
||||
free(x);
|
||||
delete random;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MC::run()
|
||||
{
|
||||
int iatom,accept,msgID,nfield;
|
||||
double pe_initial,pe_final,edelta;
|
||||
double dx,dy,dz;
|
||||
double xold[3],xnew[3];
|
||||
int *fieldID,*fieldtype,*fieldlen;
|
||||
|
||||
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
|
||||
|
||||
CSlib *cs = (CSlib *) cs_void;
|
||||
|
||||
// one-time request for atom count from MD
|
||||
// allocate 1d coord buffer
|
||||
|
||||
cs->send(NATOMS,0);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
natoms = cs->unpack_int(1);
|
||||
|
||||
x = (double *) malloc(3*natoms*sizeof(double));
|
||||
|
||||
// loop over MC moves
|
||||
|
||||
naccept = nattempt = 0;
|
||||
|
||||
for (int iloop = 0; iloop < nloop; iloop++) {
|
||||
|
||||
// request current energy from MD
|
||||
// recv energy, coords from MD
|
||||
|
||||
cs->send(EINIT,0);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
pe_initial = cs->unpack_double(1);
|
||||
double *x = (double *) cs->unpack(2);
|
||||
|
||||
// perform simple MC event
|
||||
// displace a single atom by random amount
|
||||
|
||||
iatom = (int) natoms*random->uniform();
|
||||
xold[0] = x[3*iatom+0];
|
||||
xold[1] = x[3*iatom+1];
|
||||
xold[2] = x[3*iatom+2];
|
||||
|
||||
dx = 2.0*delta*random->uniform() - delta;
|
||||
dy = 2.0*delta*random->uniform() - delta;
|
||||
dz = 2.0*delta*random->uniform() - delta;
|
||||
|
||||
xnew[0] = xold[0] + dx;
|
||||
xnew[1] = xold[1] + dx;
|
||||
xnew[2] = xold[2] + dx;
|
||||
|
||||
// send atom ID and its new coords to MD
|
||||
// recv new energy
|
||||
|
||||
cs->send(DISPLACE,2);
|
||||
cs->pack_int(1,iatom+1);
|
||||
cs->pack(2,4,3,xnew);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
pe_final = cs->unpack_double(1);
|
||||
|
||||
// decide whether to accept/reject MC event
|
||||
|
||||
if (pe_final <= pe_initial) accept = 1;
|
||||
else if (temperature == 0.0) accept = 0;
|
||||
else if (random->uniform() >
|
||||
exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
|
||||
else accept = 1;
|
||||
|
||||
nattempt++;
|
||||
if (accept) naccept++;
|
||||
|
||||
// send accept (1) or reject (0) flag to MD
|
||||
|
||||
cs->send(ACCEPT,1);
|
||||
cs->pack_int(1,accept);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
|
||||
// send dynamics timesteps
|
||||
|
||||
cs->send(RUN,1);
|
||||
cs->pack_int(1,ndynamics);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
}
|
||||
|
||||
// send exit message to MD
|
||||
|
||||
cs->send(-1,0);
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MC::options(char *filename)
|
||||
{
|
||||
// default params
|
||||
|
||||
nsteps = 0;
|
||||
ndynamics = 100;
|
||||
delta = 0.1;
|
||||
temperature = 1.0;
|
||||
seed = 12345;
|
||||
|
||||
// read and parse file
|
||||
|
||||
FILE *fp = fopen(filename,"r");
|
||||
if (fp == NULL) error("Could not open MC file");
|
||||
|
||||
char line[MAXLINE];
|
||||
char *keyword,*value;
|
||||
char *eof = fgets(line,MAXLINE,fp);
|
||||
|
||||
while (eof) {
|
||||
if (line[0] == '#') { // comment line
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
continue;
|
||||
}
|
||||
|
||||
value = strtok(line," \t\n\r\f");
|
||||
if (value == NULL) { // blank line
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
continue;
|
||||
}
|
||||
|
||||
keyword = strtok(NULL," \t\n\r\f");
|
||||
if (keyword == NULL) error("Missing keyword in MC file");
|
||||
|
||||
if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
|
||||
else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
|
||||
else if (strcmp(keyword,"delta") == 0) delta = atof(value);
|
||||
else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
|
||||
else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
|
||||
else error("Unknown param in MC file");
|
||||
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
}
|
||||
|
||||
// derived params
|
||||
|
||||
nloop = nsteps/ndynamics;
|
||||
}
|
||||
40
examples/COUPLE/lammps_mc/mc.h
Normal file
40
examples/COUPLE/lammps_mc/mc.h
Normal file
@ -0,0 +1,40 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef MC_H
|
||||
#define MC_H
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
class MC {
|
||||
public:
|
||||
int naccept; // # of accepted MC events
|
||||
int nattempt; // # of attempted MC events
|
||||
|
||||
MC(char *, void *);
|
||||
~MC();
|
||||
void run();
|
||||
|
||||
private:
|
||||
int nsteps; // total # of MD steps
|
||||
int ndynamics; // steps in one short dynamics run
|
||||
int nloop; // nsteps/ndynamics
|
||||
int natoms; // # of MD atoms
|
||||
|
||||
double delta; // MC displacement distance
|
||||
double temperature; // MC temperature for Boltzmann criterion
|
||||
double *x; // atom coords as 3N 1d vector
|
||||
double energy; // global potential energy
|
||||
|
||||
int seed; // RNG seed
|
||||
class RanPark *random;
|
||||
|
||||
void *cs_void; // messaging library
|
||||
|
||||
void options(char *);
|
||||
};
|
||||
|
||||
#endif
|
||||
72
examples/COUPLE/lammps_mc/random_park.cpp
Normal file
72
examples/COUPLE/lammps_mc/random_park.cpp
Normal file
@ -0,0 +1,72 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// Park/Miller RNG
|
||||
|
||||
#include <math.h>
|
||||
#include "random_park.h"
|
||||
//#include "error.h"
|
||||
|
||||
#define IA 16807
|
||||
#define IM 2147483647
|
||||
#define AM (1.0/IM)
|
||||
#define IQ 127773
|
||||
#define IR 2836
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
RanPark::RanPark(int seed_init)
|
||||
{
|
||||
//if (seed_init <= 0)
|
||||
// error->one(FLERR,"Invalid seed for Park random # generator");
|
||||
seed = seed_init;
|
||||
save = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
uniform RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double RanPark::uniform()
|
||||
{
|
||||
int k = seed/IQ;
|
||||
seed = IA*(seed-k*IQ) - IR*k;
|
||||
if (seed < 0) seed += IM;
|
||||
double ans = AM*seed;
|
||||
return ans;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
gaussian RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double RanPark::gaussian()
|
||||
{
|
||||
double first,v1,v2,rsq,fac;
|
||||
|
||||
if (!save) {
|
||||
do {
|
||||
v1 = 2.0*uniform()-1.0;
|
||||
v2 = 2.0*uniform()-1.0;
|
||||
rsq = v1*v1 + v2*v2;
|
||||
} while ((rsq >= 1.0) || (rsq == 0.0));
|
||||
fac = sqrt(-2.0*log(rsq)/rsq);
|
||||
second = v1*fac;
|
||||
first = v2*fac;
|
||||
save = 1;
|
||||
} else {
|
||||
first = second;
|
||||
save = 0;
|
||||
}
|
||||
return first;
|
||||
}
|
||||
28
examples/COUPLE/lammps_mc/random_park.h
Normal file
28
examples/COUPLE/lammps_mc/random_park.h
Normal file
@ -0,0 +1,28 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef RANPARK_H
|
||||
#define RANPARK_H
|
||||
|
||||
class RanPark {
|
||||
public:
|
||||
RanPark(int);
|
||||
double uniform();
|
||||
double gaussian();
|
||||
|
||||
private:
|
||||
int seed,save;
|
||||
double second;
|
||||
};
|
||||
|
||||
#endif
|
||||
53
examples/COUPLE/lammps_vasp/INCAR
Normal file
53
examples/COUPLE/lammps_vasp/INCAR
Normal file
@ -0,0 +1,53 @@
|
||||
# Startparameter for this run:
|
||||
NWRITE = 2 write-flag & timer
|
||||
PREC = normal normal or accurate (medium, high low for compatibility)
|
||||
ISTART = 0 job : 0-new 1-cont 2-samecut
|
||||
ICHARG = 2 charge: 1-file 2-atom 10-const
|
||||
ISPIN = 1 spin polarized calculation?
|
||||
LSORBIT = F spin-orbit coupling
|
||||
INIWAV = 1 electr: 0-lowe 1-rand 2-diag
|
||||
|
||||
# Electronic Relaxation 1
|
||||
ENCUT = 600.0 eV #Plane wave energy cutoff
|
||||
ENINI = 600.0 initial cutoff
|
||||
NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
|
||||
EDIFF = 0.1E-05 stopping-criterion for ELM
|
||||
# Ionic relaxation
|
||||
EDIFFG = 0.1E-02 stopping-criterion for IOM
|
||||
NSW = 0 number of steps for IOM
|
||||
NBLOCK = 1; KBLOCK = 1 inner block; outer block
|
||||
IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
|
||||
NFREE = 0 steps in history (QN), initial steepest desc. (CG)
|
||||
ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
|
||||
IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
|
||||
|
||||
POTIM = 0.5000 time-step for ionic-motion
|
||||
TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
|
||||
SMASS = -3.00 Nose mass-parameter (am)
|
||||
estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
|
||||
PSTRESS= 0.0 pullay stress
|
||||
|
||||
# DOS related values:
|
||||
EMIN = 10.00; EMAX =-10.00 energy-range for DOS
|
||||
EFERMI = 0.00
|
||||
ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
|
||||
|
||||
# Electronic relaxation 2 (details)
|
||||
IALGO = 48 algorithm
|
||||
|
||||
# Write flags
|
||||
LWAVE = T write WAVECAR
|
||||
LCHARG = T write CHGCAR
|
||||
LVTOT = F write LOCPOT, total local potential
|
||||
LVHAR = F write LOCPOT, Hartree potential only
|
||||
LELF = F write electronic localiz. function (ELF)
|
||||
|
||||
# Dipole corrections
|
||||
LMONO = F monopole corrections only (constant potential shift)
|
||||
LDIPOL = F correct potential (dipole corrections)
|
||||
IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
|
||||
EPSILON= 1.0000000 bulk dielectric constant
|
||||
|
||||
# Exchange correlation treatment:
|
||||
GGA = -- GGA type
|
||||
|
||||
6
examples/COUPLE/lammps_vasp/KPOINTS
Normal file
6
examples/COUPLE/lammps_vasp/KPOINTS
Normal file
@ -0,0 +1,6 @@
|
||||
K-Points
|
||||
0
|
||||
Monkhorst Pack
|
||||
15 15 15
|
||||
0 0 0
|
||||
|
||||
11
examples/COUPLE/lammps_vasp/POSCAR_W
Normal file
11
examples/COUPLE/lammps_vasp/POSCAR_W
Normal file
@ -0,0 +1,11 @@
|
||||
W unit cell
|
||||
1.0
|
||||
3.16 0.00000000 0.00000000
|
||||
0.00000000 3.16 0.00000000
|
||||
0.00000000 0.00000000 3.16
|
||||
W
|
||||
2
|
||||
Direct
|
||||
0.00000000 0.00000000 0.00000000
|
||||
0.50000000 0.50000000 0.50000000
|
||||
|
||||
149
examples/COUPLE/lammps_vasp/README
Normal file
149
examples/COUPLE/lammps_vasp/README
Normal file
@ -0,0 +1,149 @@
|
||||
Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
|
||||
coupling
|
||||
|
||||
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
|
||||
Section_howto.html#howto10 for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
|
||||
code so it can work as a "server" code which LAMMPS drives as a
|
||||
"client" code to perform ab initio MD. LAMMPS performs the MD
|
||||
timestepping, sends VASP a current set of coordinates each timestep,
|
||||
VASP computes forces and energy and virial and returns that info to
|
||||
LAMMPS.
|
||||
|
||||
Messages are exchanged between MC and LAMMPS via a client/server
|
||||
library (CSlib), which is included in the LAMMPS distribution in
|
||||
lib/message. As explained below you can choose to exchange data
|
||||
between the two programs either via files or sockets (ZMQ). If the
|
||||
vasp_wrap.py program became parallel, or the CSlib library calls were
|
||||
integrated into VASP directly, then data could also be exchanged via
|
||||
MPI.
|
||||
|
||||
----------------
|
||||
|
||||
Build LAMMPS with its MESSAGE package installed:
|
||||
|
||||
See the Build extras doc page and its MESSAGE package
|
||||
section for details.
|
||||
|
||||
CMake:
|
||||
|
||||
-D PKG_MESSAGE=yes # include the MESSAGE package
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
Traditional make:
|
||||
|
||||
cd lammps/lib/message
|
||||
python Install.py -m -z # build CSlib with MPI and ZMQ support
|
||||
cd lammps/src
|
||||
make yes-message
|
||||
make mpi
|
||||
|
||||
You can leave off the -z if you do not have ZMQ on your system.
|
||||
|
||||
----------------
|
||||
|
||||
Build the CSlib in a form usable by the vasp_wrapper.py script:
|
||||
|
||||
% cd lammps/lib/message/cslib/src
|
||||
% make shlib # build serial and parallel shared lib with ZMQ support
|
||||
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
|
||||
|
||||
This will make a shared library versions of the CSlib, which Python
|
||||
requires. Python must be able to find both the cslib.py script and
|
||||
the libcsnompi.so library in your lammps/lib/message/cslib/src
|
||||
directory. If it is not able to do this, you will get an error when
|
||||
you run vasp_wrapper.py.
|
||||
|
||||
You can do this by augmenting two environment variables, either
|
||||
from the command line, or in your shell start-up script.
|
||||
Here is the sample syntax for the csh or tcsh shells:
|
||||
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
|
||||
----------------
|
||||
|
||||
Prepare to use VASP and the vasp_wrapper.py script
|
||||
|
||||
You can run the vasp_wrap.py script as-is to test that the coupling
|
||||
between it and LAMMPS is functional. This will use the included
|
||||
vasprun.xml file output by a previous VASP run.
|
||||
|
||||
But note that the as-is version of vasp_wrap.py will not attempt to
|
||||
run VASP.
|
||||
|
||||
To do this, you must edit the 1st vaspcmd line at the top of
|
||||
vasp_wrapper.py to be the launch command needed to run VASP on your
|
||||
system. It can be a command to run VASP in serial or in parallel,
|
||||
e.g. an mpirun command. Then comment out the 2nd vaspcmd line
|
||||
immediately following it.
|
||||
|
||||
Insure you have the necessary VASP input files in this
|
||||
directory, suitable for the VASP calculation you want to perform:
|
||||
|
||||
INCAR
|
||||
KPOINTS
|
||||
POSCAR_template
|
||||
POTCAR
|
||||
|
||||
Examples of all but the POTCAR file are provided. As explained below,
|
||||
POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
|
||||
be used to test the LAMMPS/VASP coupling. The POTCAR file is a
|
||||
proprietary VASP file, so use one from your VASP installation.
|
||||
|
||||
Note that the POSCAR_template file should be matched to the LAMMPS
|
||||
input script (# of atoms and atom types, box size, etc). The provided
|
||||
POSCAR_W matches in.client.W.
|
||||
|
||||
Once you run VASP yourself, the vasprun.xml file will be overwritten.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
NOTE: The vasp_wrap.py script must be run with Python version 2, not
|
||||
3. This is because it used the CSlib python wrapper, which only
|
||||
supports version 2. We plan to upgrade CSlib to support Python 3.
|
||||
|
||||
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
|
||||
messaging mode, namely file or zmq. This is an argument to the
|
||||
vasp_wrap.py code; it can be selected by setting the "mode" variable
|
||||
when you run LAMMPS. The default mode = file.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means either of
|
||||
the messaging modes can be used and LAMMPS can be run in serial or
|
||||
parallel. The vasp_wrap.py code is always run in serial, but it
|
||||
launches VASP from Python via an mpirun command which can run VASP
|
||||
itself in parallel.
|
||||
|
||||
When you run, the server should print out thermodynamic info every
|
||||
timestep which corresponds to the forces and virial computed by VASP.
|
||||
VASP will also generate output files each timestep. The vasp_wrapper.py
|
||||
script could be generalized to archive these.
|
||||
|
||||
The examples below are commands you should use in two different
|
||||
terminal windows. The order of the two commands (client or server
|
||||
launch) does not matter. You can run them both in the same window if
|
||||
you append a "&" character to the first one to run it in the
|
||||
background.
|
||||
|
||||
--------------
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file < in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
15
examples/COUPLE/lammps_vasp/data.W
Normal file
15
examples/COUPLE/lammps_vasp/data.W
Normal file
@ -0,0 +1,15 @@
|
||||
LAMMPS W data file
|
||||
|
||||
2 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
0.0 3.16 xlo xhi
|
||||
0.0 3.16 ylo yhi
|
||||
0.0 3.16 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.000 0.000 0.000
|
||||
2 1 1.58 1.58 1.58
|
||||
|
||||
34
examples/COUPLE/lammps_vasp/in.client.W
Normal file
34
examples/COUPLE/lammps_vasp/in.client.W
Normal file
@ -0,0 +1,34 @@
|
||||
# small W unit cell for use with VASP
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
|
||||
76
examples/COUPLE/lammps_vasp/log.client.output
Normal file
76
examples/COUPLE/lammps_vasp/log.client.output
Normal file
@ -0,0 +1,76 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# small W unit cell for use with VASP
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md zmq localhost:5555
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
2 atoms
|
||||
Time spent = 0.000148058 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -48.030793 -78159.503
|
||||
1 298.24318 0 0 -48.03102 -78167.19
|
||||
2 296.85584 0 0 -48.031199 -78173.26
|
||||
3 295.83795 0 0 -48.031331 -78177.714
|
||||
Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
|
||||
50.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
|
||||
Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
|
||||
Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
|
||||
Other | | 1.204e-05 | | | 0.00
|
||||
|
||||
Nlocal: 1 ave 1 max 1 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4 ave 4 max 4 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:01:21
|
||||
300
examples/COUPLE/lammps_vasp/vasp_wrap.py
Normal file
300
examples/COUPLE/lammps_vasp/vasp_wrap.py
Normal file
@ -0,0 +1,300 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# http://lammps.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# ----------------------------------------------------------------------
|
||||
|
||||
# Syntax: vasp_wrap.py file/zmq POSCARfile
|
||||
|
||||
# wrapper on VASP to act as server program using CSlib
|
||||
# receives message with list of coords from client
|
||||
# creates VASP inputs
|
||||
# invokes VASP to calculate self-consistent energy of that config
|
||||
# reads VASP outputs
|
||||
# sends message with energy, forces, pressure to client
|
||||
|
||||
# NOTES:
|
||||
# check to insure basic VASP input files are in place?
|
||||
# could archive VASP input/output in special filenames or dirs?
|
||||
# need to check that POTCAR file is consistent with atom ordering?
|
||||
# could make syntax for launching VASP more flexible
|
||||
# e.g. command-line arg for # of procs
|
||||
# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
|
||||
|
||||
from __future__ import print_function
|
||||
import sys
|
||||
|
||||
version = sys.version_info[0]
|
||||
if version == 3:
|
||||
sys.exit("The CSlib python wrapper does not yet support python 3")
|
||||
|
||||
import subprocess
|
||||
import xml.etree.ElementTree as ET
|
||||
from cslib import CSlib
|
||||
|
||||
# comment out 2nd line once 1st line is correct for your system
|
||||
|
||||
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
|
||||
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
|
||||
vaspcmd = "touch tmp"
|
||||
|
||||
# enums matching FixClientMD class in LAMMPS
|
||||
|
||||
SETUP,STEP = range(1,2+1)
|
||||
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
|
||||
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
|
||||
|
||||
# -------------------------------------
|
||||
# functions
|
||||
|
||||
# error message and exit
|
||||
|
||||
def error(txt):
|
||||
print("ERROR:",txt)
|
||||
sys.exit(1)
|
||||
|
||||
# -------------------------------------
|
||||
# read initial VASP POSCAR file to setup problem
|
||||
# return natoms,ntypes,box
|
||||
|
||||
def vasp_setup(poscar):
|
||||
|
||||
ps = open(poscar,'r').readlines()
|
||||
|
||||
# box size
|
||||
|
||||
words = ps[2].split()
|
||||
xbox = float(words[0])
|
||||
words = ps[3].split()
|
||||
ybox = float(words[1])
|
||||
words = ps[4].split()
|
||||
zbox = float(words[2])
|
||||
box = [xbox,ybox,zbox]
|
||||
|
||||
ntypes = 0
|
||||
natoms = 0
|
||||
words = ps[6].split()
|
||||
for word in words:
|
||||
if word == '#': break
|
||||
ntypes += 1
|
||||
natoms += int(word)
|
||||
|
||||
return natoms,ntypes,box
|
||||
|
||||
# -------------------------------------
|
||||
# write a new POSCAR file for VASP
|
||||
|
||||
def poscar_write(poscar,natoms,ntypes,types,coords,box):
|
||||
|
||||
psold = open(poscar,'r').readlines()
|
||||
psnew = open("POSCAR",'w')
|
||||
|
||||
# header, including box size
|
||||
|
||||
psnew.write(psold[0])
|
||||
psnew.write(psold[1])
|
||||
psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
|
||||
psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
|
||||
psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
|
||||
psnew.write(psold[5])
|
||||
psnew.write(psold[6])
|
||||
|
||||
# per-atom coords
|
||||
# grouped by types
|
||||
|
||||
psnew.write("Cartesian\n")
|
||||
|
||||
for itype in range(1,ntypes+1):
|
||||
for i in range(natoms):
|
||||
if types[i] != itype: continue
|
||||
x = coords[3*i+0]
|
||||
y = coords[3*i+1]
|
||||
z = coords[3*i+2]
|
||||
aline = " %g %g %g\n" % (x,y,z)
|
||||
psnew.write(aline)
|
||||
|
||||
psnew.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a VASP output vasprun.xml file
|
||||
# uses ElementTree module
|
||||
# see https://docs.python.org/2/library/xml.etree.elementtree.html
|
||||
|
||||
def vasprun_read():
|
||||
tree = ET.parse('vasprun.xml')
|
||||
root = tree.getroot()
|
||||
|
||||
#fp = open("vasprun.xml","r")
|
||||
#root = ET.parse(fp)
|
||||
|
||||
scsteps = root.findall('calculation/scstep')
|
||||
energy = scsteps[-1].find('energy')
|
||||
for child in energy:
|
||||
if child.attrib["name"] == "e_0_energy":
|
||||
eout = float(child.text)
|
||||
|
||||
fout = []
|
||||
sout = []
|
||||
|
||||
varrays = root.findall('calculation/varray')
|
||||
for varray in varrays:
|
||||
if varray.attrib["name"] == "forces":
|
||||
forces = varray.findall("v")
|
||||
for line in forces:
|
||||
fxyz = line.text.split()
|
||||
fxyz = [float(value) for value in fxyz]
|
||||
fout += fxyz
|
||||
if varray.attrib["name"] == "stress":
|
||||
tensor = varray.findall("v")
|
||||
stensor = []
|
||||
for line in tensor:
|
||||
sxyz = line.text.split()
|
||||
sxyz = [float(value) for value in sxyz]
|
||||
stensor.append(sxyz)
|
||||
sxx = stensor[0][0]
|
||||
syy = stensor[1][1]
|
||||
szz = stensor[2][2]
|
||||
# symmetrize off-diagonal components
|
||||
sxy = 0.5 * (stensor[0][1] + stensor[1][0])
|
||||
sxz = 0.5 * (stensor[0][2] + stensor[2][0])
|
||||
syz = 0.5 * (stensor[1][2] + stensor[2][1])
|
||||
sout = [sxx,syy,szz,sxy,sxz,syz]
|
||||
|
||||
#fp.close()
|
||||
|
||||
return eout,fout,sout
|
||||
|
||||
# -------------------------------------
|
||||
# main program
|
||||
|
||||
# command-line args
|
||||
|
||||
if len(sys.argv) != 3:
|
||||
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
|
||||
sys.exit(1)
|
||||
|
||||
mode = sys.argv[1]
|
||||
poscar_template = sys.argv[2]
|
||||
|
||||
if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
|
||||
elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
|
||||
else:
|
||||
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
|
||||
sys.exit(1)
|
||||
|
||||
natoms,ntypes,box = vasp_setup(poscar_template)
|
||||
|
||||
# initial message for MD protocol
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID != 0: error("Bad initial client/server handshake")
|
||||
protocol = cs.unpack_string(1)
|
||||
if protocol != "md": error("Mismatch in client/server protocol")
|
||||
cs.send(0,0)
|
||||
|
||||
# endless server loop
|
||||
|
||||
while 1:
|
||||
|
||||
# recv message from client
|
||||
# msgID = 0 = all-done message
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID < 0: break
|
||||
|
||||
# SETUP receive at beginning of each run
|
||||
# required fields: DIM, PERIODICTY, ORIGIN, BOX,
|
||||
# NATOMS, NTYPES, TYPES, COORDS
|
||||
# optional fields: others in enum above, but VASP ignores them
|
||||
|
||||
if msgID == SETUP:
|
||||
|
||||
origin = []
|
||||
box = []
|
||||
natoms_recv = ntypes_recv = 0
|
||||
types = []
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == DIM:
|
||||
dim = cs.unpack_int(DIM)
|
||||
if dim != 3: error("VASP only performs 3d simulations")
|
||||
elif field == PERIODICITY:
|
||||
periodicity = cs.unpack(PERIODICITY,1)
|
||||
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
|
||||
error("VASP wrapper only currently supports fully periodic systems")
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box = cs.unpack(BOX,1)
|
||||
elif field == NATOMS:
|
||||
natoms_recv = cs.unpack_int(NATOMS)
|
||||
if natoms != natoms_recv:
|
||||
error("VASP wrapper mis-match in number of atoms")
|
||||
elif field == NTYPES:
|
||||
ntypes_recv = cs.unpack_int(NTYPES)
|
||||
if ntypes != ntypes_recv:
|
||||
error("VASP wrapper mis-match in number of atom types")
|
||||
elif field == TYPES:
|
||||
types = cs.unpack(TYPES,1)
|
||||
elif field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
|
||||
if not origin or not box or not natoms or not ntypes or \
|
||||
not types or not coords:
|
||||
error("Required VASP wrapper setup field not received");
|
||||
|
||||
# STEP receive at each timestep of run or minimization
|
||||
# required fields: COORDS
|
||||
# optional fields: ORIGIN, BOX
|
||||
|
||||
elif msgID == STEP:
|
||||
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box = cs.unpack(BOX,1)
|
||||
|
||||
if not coords: error("Required VASP wrapper step field not received");
|
||||
|
||||
else: error("VASP wrapper received unrecognized message")
|
||||
|
||||
# create POSCAR file
|
||||
|
||||
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
|
||||
|
||||
# invoke VASP
|
||||
|
||||
print("\nLaunching VASP ...")
|
||||
print(vaspcmd)
|
||||
subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
|
||||
|
||||
# process VASP output
|
||||
|
||||
energy,forces,virial = vasprun_read()
|
||||
|
||||
# convert VASP kilobars to bars
|
||||
|
||||
for i,value in enumerate(virial): virial[i] *= 1000.0
|
||||
|
||||
# return forces, energy, pressure to client
|
||||
|
||||
cs.send(msgID,3);
|
||||
cs.pack(FORCES,4,3*natoms,forces)
|
||||
cs.pack_double(ENERGY,energy)
|
||||
cs.pack(VIRIAL,4,6,virial)
|
||||
|
||||
# final reply to client
|
||||
|
||||
cs.send(0,0)
|
||||
|
||||
# clean-up
|
||||
|
||||
del cs
|
||||
12329
examples/COUPLE/lammps_vasp/vasprun.xml
Normal file
12329
examples/COUPLE/lammps_vasp/vasprun.xml
Normal file
File diff suppressed because it is too large
Load Diff
@ -83,6 +83,7 @@ kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
||||
latte: use of LATTE density-functional tight-binding quantum code
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
message: client/server coupling of 2 codes
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
mscg: parameterize a multi-scale coarse-graining (MSCG) model
|
||||
|
||||
117
examples/message/README
Normal file
117
examples/message/README
Normal file
@ -0,0 +1,117 @@
|
||||
This dir contains scripts that demonstrate how to use LAMMPS as both a
|
||||
client and server code to run a simple MD simulation. LAMMPS as a
|
||||
client performs the MD timestepping. LAMMPS as a server provides the
|
||||
energy and forces between interacting particles. Every timestep the
|
||||
LAMMPS client sends a message to the LAMMPS server and receives a
|
||||
response message in return.
|
||||
|
||||
Another code could replace LAMMPS as the client, e.g. another MD code
|
||||
which wants to use a LAMMPS potential. Another code could replace
|
||||
LAMMPS as the server, e.g. a quantum code computing quantum forces, so
|
||||
that ab initio MD could be performed. See an example of the latter in
|
||||
examples/COUPLE/lammps_vasp.
|
||||
|
||||
See the doc pages for the "MESSAGE package"
|
||||
(Package_details.html#PKG-MESSAGE) and "Howto client/server"
|
||||
(Howto_client_server.html) for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
--------------
|
||||
|
||||
Note that you can adjust the problem size run by these scripts by
|
||||
setting "x,y,z" variables when you run LAMMPS. The default problem size
|
||||
is x = y = z = 5, which is 500 particles.
|
||||
|
||||
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
|
||||
|
||||
This applies to either in.message or in.message.client
|
||||
|
||||
You can also run the in.message scripts with an NPT integrator
|
||||
instead of NVE, if you comment/uncomment the correct lines.
|
||||
|
||||
The client and server script define a "mode" variable
|
||||
which can be set to file, zmq, mpi/one, or mpi/two,
|
||||
as illustrated below.
|
||||
|
||||
--------------
|
||||
|
||||
To run this problem in the traditional way (no client/server coupling)
|
||||
do one of these:
|
||||
|
||||
% lmp_serial < in.message
|
||||
% mpirun -np 4 lmp_mpi < in.message
|
||||
|
||||
Or run with in.message.tilt.
|
||||
|
||||
--------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
Both the client and server script must use the same messaging mode.
|
||||
This can be selected by setting the "mode" variable when you run
|
||||
LAMMPS. The default mode = file. The other options for the mode
|
||||
variable are zmq, mpione, mpitwo.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means any of
|
||||
the 4 messaging modes can be used.
|
||||
|
||||
The next sections illustrate how to launch LAMMPS twice, once as a
|
||||
client, once as a server, for each of the messaging modes.
|
||||
|
||||
In all cases, the client should print out thermodynamic info for 50
|
||||
steps. The server should print out setup info, print nothing until
|
||||
the client exits, at which point the server should also exit.
|
||||
|
||||
The examples below show launching LAMMPS twice from the same window
|
||||
(or batch script), using the "&" character to launch the first time in
|
||||
the background. For all modes except {mpi/one}, you could also launch
|
||||
twice in separate windows on your desktop machine. It does not matter
|
||||
whether you launch the client or server first.
|
||||
|
||||
In these examples either the client or server can be run on one or
|
||||
more processors. If running in a non-MPI mode (file or zmq) you can
|
||||
launch LAMMPS on a single processor without using mpirun.
|
||||
|
||||
IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both
|
||||
times via mpirun, even if one or both of them runs on a single
|
||||
processor. This is so that MPI can figure out how to connect both MPI
|
||||
processes together to exchange MPI messages between them.
|
||||
|
||||
--------------
|
||||
|
||||
NOTE: the Script.sh file has comands to perform all the
|
||||
runs listed below.
|
||||
|
||||
--------------
|
||||
|
||||
File or ZMQ or mpi/two modes of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
|
||||
% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
|
||||
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client &
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
|
||||
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
Don't run the tilt files with the "file" mode; they run too slow.
|
||||
|
||||
--------------
|
||||
|
||||
Mpi/one mode of messaging:
|
||||
|
||||
Launch LAMMPS twice in a single mpirun command:
|
||||
|
||||
% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
|
||||
The two -np values determine how many procs the client and the server
|
||||
run on.
|
||||
|
||||
A LAMMPS executable run in this manner must use the -mpicolor color
|
||||
command-line option as its first option, where color is set to one
|
||||
integer value for the 1st app, and another value for the 2nd app.
|
||||
55
examples/message/Script.sh
Normal file
55
examples/message/Script.sh
Normal file
@ -0,0 +1,55 @@
|
||||
# sample launch script
|
||||
|
||||
# message on 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
|
||||
|
||||
# message on 2/4 procs each
|
||||
|
||||
mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
|
||||
|
||||
# message.tilt on 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client &
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
|
||||
|
||||
# message.tilt on 2/4 procs each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client &
|
||||
mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
|
||||
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
|
||||
29
examples/message/in.message
Normal file
29
examples/message/in.message
Normal file
@ -0,0 +1,29 @@
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
41
examples/message/in.message.client
Normal file
41
examples/message/in.message.client
Normal file
@ -0,0 +1,41 @@
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message client md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message client md mpi/two tmp.couple"
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
29
examples/message/in.message.server
Normal file
29
examples/message/in.message.server
Normal file
@ -0,0 +1,29 @@
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server md zmq *:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message server md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message server md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
30
examples/message/in.message.tilt
Normal file
30
examples/message/in.message.tilt
Normal file
@ -0,0 +1,30 @@
|
||||
# 2d NEMD simulation - no client/server mode
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
42
examples/message/in.message.tilt.client
Normal file
42
examples/message/in.message.tilt.client
Normal file
@ -0,0 +1,42 @@
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message client md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message client md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
31
examples/message/in.message.tilt.server
Normal file
31
examples/message/in.message.tilt.server
Normal file
@ -0,0 +1,31 @@
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server md zmq *:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message server md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message server md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
79
examples/message/log.28Aug18.message.client.file.g++.1
Normal file
79
examples/message/log.28Aug18.message.client.file.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md file tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000752926 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 4298.421 tau/day, 9.950 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
|
||||
Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00
|
||||
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
|
||||
Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98
|
||||
Other | | 0.0004668 | | | 0.01
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
79
examples/message/log.28Aug18.message.client.file.g++.2
Normal file
79
examples/message/log.28Aug18.message.client.file.g++.2
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md file tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000613928 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 4299.499 tau/day, 9.953 timesteps/s
|
||||
50.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00
|
||||
Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00
|
||||
Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01
|
||||
Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92
|
||||
Other | | 0.003203 | | | 0.06
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
79
examples/message/log.28Aug18.message.client.mpione.g++.1
Normal file
79
examples/message/log.28Aug18.message.client.mpione.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000540018 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 534798.272 tau/day, 1237.959 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01
|
||||
Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16
|
||||
Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24
|
||||
Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17
|
||||
Other | | 0.0001726 | | | 0.43
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/message/log.28Aug18.message.client.mpione.g++.2
Normal file
79
examples/message/log.28Aug18.message.client.mpione.g++.2
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000475883 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1035997.740 tau/day, 2398.143 timesteps/s
|
||||
99.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02
|
||||
Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60
|
||||
Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38
|
||||
Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15
|
||||
Other | | 0.0001761 | | | 0.84
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/message/log.28Aug18.message.client.mpitwo.g++.1
Normal file
79
examples/message/log.28Aug18.message.client.mpitwo.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000603914 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 312504.627 tau/day, 723.390 timesteps/s
|
||||
42.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01
|
||||
Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15
|
||||
Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20
|
||||
Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25
|
||||
Other | | 0.0002651 | | | 0.38
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/message/log.28Aug18.message.client.mpitwo.g++.2
Normal file
79
examples/message/log.28Aug18.message.client.mpitwo.g++.2
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000667095 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1135563.588 tau/day, 2628.619 timesteps/s
|
||||
58.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02
|
||||
Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95
|
||||
Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81
|
||||
Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58
|
||||
Other | | 0.0005029 | | | 2.64
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
79
examples/message/log.28Aug18.message.client.zmq.g++.1
Normal file
79
examples/message/log.28Aug18.message.client.zmq.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000734091 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 277513.222 tau/day, 642.392 timesteps/s
|
||||
11.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01
|
||||
Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11
|
||||
Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15
|
||||
Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37
|
||||
Other | | 0.0002885 | | | 0.37
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/message/log.28Aug18.message.client.zmq.g++.2
Normal file
79
examples/message/log.28Aug18.message.client.zmq.g++.2
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000570059 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 518489.499 tau/day, 1200.207 timesteps/s
|
||||
56.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01
|
||||
Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33
|
||||
Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27
|
||||
Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49
|
||||
Other | | 0.0003769 | | | 0.90
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
85
examples/message/log.28Aug18.message.g++.1
Normal file
85
examples/message/log.28Aug18.message.g++.1
Normal file
@ -0,0 +1,85 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000682831 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
|
||||
20 0.628166 -5.5624945 0 -4.62213 1.0186262
|
||||
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
|
||||
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
|
||||
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
|
||||
Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 544341.699 tau/day, 1260.050 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59
|
||||
Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41
|
||||
Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21
|
||||
Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32
|
||||
Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34
|
||||
Other | | 0.000448 | | | 1.13
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1946 ave 1946 max 1946 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18820 ave 18820 max 18820 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18820
|
||||
Ave neighs/atom = 37.64
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
85
examples/message/log.28Aug18.message.g++.4
Normal file
85
examples/message/log.28Aug18.message.g++.4
Normal file
@ -0,0 +1,85 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000656843 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
|
||||
20 0.628166 -5.5624945 0 -4.62213 1.0186262
|
||||
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
|
||||
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
|
||||
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1642350.242 tau/day, 3801.737 timesteps/s
|
||||
97.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71
|
||||
Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82
|
||||
Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41
|
||||
Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98
|
||||
Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14
|
||||
Other | | 0.0003865 | | | 2.94
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 1091 ave 1094 max 1089 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 4705 ave 4849 max 4648 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18820
|
||||
Ave neighs/atom = 37.64
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.file.g++.1
Normal file
44
examples/message/log.28Aug18.message.server.file.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md file tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:05
|
||||
44
examples/message/log.28Aug18.message.server.file.g++.4
Normal file
44
examples/message/log.28Aug18.message.server.file.g++.4
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md file tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:05
|
||||
44
examples/message/log.28Aug18.message.server.mpione.g++.1
Normal file
44
examples/message/log.28Aug18.message.server.mpione.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.mpione.g++.4
Normal file
44
examples/message/log.28Aug18.message.server.mpione.g++.4
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.mpitwo.g++.1
Normal file
44
examples/message/log.28Aug18.message.server.mpitwo.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.mpitwo.g++.4
Normal file
44
examples/message/log.28Aug18.message.server.mpitwo.g++.4
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.zmq.g++.1
Normal file
44
examples/message/log.28Aug18.message.server.zmq.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
44
examples/message/log.28Aug18.message.server.zmq.g++.4
Normal file
44
examples/message/log.28Aug18.message.server.zmq.g++.4
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
130
examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
Normal file
130
examples/message/log.28Aug18.message.tilt.client.mpione.g++.1
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000485897 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0086399 0 1.3760711 6.8772078 0.61567613
|
||||
2000 1.0707188 0 1.3744107 6.628097 1.2313523
|
||||
3000 1.0627515 0 1.310096 6.1647179 1.8470284
|
||||
4000 0.94091054 0 1.268976 6.4723215 2.4627045
|
||||
5000 1.0218949 0 1.2430242 5.6945977 3.0783806
|
||||
6000 0.98649481 0 1.1997565 5.2870413 3.6940568
|
||||
7000 0.9047957 0 1.1461262 5.9291636 4.3097329
|
||||
8000 0.85697614 0 1.0437412 5.0652097 4.925409
|
||||
9000 0.84208329 0 1.109218 6.1749808 5.5410852
|
||||
10000 0.86418108 0 1.1594773 6.2581867 6.1567613
|
||||
11000 0.95136356 0 1.1650901 5.8389085 6.7724374
|
||||
12000 0.94571583 0 1.2210342 6.2498816 7.3881135
|
||||
13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
|
||||
14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
|
||||
15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
|
||||
16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
|
||||
17000 1.0306843 0 1.3101457 6.4750102 -4.925409
|
||||
18000 1.071154 0 1.2947547 5.695888 -4.3097329
|
||||
19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
|
||||
20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
|
||||
21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
|
||||
22000 0.98550707 0 1.1768148 5.019967 -1.8470284
|
||||
23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
|
||||
24000 0.94069959 0 1.184119 5.8434876 -0.61567613
|
||||
25000 0.91569312 0 1.1642118 5.668997 0
|
||||
26000 0.98882932 0 1.1999248 5.0115507 0.61567613
|
||||
27000 0.8972608 0 1.2556546 7.0837158 1.2313523
|
||||
28000 0.93554756 0 1.2221911 5.9302841 1.8470284
|
||||
29000 0.97894608 0 1.2168736 5.5766766 2.4627045
|
||||
30000 0.97877055 0 1.2575839 6.4308887 3.0783806
|
||||
31000 1.0002387 0 1.2338069 5.3873124 3.6940568
|
||||
32000 0.89608618 0 1.2382021 6.7892204 4.3097329
|
||||
33000 0.87439302 0 1.2252635 7.078134 4.925409
|
||||
34000 1.076102 0 1.2991393 5.5556892 5.5410852
|
||||
35000 1.0018689 0 1.272105 6.1320483 6.1567613
|
||||
36000 0.93327214 0 1.2428039 7.0030867 6.7724374
|
||||
37000 1.0770236 0 1.3002931 5.4996076 7.3881135
|
||||
38000 0.98715132 0 1.215562 5.5958335 -7.3881135
|
||||
39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
|
||||
40000 1.0445585 0 1.241151 5.3589806 -6.1567613
|
||||
41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
|
||||
42000 0.99231038 0 1.2228781 5.9363471 -4.925409
|
||||
43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
|
||||
44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
|
||||
45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
|
||||
46000 0.98701623 0 1.170581 4.9719567 -2.4627045
|
||||
47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
|
||||
48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
|
||||
49000 1.0187472 0 1.271608 5.3355092 -0.61567613
|
||||
50000 1.0194881 0 1.2831094 6.2449759 0
|
||||
Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 12374053.445 tau/day, 28643.642 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12
|
||||
Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89
|
||||
Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03
|
||||
Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15
|
||||
Other | | 0.04905 | | | 2.81
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5270
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
130
examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
Normal file
130
examples/message/log.28Aug18.message.tilt.client.mpione.g++.2
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000453949 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0876599 0 1.3637783 6.063363 0.61567613
|
||||
2000 1.0722996 0 1.4108622 7.0518942 1.2313523
|
||||
3000 1.0580774 0 1.3845895 6.0395275 1.8470284
|
||||
4000 1.0068006 0 1.3804387 7.0944598 2.4627045
|
||||
5000 0.95391814 0 1.2578438 6.1878831 3.0783806
|
||||
6000 0.93492945 0 1.2711287 7.0440517 3.6940568
|
||||
7000 0.94107853 0 1.2384371 6.1438077 4.3097329
|
||||
8000 0.89711744 0 1.145748 6.3558305 4.925409
|
||||
9000 0.90190304 0 1.0860684 4.957098 5.5410852
|
||||
10000 0.84255749 0 1.0376892 5.2351795 6.1567613
|
||||
11000 0.90250882 0 1.0497695 4.3844838 6.7724374
|
||||
12000 0.83461274 0 1.0281949 5.1534361 7.3881135
|
||||
13000 0.80315331 0 1.0226333 5.757222 -7.3881135
|
||||
14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
|
||||
15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
|
||||
16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
|
||||
17000 0.98268136 0 1.2086981 5.6302847 -4.925409
|
||||
18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
|
||||
19000 1.0795086 0 1.4562691 7.639418 -3.6940568
|
||||
20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
|
||||
21000 1.2424296 0 1.6048792 7.959585 -2.4627045
|
||||
22000 1.297169 0 1.7421262 8.9432388 -1.8470284
|
||||
23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
|
||||
24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
|
||||
25000 1.3339728 0 1.6883255 7.529098 0
|
||||
26000 1.1483243 0 1.5155578 7.3869994 0.61567613
|
||||
27000 1.1372606 0 1.4368323 7.0580136 1.2313523
|
||||
28000 1.0518579 0 1.355311 6.478857 1.8470284
|
||||
29000 1.0581145 0 1.2535509 5.3697479 2.4627045
|
||||
30000 0.93612564 0 1.185532 5.5520142 3.0783806
|
||||
31000 0.94387516 0 1.1716454 5.8655485 3.6940568
|
||||
32000 0.83953515 0 1.0737746 5.5551953 4.3097329
|
||||
33000 0.84862926 0 1.0564042 5.7795428 4.925409
|
||||
34000 0.83621877 0 1.079387 5.7514243 5.5410852
|
||||
35000 0.86938506 0 1.031783 4.5897825 6.1567613
|
||||
36000 0.88990609 0 1.0807597 5.3751744 6.7724374
|
||||
37000 0.89534631 0 1.1238882 5.2400355 7.3881135
|
||||
38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
|
||||
39000 0.96737778 0 1.2472934 6.1139 -6.7724374
|
||||
40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
|
||||
41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
|
||||
42000 1.0875422 0 1.3963739 7.1208066 -4.925409
|
||||
43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
|
||||
44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
|
||||
45000 1.1243261 0 1.432186 6.884782 -3.0783806
|
||||
46000 1.039713 0 1.4389721 7.5585257 -2.4627045
|
||||
47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
|
||||
48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
|
||||
49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
|
||||
50000 0.92367087 0 1.1875669 6.4685214 0
|
||||
Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 7638300.565 tau/day, 17681.251 timesteps/s
|
||||
100.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04
|
||||
Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89
|
||||
Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02
|
||||
Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41
|
||||
Other | | 0.07465 | | | 2.64
|
||||
|
||||
Nlocal: 80 ave 80 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5257
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
130
examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
Normal file
130
examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.1
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000543118 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0086399 0 1.3760711 6.8772078 0.61567613
|
||||
2000 1.0707188 0 1.3744107 6.628097 1.2313523
|
||||
3000 1.0627515 0 1.310096 6.1647179 1.8470284
|
||||
4000 0.94091054 0 1.268976 6.4723215 2.4627045
|
||||
5000 1.0218949 0 1.2430242 5.6945977 3.0783806
|
||||
6000 0.98649481 0 1.1997565 5.2870413 3.6940568
|
||||
7000 0.9047957 0 1.1461262 5.9291636 4.3097329
|
||||
8000 0.85697614 0 1.0437412 5.0652097 4.925409
|
||||
9000 0.84208329 0 1.109218 6.1749808 5.5410852
|
||||
10000 0.86418108 0 1.1594773 6.2581867 6.1567613
|
||||
11000 0.95136356 0 1.1650901 5.8389085 6.7724374
|
||||
12000 0.94571583 0 1.2210342 6.2498816 7.3881135
|
||||
13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
|
||||
14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
|
||||
15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
|
||||
16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
|
||||
17000 1.0306843 0 1.3101457 6.4750102 -4.925409
|
||||
18000 1.071154 0 1.2947547 5.695888 -4.3097329
|
||||
19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
|
||||
20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
|
||||
21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
|
||||
22000 0.98550707 0 1.1768148 5.019967 -1.8470284
|
||||
23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
|
||||
24000 0.94069959 0 1.184119 5.8434876 -0.61567613
|
||||
25000 0.91569312 0 1.1642118 5.668997 0
|
||||
26000 0.98882932 0 1.1999248 5.0115507 0.61567613
|
||||
27000 0.8972608 0 1.2556546 7.0837158 1.2313523
|
||||
28000 0.93554756 0 1.2221911 5.9302841 1.8470284
|
||||
29000 0.97894608 0 1.2168736 5.5766766 2.4627045
|
||||
30000 0.97877055 0 1.2575839 6.4308887 3.0783806
|
||||
31000 1.0002387 0 1.2338069 5.3873124 3.6940568
|
||||
32000 0.89608618 0 1.2382021 6.7892204 4.3097329
|
||||
33000 0.87439302 0 1.2252635 7.078134 4.925409
|
||||
34000 1.076102 0 1.2991393 5.5556892 5.5410852
|
||||
35000 1.0018689 0 1.272105 6.1320483 6.1567613
|
||||
36000 0.93327214 0 1.2428039 7.0030867 6.7724374
|
||||
37000 1.0770236 0 1.3002931 5.4996076 7.3881135
|
||||
38000 0.98715132 0 1.215562 5.5958335 -7.3881135
|
||||
39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
|
||||
40000 1.0445585 0 1.241151 5.3589806 -6.1567613
|
||||
41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
|
||||
42000 0.99231038 0 1.2228781 5.9363471 -4.925409
|
||||
43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
|
||||
44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
|
||||
45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
|
||||
46000 0.98701623 0 1.170581 4.9719567 -2.4627045
|
||||
47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
|
||||
48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
|
||||
49000 1.0187472 0 1.271608 5.3355092 -0.61567613
|
||||
50000 1.0194881 0 1.2831094 6.2449759 0
|
||||
Loop time of 4.80282 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 4497356.047 tau/day, 10410.546 timesteps/s
|
||||
50.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0032325 | 0.0032325 | 0.0032325 | 0.0 | 0.07
|
||||
Comm | 0.033613 | 0.033613 | 0.033613 | 0.0 | 0.70
|
||||
Output | 0.00089812 | 0.00089812 | 0.00089812 | 0.0 | 0.02
|
||||
Modify | 4.6706 | 4.6706 | 4.6706 | 0.0 | 97.25
|
||||
Other | | 0.09449 | | | 1.97
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5270
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
130
examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
Normal file
130
examples/message/log.28Aug18.message.tilt.client.mpitwo.g++.2
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000574827 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0876599 0 1.3637783 6.063363 0.61567613
|
||||
2000 1.0722996 0 1.4108622 7.0518942 1.2313523
|
||||
3000 1.0580774 0 1.3845895 6.0395275 1.8470284
|
||||
4000 1.0068006 0 1.3804387 7.0944598 2.4627045
|
||||
5000 0.95391814 0 1.2578438 6.1878831 3.0783806
|
||||
6000 0.93492945 0 1.2711287 7.0440517 3.6940568
|
||||
7000 0.94107853 0 1.2384371 6.1438077 4.3097329
|
||||
8000 0.89711744 0 1.145748 6.3558305 4.925409
|
||||
9000 0.90190304 0 1.0860684 4.957098 5.5410852
|
||||
10000 0.84255749 0 1.0376892 5.2351795 6.1567613
|
||||
11000 0.90250882 0 1.0497695 4.3844838 6.7724374
|
||||
12000 0.83461274 0 1.0281949 5.1534361 7.3881135
|
||||
13000 0.80315331 0 1.0226333 5.757222 -7.3881135
|
||||
14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
|
||||
15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
|
||||
16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
|
||||
17000 0.98268136 0 1.2086981 5.6302847 -4.925409
|
||||
18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
|
||||
19000 1.0795086 0 1.4562691 7.639418 -3.6940568
|
||||
20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
|
||||
21000 1.2424296 0 1.6048792 7.959585 -2.4627045
|
||||
22000 1.297169 0 1.7421262 8.9432388 -1.8470284
|
||||
23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
|
||||
24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
|
||||
25000 1.3339728 0 1.6883255 7.529098 0
|
||||
26000 1.1483243 0 1.5155578 7.3869994 0.61567613
|
||||
27000 1.1372606 0 1.4368323 7.0580136 1.2313523
|
||||
28000 1.0518579 0 1.355311 6.478857 1.8470284
|
||||
29000 1.0581145 0 1.2535509 5.3697479 2.4627045
|
||||
30000 0.93612564 0 1.185532 5.5520142 3.0783806
|
||||
31000 0.94387516 0 1.1716454 5.8655485 3.6940568
|
||||
32000 0.83953515 0 1.0737746 5.5551953 4.3097329
|
||||
33000 0.84862926 0 1.0564042 5.7795428 4.925409
|
||||
34000 0.83621877 0 1.079387 5.7514243 5.5410852
|
||||
35000 0.86938506 0 1.031783 4.5897825 6.1567613
|
||||
36000 0.88990609 0 1.0807597 5.3751744 6.7724374
|
||||
37000 0.89534631 0 1.1238882 5.2400355 7.3881135
|
||||
38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
|
||||
39000 0.96737778 0 1.2472934 6.1139 -6.7724374
|
||||
40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
|
||||
41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
|
||||
42000 1.0875422 0 1.3963739 7.1208066 -4.925409
|
||||
43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
|
||||
44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
|
||||
45000 1.1243261 0 1.432186 6.884782 -3.0783806
|
||||
46000 1.039713 0 1.4389721 7.5585257 -2.4627045
|
||||
47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
|
||||
48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
|
||||
49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
|
||||
50000 0.92367087 0 1.1875669 6.4685214 0
|
||||
Loop time of 5.66536 on 2 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 3812643.232 tau/day, 8825.563 timesteps/s
|
||||
48.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0012836 | 0.0015377 | 0.0017917 | 0.6 | 0.03
|
||||
Comm | 0.037211 | 0.037922 | 0.038633 | 0.4 | 0.67
|
||||
Output | 0.00052023 | 0.00073683 | 0.00095344 | 0.0 | 0.01
|
||||
Modify | 5.5101 | 5.5105 | 5.511 | 0.0 | 97.27
|
||||
Other | | 0.1146 | | | 2.02
|
||||
|
||||
Nlocal: 80 ave 80 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5257
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
130
examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
Normal file
130
examples/message/log.28Aug18.message.tilt.client.zmq.g++.1
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000530005 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0086399 0 1.3760711 6.8772078 0.61567613
|
||||
2000 1.0707188 0 1.3744107 6.628097 1.2313523
|
||||
3000 1.0627515 0 1.310096 6.1647179 1.8470284
|
||||
4000 0.94091054 0 1.268976 6.4723215 2.4627045
|
||||
5000 1.0218949 0 1.2430242 5.6945977 3.0783806
|
||||
6000 0.98649481 0 1.1997565 5.2870413 3.6940568
|
||||
7000 0.9047957 0 1.1461262 5.9291636 4.3097329
|
||||
8000 0.85697614 0 1.0437412 5.0652097 4.925409
|
||||
9000 0.84208329 0 1.109218 6.1749808 5.5410852
|
||||
10000 0.86418108 0 1.1594773 6.2581867 6.1567613
|
||||
11000 0.95136356 0 1.1650901 5.8389085 6.7724374
|
||||
12000 0.94571583 0 1.2210342 6.2498816 7.3881135
|
||||
13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
|
||||
14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
|
||||
15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
|
||||
16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
|
||||
17000 1.0306843 0 1.3101457 6.4750102 -4.925409
|
||||
18000 1.071154 0 1.2947547 5.695888 -4.3097329
|
||||
19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
|
||||
20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
|
||||
21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
|
||||
22000 0.98550707 0 1.1768148 5.019967 -1.8470284
|
||||
23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
|
||||
24000 0.94069959 0 1.184119 5.8434876 -0.61567613
|
||||
25000 0.91569312 0 1.1642118 5.668997 0
|
||||
26000 0.98882932 0 1.1999248 5.0115507 0.61567613
|
||||
27000 0.8972608 0 1.2556546 7.0837158 1.2313523
|
||||
28000 0.93554756 0 1.2221911 5.9302841 1.8470284
|
||||
29000 0.97894608 0 1.2168736 5.5766766 2.4627045
|
||||
30000 0.97877055 0 1.2575839 6.4308887 3.0783806
|
||||
31000 1.0002387 0 1.2338069 5.3873124 3.6940568
|
||||
32000 0.89608618 0 1.2382021 6.7892204 4.3097329
|
||||
33000 0.87439302 0 1.2252635 7.078134 4.925409
|
||||
34000 1.076102 0 1.2991393 5.5556892 5.5410852
|
||||
35000 1.0018689 0 1.272105 6.1320483 6.1567613
|
||||
36000 0.93327214 0 1.2428039 7.0030867 6.7724374
|
||||
37000 1.0770236 0 1.3002931 5.4996076 7.3881135
|
||||
38000 0.98715132 0 1.215562 5.5958335 -7.3881135
|
||||
39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
|
||||
40000 1.0445585 0 1.241151 5.3589806 -6.1567613
|
||||
41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
|
||||
42000 0.99231038 0 1.2228781 5.9363471 -4.925409
|
||||
43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
|
||||
44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
|
||||
45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
|
||||
46000 0.98701623 0 1.170581 4.9719567 -2.4627045
|
||||
47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
|
||||
48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
|
||||
49000 1.0187472 0 1.271608 5.3355092 -0.61567613
|
||||
50000 1.0194881 0 1.2831094 6.2449759 0
|
||||
Loop time of 12.9652 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 1666000.147 tau/day, 3856.482 timesteps/s
|
||||
23.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0018659 | 0.0018659 | 0.0018659 | 0.0 | 0.01
|
||||
Comm | 0.020679 | 0.020679 | 0.020679 | 0.0 | 0.16
|
||||
Output | 0.00052547 | 0.00052547 | 0.00052547 | 0.0 | 0.00
|
||||
Modify | 12.871 | 12.871 | 12.871 | 0.0 | 99.28
|
||||
Other | | 0.07062 | | | 0.54
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5270
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:12
|
||||
130
examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
Normal file
130
examples/message/log.28Aug18.message.tilt.client.zmq.g++.2
Normal file
@ -0,0 +1,130 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000673056 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0876599 0 1.3637783 6.063363 0.61567613
|
||||
2000 1.0722996 0 1.4108622 7.0518942 1.2313523
|
||||
3000 1.0580774 0 1.3845895 6.0395275 1.8470284
|
||||
4000 1.0068006 0 1.3804387 7.0944598 2.4627045
|
||||
5000 0.95391814 0 1.2578438 6.1878831 3.0783806
|
||||
6000 0.93492945 0 1.2711287 7.0440517 3.6940568
|
||||
7000 0.94107853 0 1.2384371 6.1438077 4.3097329
|
||||
8000 0.89711744 0 1.145748 6.3558305 4.925409
|
||||
9000 0.90190304 0 1.0860684 4.957098 5.5410852
|
||||
10000 0.84255749 0 1.0376892 5.2351795 6.1567613
|
||||
11000 0.90250882 0 1.0497695 4.3844838 6.7724374
|
||||
12000 0.83461274 0 1.0281949 5.1534361 7.3881135
|
||||
13000 0.80315331 0 1.0226333 5.757222 -7.3881135
|
||||
14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
|
||||
15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
|
||||
16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
|
||||
17000 0.98268136 0 1.2086981 5.6302847 -4.925409
|
||||
18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
|
||||
19000 1.0795086 0 1.4562691 7.639418 -3.6940568
|
||||
20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
|
||||
21000 1.2424296 0 1.6048792 7.959585 -2.4627045
|
||||
22000 1.297169 0 1.7421262 8.9432388 -1.8470284
|
||||
23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
|
||||
24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
|
||||
25000 1.3339728 0 1.6883255 7.529098 0
|
||||
26000 1.1483243 0 1.5155578 7.3869994 0.61567613
|
||||
27000 1.1372606 0 1.4368323 7.0580136 1.2313523
|
||||
28000 1.0518579 0 1.355311 6.478857 1.8470284
|
||||
29000 1.0581145 0 1.2535509 5.3697479 2.4627045
|
||||
30000 0.93612564 0 1.185532 5.5520142 3.0783806
|
||||
31000 0.94387516 0 1.1716454 5.8655485 3.6940568
|
||||
32000 0.83953515 0 1.0737746 5.5551953 4.3097329
|
||||
33000 0.84862926 0 1.0564042 5.7795428 4.925409
|
||||
34000 0.83621877 0 1.079387 5.7514243 5.5410852
|
||||
35000 0.86938506 0 1.031783 4.5897825 6.1567613
|
||||
36000 0.88990609 0 1.0807597 5.3751744 6.7724374
|
||||
37000 0.89534631 0 1.1238882 5.2400355 7.3881135
|
||||
38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
|
||||
39000 0.96737778 0 1.2472934 6.1139 -6.7724374
|
||||
40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
|
||||
41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
|
||||
42000 1.0875422 0 1.3963739 7.1208066 -4.925409
|
||||
43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
|
||||
44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
|
||||
45000 1.1243261 0 1.432186 6.884782 -3.0783806
|
||||
46000 1.039713 0 1.4389721 7.5585257 -2.4627045
|
||||
47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
|
||||
48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
|
||||
49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
|
||||
50000 0.92367087 0 1.1875669 6.4685214 0
|
||||
Loop time of 13.6129 on 2 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 1586733.497 tau/day, 3672.994 timesteps/s
|
||||
59.3% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0015125 | 0.0015551 | 0.0015976 | 0.1 | 0.01
|
||||
Comm | 0.026598 | 0.028413 | 0.030227 | 1.1 | 0.21
|
||||
Output | 0.00046492 | 0.00063884 | 0.00081277 | 0.0 | 0.00
|
||||
Modify | 13.465 | 13.483 | 13.501 | 0.5 | 99.04
|
||||
Other | | 0.0994 | | | 0.73
|
||||
|
||||
Nlocal: 80 ave 80 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5257
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:13
|
||||
129
examples/message/log.28Aug18.message.tilt.g++.1
Normal file
129
examples/message/log.28Aug18.message.tilt.g++.1
Normal file
@ -0,0 +1,129 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - no client/server mode
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000437021 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
|
||||
2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
|
||||
3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
|
||||
4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
|
||||
5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
|
||||
6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
|
||||
7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
|
||||
8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
|
||||
9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
|
||||
10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
|
||||
11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
|
||||
12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
|
||||
13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
|
||||
14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
|
||||
15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
|
||||
16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
|
||||
17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
|
||||
18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
|
||||
19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
|
||||
20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
|
||||
21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
|
||||
22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
|
||||
23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
|
||||
24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
|
||||
25000 1.0946409 0.33366032 1.4214597 7.1907559 0
|
||||
26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
|
||||
27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
|
||||
28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
|
||||
29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
|
||||
30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
|
||||
31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
|
||||
32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
|
||||
33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
|
||||
34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
|
||||
35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
|
||||
36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
|
||||
37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
|
||||
38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
|
||||
39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
|
||||
40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
|
||||
41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
|
||||
42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
|
||||
43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
|
||||
44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
|
||||
45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
|
||||
46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
|
||||
47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
|
||||
48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
|
||||
49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
|
||||
50000 1.0566272 0.28657142 1.3365947 6.261203 0
|
||||
Loop time of 1.15672 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 18673426.371 tau/day, 43225.524 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.19267 | 0.19267 | 0.19267 | 0.0 | 16.66
|
||||
Neigh | 0.15156 | 0.15156 | 0.15156 | 0.0 | 13.10
|
||||
Comm | 0.044569 | 0.044569 | 0.044569 | 0.0 | 3.85
|
||||
Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.05
|
||||
Modify | 0.71051 | 0.71051 | 0.71051 | 0.0 | 61.42
|
||||
Other | | 0.05684 | | | 4.91
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 71 ave 71 max 71 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 362 ave 362 max 362 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 362
|
||||
Ave neighs/atom = 2.2625
|
||||
Neighbor list builds = 5256
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
129
examples/message/log.28Aug18.message.tilt.g++.4
Normal file
129
examples/message/log.28Aug18.message.tilt.g++.4
Normal file
@ -0,0 +1,129 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - no client/server mode
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000396967 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.1326992 0.25863754 1.3842573 6.0588079 0.61567613
|
||||
2000 1.0158438 0.33502643 1.3445212 7.2638652 1.2313523
|
||||
3000 1.0968167 0.3149227 1.4048843 7.0653223 1.8470284
|
||||
4000 1.0070993 0.40611915 1.4069241 7.7283521 2.4627045
|
||||
5000 1.1153133 0.2674828 1.3758254 6.2949171 3.0783806
|
||||
6000 1.0170665 0.25843673 1.2691466 6.049412 3.6940568
|
||||
7000 1.0224605 0.20974914 1.2258193 5.5104976 4.3097329
|
||||
8000 0.96149374 0.24035439 1.1958388 5.4179146 4.925409
|
||||
9000 0.87759014 0.2590493 1.1311545 5.8711239 5.5410852
|
||||
10000 0.83791968 0.23477897 1.0674617 5.666904 6.1567613
|
||||
11000 0.87702487 0.22958877 1.1011322 5.9068062 6.7724374
|
||||
12000 0.81507294 0.26375817 1.0737369 5.9166925 7.3881135
|
||||
13000 0.85655284 0.24676491 1.0979643 5.6918734 -7.3881135
|
||||
14000 0.84369293 0.27818471 1.1166046 6.4146184 -6.7724374
|
||||
15000 0.90052173 0.19836095 1.0932544 5.2690913 -6.1567613
|
||||
16000 0.83836874 0.26921637 1.1023453 5.9579526 -5.5410852
|
||||
17000 0.90492897 0.21933098 1.1186041 5.6042194 -4.925409
|
||||
18000 0.90113412 0.24880908 1.1443111 6.0634846 -4.3097329
|
||||
19000 1.0160445 0.17252962 1.1822239 5.3149334 -3.6940568
|
||||
20000 0.96217234 0.2414377 1.1975965 5.476653 -3.0783806
|
||||
21000 0.98229664 0.27569118 1.2518485 5.9340174 -2.4627045
|
||||
22000 1.0551763 0.26997615 1.3185576 6.2094112 -1.8470284
|
||||
23000 1.051999 0.34076639 1.3861904 7.082385 -1.2313523
|
||||
24000 1.1350071 0.23701844 1.3649317 6.1829742 -0.61567613
|
||||
25000 1.0946409 0.33366032 1.4214597 7.1907559 0
|
||||
26000 1.1511799 0.24626808 1.3902531 5.8469984 0.61567613
|
||||
27000 1.1009203 0.25653085 1.3505704 6.1504287 1.2313523
|
||||
28000 1.0521302 0.2876798 1.3332342 5.9906187 1.8470284
|
||||
29000 1.0518465 0.21853 1.2638025 5.6577549 2.4627045
|
||||
30000 0.97264625 0.28758145 1.2541487 6.5769804 3.0783806
|
||||
31000 1.0133579 0.31575837 1.3227828 6.6650893 3.6940568
|
||||
32000 1.0714324 0.28757036 1.3523063 6.2682059 4.3097329
|
||||
33000 1.0739451 0.28062459 1.3478575 6.6862746 4.925409
|
||||
34000 1.0056867 0.38289586 1.382297 7.1120131 5.5410852
|
||||
35000 1.0911349 0.26370939 1.3480247 6.1476048 6.1567613
|
||||
36000 1.0618618 0.28269593 1.3379211 6.9414608 6.7724374
|
||||
37000 1.0704991 0.29974994 1.3635585 7.0834346 7.3881135
|
||||
38000 1.1087507 0.2682201 1.3700411 5.8506019 -7.3881135
|
||||
39000 1.1303733 0.22362416 1.3469326 5.2500269 -6.7724374
|
||||
40000 1.0174248 0.28956571 1.3006316 6.4491571 -6.1567613
|
||||
41000 0.95981887 0.29162143 1.2454414 6.4658646 -5.5410852
|
||||
42000 0.88302144 0.30432252 1.1818251 6.7401923 -4.925409
|
||||
43000 0.93164419 0.25110308 1.1769245 5.9067383 -4.3097329
|
||||
44000 0.98352598 0.23322873 1.2106077 5.5606585 -3.6940568
|
||||
45000 1.0247245 0.26503082 1.2833508 6.533394 -3.0783806
|
||||
46000 0.93004532 0.32277782 1.2470104 6.4689179 -2.4627045
|
||||
47000 1.0653176 0.29185413 1.3505135 6.9534569 -1.8470284
|
||||
48000 1.0401524 0.3420245 1.3756759 6.8016042 -1.2313523
|
||||
49000 1.0023407 0.31833091 1.314407 6.7385662 -0.61567613
|
||||
50000 1.0566272 0.28657142 1.3365947 6.261203 0
|
||||
Loop time of 0.92653 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 23312793.646 tau/day, 53964.800 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.15063 | 0.15063 | 0.15063 | 0.0 | 16.26
|
||||
Neigh | 0.11869 | 0.11869 | 0.11869 | 0.0 | 12.81
|
||||
Comm | 0.035839 | 0.035839 | 0.035839 | 0.0 | 3.87
|
||||
Output | 0.00064468 | 0.00064468 | 0.00064468 | 0.0 | 0.07
|
||||
Modify | 0.57422 | 0.57422 | 0.57422 | 0.0 | 61.98
|
||||
Other | | 0.0465 | | | 5.02
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 71 ave 71 max 71 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 362 ave 362 max 362 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 362
|
||||
Ave neighs/atom = 2.2625
|
||||
Neighbor list builds = 5256
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000438929 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5073
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000455141 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
2 by 2 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5066
|
||||
Total wall time: 0:00:02
|
||||
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000521898 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5073
|
||||
Total wall time: 0:00:04
|
||||
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000378847 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
2 by 2 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5066
|
||||
Total wall time: 0:00:06
|
||||
48
examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
Normal file
48
examples/message/log.28Aug18.message.tilt.server.zmq.g++.1
Normal file
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000557184 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5073
|
||||
Total wall time: 0:00:12
|
||||
48
examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
Normal file
48
examples/message/log.28Aug18.message.tilt.server.zmq.g++.4
Normal file
@ -0,0 +1,48 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000586987 secs
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
2 by 2 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 1.3
|
||||
binsize = 0.65, bins = 24 19 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/2d/newton/tri
|
||||
bin: standard
|
||||
Server MD calls = 50001
|
||||
Server MD reneighborings 5066
|
||||
Total wall time: 0:00:13
|
||||
@ -35,6 +35,8 @@ linalg set of BLAS and LAPACK routines needed by USER-ATC package
|
||||
from Axel Kohlmeyer (Temple U)
|
||||
meam modified embedded atom method (MEAM) potential, MEAM package
|
||||
from Greg Wagner (Sandia)
|
||||
message client/server communication library via MPI, sockets, files
|
||||
from Steve Plimpton (Sandia)
|
||||
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
|
||||
from Axel Kohlmeyer (Temple U) and the VMD development team
|
||||
mscg hooks to the MSCG library, used by fix_mscg command
|
||||
|
||||
118
lib/message/Install.py
Normal file
118
lib/message/Install.py
Normal file
@ -0,0 +1,118 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# Install.py tool to build the CSlib library
|
||||
# used to automate the steps described in the README file in this dir
|
||||
|
||||
from __future__ import print_function
|
||||
import sys,os,re,subprocess
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax from src dir: make lib-message args="-m"
|
||||
or: make lib-message args="-s -z"
|
||||
Syntax from lib dir: python Install.py -m
|
||||
or: python Install.py -s -z
|
||||
|
||||
specify zero or more options, order does not matter
|
||||
|
||||
-m = parallel build of CSlib library
|
||||
-s = serial build of CSlib library
|
||||
-z = build CSlib library with ZMQ socket support, default = no ZMQ support
|
||||
|
||||
Example:
|
||||
|
||||
make lib-message args="-m -z" # build parallel CSlib with ZMQ support
|
||||
make lib-message args="-s" # build serial CSlib with no ZMQ support
|
||||
"""
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR",str)
|
||||
sys.exit()
|
||||
|
||||
# expand to full path name
|
||||
# process leading '~' or relative path
|
||||
|
||||
def fullpath(path):
|
||||
return os.path.abspath(os.path.expanduser(path))
|
||||
|
||||
def which(program):
|
||||
def is_exe(fpath):
|
||||
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
|
||||
|
||||
fpath, fname = os.path.split(program)
|
||||
if fpath:
|
||||
if is_exe(program):
|
||||
return program
|
||||
else:
|
||||
for path in os.environ["PATH"].split(os.pathsep):
|
||||
path = path.strip('"')
|
||||
exe_file = os.path.join(path, program)
|
||||
if is_exe(exe_file):
|
||||
return exe_file
|
||||
|
||||
return None
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
mpiflag = False
|
||||
serialflag = False
|
||||
zmqflag = False
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
mpiflag = True
|
||||
iarg += 1
|
||||
elif args[iarg] == "-s":
|
||||
serialflag = True
|
||||
iarg += 1
|
||||
elif args[iarg] == "-z":
|
||||
zmqflag = True
|
||||
iarg += 1
|
||||
else: error()
|
||||
|
||||
if (not mpiflag and not serialflag):
|
||||
error("Must use either -m or -s flag")
|
||||
|
||||
if (mpiflag and serialflag):
|
||||
error("Cannot use -m and -s flag at the same time")
|
||||
|
||||
# build CSlib
|
||||
# copy resulting lib to cslib/src/libmessage.a
|
||||
# copy appropriate Makefile.lammps.* to Makefile.lammps
|
||||
|
||||
print("Building CSlib ...")
|
||||
srcdir = fullpath("./cslib/src")
|
||||
|
||||
if mpiflag and zmqflag:
|
||||
cmd = "cd %s; make lib_parallel" % srcdir
|
||||
elif mpiflag and not zmqflag:
|
||||
cmd = "cd %s; make lib_parallel zmq=no" % srcdir
|
||||
elif not mpiflag and zmqflag:
|
||||
cmd = "cd %s; make lib_serial" % srcdir
|
||||
elif not mpiflag and not zmqflag:
|
||||
cmd = "cd %s; make lib_serial zmq=no" % srcdir
|
||||
|
||||
print(cmd)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
|
||||
if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir
|
||||
else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir
|
||||
print(cmd)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
|
||||
if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps"
|
||||
else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps"
|
||||
print(cmd)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
print(txt.decode('UTF-8'))
|
||||
5
lib/message/Makefile.lammps.nozmq
Normal file
5
lib/message/Makefile.lammps.nozmq
Normal file
@ -0,0 +1,5 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
message_SYSINC =
|
||||
message_SYSLIB =
|
||||
message_SYSPATH =
|
||||
5
lib/message/Makefile.lammps.zmq
Normal file
5
lib/message/Makefile.lammps.zmq
Normal file
@ -0,0 +1,5 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
message_SYSINC =
|
||||
message_SYSLIB = -lzmq
|
||||
message_SYSPATH =
|
||||
51
lib/message/README
Normal file
51
lib/message/README
Normal file
@ -0,0 +1,51 @@
|
||||
This directory contains the CSlib library which is required
|
||||
to use the MESSAGE package and its client/server commands
|
||||
in a LAMMPS input script.
|
||||
|
||||
The CSlib libary is included in the LAMMPS distribution. A fuller
|
||||
version including documentation and test programs is available at
|
||||
http://cslib.sandia.gov. It was developed by Steve Plimpton at Sandia
|
||||
National Laboratories.
|
||||
|
||||
You can type "make lib-message" from the src directory to see help on
|
||||
how to build this library via make commands, or you can do the same
|
||||
thing by typing "python Install.py" from within this directory, or you
|
||||
can do it manually by following the instructions below.
|
||||
|
||||
The CSlib can be optionally built with support for sockets using
|
||||
the open-source ZeroMQ (ZMQ) library. If it is not installed
|
||||
on your system, it is easy to download and install.
|
||||
|
||||
Go to the ZMQ website for details: http://zeromq.org
|
||||
|
||||
-----------------
|
||||
|
||||
Instructions:
|
||||
|
||||
1. Compile CSlib from within cslib/src with one of the following:
|
||||
% make lib_parallel # build parallel library with ZMQ socket support
|
||||
% make lib_serial # build serial library with ZMQ support
|
||||
% make lib_parallel zmq=no # build parallel lib with no ZMQ support
|
||||
% make lib_serial zmq=no # build serial lib with no ZMQ support
|
||||
|
||||
2. Copy the produced cslib/src/libcsmpi.a or libscnompi.a file to
|
||||
cslib/src/libmessage.a
|
||||
|
||||
3. Copy either lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq
|
||||
to lib/message/Makefile.lammps, depending on whether you
|
||||
build the library with ZMQ support or not.
|
||||
If your ZMQ library is not in a place your shell path finds,
|
||||
you can set the INCLUDE and PATH variables in Makefile.lammps
|
||||
to point to the dirs where the ZMQ include and library files are.
|
||||
|
||||
-----------------
|
||||
|
||||
When these steps are complete you can build LAMMPS
|
||||
with the MESSAGAE package installed:
|
||||
|
||||
% cd lammps/src
|
||||
% make yes-message
|
||||
% make mpi (or whatever target you wish)
|
||||
|
||||
Note that if you download and unpack a new LAMMPS tarball, you will
|
||||
need to re-build the CSlib in this dir.
|
||||
32
lib/message/cslib/LICENSE
Normal file
32
lib/message/cslib/LICENSE
Normal file
@ -0,0 +1,32 @@
|
||||
Program: CSlib client/server coupling library
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of Sandia,
|
||||
LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
|
||||
U.S. Government retains certain rights in this software. This
|
||||
software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions are met:
|
||||
|
||||
* Redistributions of source code must retain the above copyright notice,
|
||||
this list of conditions and the following disclaimer.
|
||||
|
||||
* Redistributions in binary form must reproduce the above copyright notice,
|
||||
this list of conditions and the following disclaimer in the documentation
|
||||
and/or other materials provided with the distribution.
|
||||
|
||||
* Neither the name of Sandia Corporation nor the names of contributors
|
||||
to this software may be used to endorse or promote products derived
|
||||
from this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
|
||||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
|
||||
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
||||
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
23
lib/message/cslib/README
Normal file
23
lib/message/cslib/README
Normal file
@ -0,0 +1,23 @@
|
||||
This is the the Client/Server messaging library (CSlib).
|
||||
|
||||
Only the source directory and license file are included here as part
|
||||
of the LAMMPS distribution. The full CSlib distribution, including
|
||||
documentation and test codes, can be found at the website:
|
||||
http://cslib.sandia.gov (as of Aug 2018).
|
||||
|
||||
The contact author is
|
||||
|
||||
Steve Plimpton
|
||||
Sandia National Laboratories
|
||||
sjplimp@sandia.gov
|
||||
http://www.sandia.gov/~sjplimp
|
||||
|
||||
The CSlib is distributed as open-source code under the modified
|
||||
Berkeley Software Distribution (BSD) License. See the accompanying
|
||||
LICENSE file.
|
||||
|
||||
This directory contains the following:
|
||||
|
||||
README this file
|
||||
LICENSE GNU LGPL license
|
||||
src source files for library
|
||||
107
lib/message/cslib/src/Makefile
Normal file
107
lib/message/cslib/src/Makefile
Normal file
@ -0,0 +1,107 @@
|
||||
# Makefile for CSlib = client/server messaging library
|
||||
# type "make help" for options
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# ----------------------------------------
|
||||
# should only need to change this section
|
||||
# compiler/linker settings
|
||||
# ----------------------------------------
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O3 -DZMQ_$(ZMQ) -DMPI_$(MPI)
|
||||
SHFLAGS = -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAGS = -rc
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# files
|
||||
|
||||
LIB = libcsmpi.a
|
||||
SHLIB = libcsmpi.so
|
||||
SRC = $(wildcard *.cpp)
|
||||
INC = $(wildcard *.h)
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# build with ZMQ support or not
|
||||
|
||||
zmq = yes
|
||||
ZMQ = $(shell echo $(zmq) | tr a-z A-Z)
|
||||
|
||||
ifeq ($(ZMQ),YES)
|
||||
ZMQLIB = -lzmq
|
||||
else
|
||||
CCFLAGS += -I./STUBS_ZMQ
|
||||
endif
|
||||
|
||||
# build with MPI support or not
|
||||
|
||||
mpi = yes
|
||||
MPI = $(shell echo $(mpi) | tr a-z A-Z)
|
||||
|
||||
ifeq ($(MPI),YES)
|
||||
CC = mpicxx
|
||||
else
|
||||
CCFLAGS += -I./STUBS_MPI
|
||||
LIB = libcsnompi.a
|
||||
SHLIB = libcsnompi.so
|
||||
endif
|
||||
|
||||
# targets
|
||||
|
||||
shlib: shlib_parallel shlib_serial
|
||||
|
||||
lib: lib_parallel lib_serial
|
||||
|
||||
all: shlib lib
|
||||
|
||||
help:
|
||||
@echo 'make default = shlib'
|
||||
@echo 'make shlib build 2 shared CSlibs: parallel & serial'
|
||||
@echo 'make lib build 2 static CSlibs: parallel & serial'
|
||||
@echo 'make all build 4 CSlibs: shlib and lib'
|
||||
@echo 'make shlib_parallel build shared parallel CSlib'
|
||||
@echo 'make shlib_serial build shared serial CSlib'
|
||||
@echo 'make lib_parallel build static parallel CSlib'
|
||||
@echo 'make lib_serial build static serial CSlib'
|
||||
@echo 'make ... zmq=no build w/out ZMQ support'
|
||||
@echo 'make clean remove all *.o files'
|
||||
@echo 'make clean-all remove *.o and lib files'
|
||||
@echo 'make tar create a tarball, 2 levels up'
|
||||
|
||||
shlib_parallel:
|
||||
$(MAKE) clean
|
||||
$(MAKE) shared zmq=$(zmq) mpi=yes
|
||||
|
||||
shlib_serial:
|
||||
$(MAKE) clean
|
||||
$(MAKE) shared zmq=$(zmq) mpi=no
|
||||
|
||||
lib_parallel:
|
||||
$(MAKE) clean
|
||||
$(MAKE) static zmq=$(zmq) mpi=yes
|
||||
|
||||
lib_serial:
|
||||
$(MAKE) clean
|
||||
$(MAKE) static zmq=$(zmq) mpi=no
|
||||
|
||||
static: $(OBJ)
|
||||
$(ARCHIVE) $(ARCHFLAGS) $(LIB) $(OBJ)
|
||||
|
||||
shared: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) -o $(SHLIB) $(OBJ) $(ZMQLIB)
|
||||
|
||||
clean:
|
||||
@rm -f *.o *.pyc
|
||||
|
||||
clean-all:
|
||||
@rm -f *.o *.pyc lib*.a lib*.so
|
||||
|
||||
tar:
|
||||
cd ../..; tar cvf cslib.tar cslib/README cslib/LICENSE \
|
||||
cslib/doc cslib/src cslib/test
|
||||
|
||||
# rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) -c $<
|
||||
96
lib/message/cslib/src/STUBS_MPI/mpi.h
Normal file
96
lib/message/cslib/src/STUBS_MPI/mpi.h
Normal file
@ -0,0 +1,96 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// MPI constants and dummy functions
|
||||
|
||||
#ifndef MPI_DUMMY_H
|
||||
#define MPI_DUMMY_H
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdint.h>
|
||||
#include <string.h>
|
||||
|
||||
namespace CSLIB_NS {
|
||||
|
||||
typedef int MPI_Comm;
|
||||
typedef int MPI_Fint;
|
||||
typedef int MPI_Datatype;
|
||||
typedef int MPI_Status;
|
||||
typedef int MPI_Op;
|
||||
typedef int MPI_Info;
|
||||
|
||||
#define MPI_COMM_WORLD 0
|
||||
#define MPI_MAX_PORT_NAME 0
|
||||
#define MPI_INFO_NULL 0
|
||||
#define MPI_INT 1
|
||||
#define MPI_LONG_LONG 2
|
||||
#define MPI_FLOAT 3
|
||||
#define MPI_DOUBLE 4
|
||||
#define MPI_CHAR 5
|
||||
#define MPI_SUM 0
|
||||
|
||||
static void MPI_Init(int *, char ***) {}
|
||||
static MPI_Comm MPI_Comm_f2c(MPI_Comm world) {return world;}
|
||||
static void MPI_Comm_rank(MPI_Comm, int *) {}
|
||||
static void MPI_Comm_size(MPI_Comm, int *) {}
|
||||
|
||||
static void MPI_Open_port(MPI_Info, char *) {}
|
||||
static void MPI_Close_port(const char *) {}
|
||||
static void MPI_Comm_accept(const char *, MPI_Info, int,
|
||||
MPI_Comm, MPI_Comm *) {}
|
||||
static void MPI_Comm_connect(const char *, MPI_Info, int,
|
||||
MPI_Comm, MPI_Comm *) {}
|
||||
|
||||
static void MPI_Comm_split(MPI_Comm, int, int, MPI_Comm *) {}
|
||||
static void MPI_Comm_free(MPI_Comm *) {}
|
||||
|
||||
static void MPI_Send(const void *, int, MPI_Datatype, int, int, MPI_Comm) {}
|
||||
static void MPI_Recv(void *, int, MPI_Datatype, int, int,
|
||||
MPI_Comm, MPI_Status *) {}
|
||||
|
||||
static void MPI_Allreduce(const void *in, void *out, int, MPI_Datatype type,
|
||||
MPI_Op op, MPI_Comm)
|
||||
{
|
||||
if (type == MPI_INT) *((int *) out) = *((int *) in);
|
||||
}
|
||||
static void MPI_Scan(const void *in, void *out, int, MPI_Datatype intype,
|
||||
MPI_Op op,MPI_Comm)
|
||||
{
|
||||
if (intype == MPI_INT) *((int *) out) = *((int *) in);
|
||||
}
|
||||
|
||||
static void MPI_Bcast(void *, int, MPI_Datatype, int, MPI_Comm) {}
|
||||
static void MPI_Allgather(const void *in, int incount, MPI_Datatype intype,
|
||||
void *out, int, MPI_Datatype, MPI_Comm)
|
||||
{
|
||||
// assuming incount = 1
|
||||
if (intype == MPI_INT) *((int *) out) = *((int *) in);
|
||||
}
|
||||
static void MPI_Allgatherv(const void *in, int incount, MPI_Datatype intype,
|
||||
void *out, const int *, const int *,
|
||||
MPI_Datatype, MPI_Comm)
|
||||
{
|
||||
if (intype == MPI_INT) memcpy(out,in,incount*sizeof(int));
|
||||
else if (intype == MPI_LONG_LONG) memcpy(out,in,incount*sizeof(int64_t));
|
||||
else if (intype == MPI_FLOAT) memcpy(out,in,incount*sizeof(float));
|
||||
else if (intype == MPI_DOUBLE) memcpy(out,in,incount*sizeof(double));
|
||||
else if (intype == MPI_CHAR) memcpy(out,in,incount*sizeof(char));
|
||||
}
|
||||
|
||||
static void MPI_Abort(MPI_Comm, int) {exit(1);}
|
||||
static void MPI_Finalize() {}
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
36
lib/message/cslib/src/STUBS_ZMQ/zmq.h
Normal file
36
lib/message/cslib/src/STUBS_ZMQ/zmq.h
Normal file
@ -0,0 +1,36 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// ZMQ constants and dummy functions
|
||||
|
||||
#ifndef ZMQ_DUMMY_H
|
||||
#define ZMQ_DUMMY_H
|
||||
|
||||
namespace CSLIB_NS {
|
||||
|
||||
#define ZMQ_REQ 0
|
||||
#define ZMQ_REP 0
|
||||
|
||||
static void *zmq_ctx_new() {return NULL;}
|
||||
static void *zmq_connect(void *, char *) {return NULL;}
|
||||
static int zmq_bind(void *, char *) {return 0;}
|
||||
static void *zmq_socket(void *,int) {return NULL;}
|
||||
static void zmq_close(void *) {}
|
||||
static void zmq_ctx_destroy(void *) {}
|
||||
static void zmq_send(void *, void *, int, int) {}
|
||||
static void zmq_recv(void *, void *, int, int) {}
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
768
lib/message/cslib/src/cslib.cpp
Normal file
768
lib/message/cslib/src/cslib.cpp
Normal file
@ -0,0 +1,768 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <mpi.h>
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
#include <limits.h>
|
||||
|
||||
#include "cslib.h"
|
||||
#include "msg_file.h"
|
||||
#include "msg_zmq.h"
|
||||
#include "msg_mpi_one.h"
|
||||
#include "msg_mpi_two.h"
|
||||
|
||||
using namespace CSLIB_NS;
|
||||
|
||||
#define MAXTYPE 5 // # of defined field data types
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
CSlib::CSlib(int csflag, const char *mode, const void *ptr, const void *pcomm)
|
||||
{
|
||||
if (pcomm) myworld = (uint64_t) *((MPI_Comm *) pcomm);
|
||||
else myworld = 0;
|
||||
|
||||
#ifdef MPI_NO
|
||||
if (pcomm)
|
||||
error_all("constructor(): CSlib invoked with MPI_Comm "
|
||||
"but built w/out MPI support");
|
||||
#endif
|
||||
#ifdef MPI_YES // NOTE: this could be OK to allow ??
|
||||
// would allow a parallel app to invoke CSlib
|
||||
// in parallel and/or in serial
|
||||
if (!pcomm)
|
||||
error_all("constructor(): CSlib invoked w/out MPI_Comm "
|
||||
"but built with MPI support");
|
||||
#endif
|
||||
|
||||
client = server = 0;
|
||||
if (csflag == 0) client = 1;
|
||||
else if (csflag == 1) server = 1;
|
||||
else error_all("constructor(): Invalid client/server arg");
|
||||
|
||||
if (pcomm == NULL) {
|
||||
me = 0;
|
||||
nprocs = 1;
|
||||
|
||||
if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr);
|
||||
else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr);
|
||||
else if (strcmp(mode,"mpi/one") == 0)
|
||||
error_all("constructor(): No mpi/one mode for serial lib usage");
|
||||
else if (strcmp(mode,"mpi/two") == 0)
|
||||
error_all("constructor(): No mpi/two mode for serial lib usage");
|
||||
else error_all("constructor(): Unknown mode");
|
||||
|
||||
} else if (pcomm) {
|
||||
MPI_Comm world = (MPI_Comm) myworld;
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_size(world,&nprocs);
|
||||
|
||||
if (strcmp(mode,"file") == 0) msg = new MsgFile(csflag,ptr,world);
|
||||
else if (strcmp(mode,"zmq") == 0) msg = new MsgZMQ(csflag,ptr,world);
|
||||
else if (strcmp(mode,"mpi/one") == 0) msg = new MsgMPIOne(csflag,ptr,world);
|
||||
else if (strcmp(mode,"mpi/two") == 0) msg = new MsgMPITwo(csflag,ptr,world);
|
||||
else error_all("constructor(): Unknown mode");
|
||||
}
|
||||
|
||||
maxfield = 0;
|
||||
fieldID = fieldtype = fieldlen = fieldoffset = NULL;
|
||||
maxheader = 0;
|
||||
header = NULL;
|
||||
maxbuf = 0;
|
||||
buf = NULL;
|
||||
|
||||
recvcounts = displs = NULL;
|
||||
maxglobal = 0;
|
||||
allids = NULL;
|
||||
maxfieldbytes = 0;
|
||||
fielddata = NULL;
|
||||
|
||||
pad = "\0\0\0\0\0\0\0"; // just length 7 since will have trailing NULL
|
||||
|
||||
nsend = nrecv = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
CSlib::~CSlib()
|
||||
{
|
||||
deallocate_fields();
|
||||
sfree(header);
|
||||
sfree(buf);
|
||||
|
||||
sfree(recvcounts);
|
||||
sfree(displs);
|
||||
sfree(allids);
|
||||
sfree(fielddata);
|
||||
|
||||
delete msg;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::send(int msgID_caller, int nfield_caller)
|
||||
{
|
||||
if (nfield_caller < 0) error_all("send(): Invalid nfield");
|
||||
|
||||
msgID = msgID_caller;
|
||||
nfield = nfield_caller;
|
||||
allocate_fields();
|
||||
|
||||
fieldcount = 0;
|
||||
nbuf = 0;
|
||||
|
||||
if (fieldcount == nfield) send_message();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_int(int id, int value)
|
||||
{
|
||||
pack(id,1,1,&value);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_int64(int id, int64_t value)
|
||||
{
|
||||
pack(id,2,1,&value);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_float(int id, float value)
|
||||
{
|
||||
pack(id,3,1,&value);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_double(int id, double value)
|
||||
{
|
||||
pack(id,4,1,&value);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_string(int id, char *value)
|
||||
{
|
||||
pack(id,5,strlen(value)+1,value);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack(int id, int ftype, int flen, void *data)
|
||||
{
|
||||
if (find_field(id,fieldcount) >= 0)
|
||||
error_all("pack(): Reuse of field ID");
|
||||
if (ftype < 1 || ftype > MAXTYPE) error_all("pack(): Invalid ftype");
|
||||
if (flen < 0) error_all("pack(): Invalid flen");
|
||||
|
||||
fieldID[fieldcount] = id;
|
||||
fieldtype[fieldcount] = ftype;
|
||||
fieldlen[fieldcount] = flen;
|
||||
|
||||
int nbytes,nbytesround;
|
||||
onefield(ftype,flen,nbytes,nbytesround);
|
||||
|
||||
memcpy(&buf[nbuf],data,nbytes);
|
||||
memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
|
||||
nbuf += nbytesround;
|
||||
|
||||
fieldcount++;
|
||||
if (fieldcount == nfield) send_message();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::pack_parallel(int id, int ftype,
|
||||
int nlocal, int *ids, int nper, void *data)
|
||||
{
|
||||
int i,j,k,m;
|
||||
|
||||
if (find_field(id,fieldcount) >= 0)
|
||||
error_all("pack_parallel(): Reuse of field ID");
|
||||
if (ftype < 1 || ftype > MAXTYPE) error_all("pack_parallel(): Invalid ftype");
|
||||
if (nlocal < 0) error_all("pack_parallel(): Invalid nlocal");
|
||||
if (nper < 1) error_all("pack_parallel(): Invalid nper");
|
||||
|
||||
MPI_Comm world = (MPI_Comm) myworld;
|
||||
|
||||
// NOTE: check for overflow of maxglobal and flen
|
||||
|
||||
int nglobal;
|
||||
MPI_Allreduce(&nlocal,&nglobal,1,MPI_INT,MPI_SUM,world);
|
||||
int flen = nper*nglobal;
|
||||
|
||||
fieldID[fieldcount] = id;
|
||||
fieldtype[fieldcount] = ftype;
|
||||
fieldlen[fieldcount] = flen;
|
||||
|
||||
// nlocal datums, each of nper length, from all procs
|
||||
// final data in buf = datums for all natoms, ordered by ids
|
||||
|
||||
if (recvcounts == NULL) {
|
||||
recvcounts = (int *) smalloc(nprocs*sizeof(int));
|
||||
displs = (int *) smalloc(nprocs*sizeof(int));
|
||||
}
|
||||
|
||||
MPI_Allgather(&nlocal,1,MPI_INT,recvcounts,1,MPI_INT,world);
|
||||
|
||||
displs[0] = 0;
|
||||
for (int iproc = 1; iproc < nprocs; iproc++)
|
||||
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
|
||||
|
||||
if (ids && nglobal > maxglobal) {
|
||||
sfree(allids);
|
||||
maxglobal = nglobal;
|
||||
// NOTE: maxglobal*sizeof(int) could overflow int
|
||||
allids = (int *) smalloc(maxglobal*sizeof(int));
|
||||
}
|
||||
|
||||
MPI_Allgatherv(ids,nlocal,MPI_INT,allids,
|
||||
recvcounts,displs,MPI_INT,world);
|
||||
|
||||
int nlocalsize = nper*nlocal;
|
||||
MPI_Allgather(&nlocalsize,1,MPI_INT,recvcounts,1,MPI_INT,world);
|
||||
|
||||
displs[0] = 0;
|
||||
for (int iproc = 1; iproc < nprocs; iproc++)
|
||||
displs[iproc] = displs[iproc-1] + recvcounts[iproc-1];
|
||||
|
||||
int nbytes,nbytesround;
|
||||
onefield(ftype,flen,nbytes,nbytesround);
|
||||
|
||||
if (ftype == 1) {
|
||||
int *alldata;
|
||||
if (ids) {
|
||||
if (nbytes > maxfieldbytes) {
|
||||
sfree(fielddata);
|
||||
maxfieldbytes = nbytes;
|
||||
fielddata = (char *) smalloc(maxfieldbytes);
|
||||
}
|
||||
alldata = (int *) fielddata;
|
||||
} else alldata = (int *) &buf[nbuf];
|
||||
MPI_Allgatherv(data,nlocalsize,MPI_INT,alldata,
|
||||
recvcounts,displs,MPI_INT,world);
|
||||
if (ids) {
|
||||
int *bufptr = (int *) &buf[nbuf];
|
||||
m = 0;
|
||||
for (i = 0; i < nglobal; i++) {
|
||||
j = (allids[i]-1) * nper;
|
||||
if (nper == 1) bufptr[j] = alldata[m++];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
bufptr[j++] = alldata[m++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (ftype == 2) {
|
||||
int64_t *alldata;
|
||||
if (ids) {
|
||||
if (nbytes > maxfieldbytes) {
|
||||
sfree(fielddata);
|
||||
maxfieldbytes = nbytes;
|
||||
fielddata = (char *) smalloc(maxfieldbytes);
|
||||
}
|
||||
alldata = (int64_t *) fielddata;
|
||||
} else alldata = (int64_t *) &buf[nbuf];
|
||||
// NOTE: may be just MPI_LONG on some machines
|
||||
MPI_Allgatherv(data,nlocalsize,MPI_LONG_LONG,alldata,
|
||||
recvcounts,displs,MPI_LONG_LONG,world);
|
||||
if (ids) {
|
||||
int64_t *bufptr = (int64_t *) &buf[nbuf];
|
||||
m = 0;
|
||||
for (i = 0; i < nglobal; i++) {
|
||||
j = (allids[i]-1) * nper;
|
||||
if (nper == 1) bufptr[j] = alldata[m++];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
bufptr[j++] = alldata[m++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (ftype == 3) {
|
||||
float *alldata;
|
||||
if (ids) {
|
||||
if (nbytes > maxfieldbytes) {
|
||||
sfree(fielddata);
|
||||
maxfieldbytes = nbytes;
|
||||
fielddata = (char *) smalloc(maxfieldbytes);
|
||||
}
|
||||
alldata = (float *) fielddata;
|
||||
} else alldata = (float *) &buf[nbuf];
|
||||
MPI_Allgatherv(data,nlocalsize,MPI_FLOAT,alldata,
|
||||
recvcounts,displs,MPI_FLOAT,world);
|
||||
if (ids) {
|
||||
float *bufptr = (float *) &buf[nbuf];
|
||||
m = 0;
|
||||
for (i = 0; i < nglobal; i++) {
|
||||
j = (allids[i]-1) * nper;
|
||||
if (nper == 1) bufptr[j] = alldata[m++];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
bufptr[j++] = alldata[m++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (ftype == 4) {
|
||||
double *alldata;
|
||||
if (ids) {
|
||||
if (nbytes > maxfieldbytes) {
|
||||
sfree(fielddata);
|
||||
maxfieldbytes = nbytes;
|
||||
fielddata = (char *) smalloc(maxfieldbytes);
|
||||
}
|
||||
alldata = (double *) fielddata;
|
||||
} else alldata = (double *) &buf[nbuf];
|
||||
MPI_Allgatherv(data,nlocalsize,MPI_DOUBLE,alldata,
|
||||
recvcounts,displs,MPI_DOUBLE,world);
|
||||
if (ids) {
|
||||
double *bufptr = (double *) &buf[nbuf];
|
||||
m = 0;
|
||||
for (i = 0; i < nglobal; i++) {
|
||||
j = (allids[i]-1) * nper;
|
||||
if (nper == 1) bufptr[j] = alldata[m++];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
bufptr[j++] = alldata[m++];
|
||||
}
|
||||
}
|
||||
|
||||
/* eventually ftype = BYTE, but not yet
|
||||
} else if (ftype == 5) {
|
||||
char *alldata;
|
||||
if (ids) {
|
||||
if (nbytes > maxfieldbytes) {
|
||||
sfree(fielddata);
|
||||
maxfieldbytes = nbytes;
|
||||
fielddata = (char *) smalloc(maxfieldbytes);
|
||||
}
|
||||
alldata = (char *) fielddata;
|
||||
} else alldata = (char *) &buf[nbuf];
|
||||
MPI_Allgatherv(data,nlocalsize,MPI_CHAR,alldata,
|
||||
recvcounts,displs,MPI_CHAR,world);
|
||||
if (ids) {
|
||||
char *bufptr = (char *) &buf[nbuf];
|
||||
m = 0;
|
||||
for (i = 0; i < nglobal; i++) {
|
||||
j = (allids[i]-1) * nper;
|
||||
memcpy(&bufptr[j],&alldata[m],nper);
|
||||
m += nper;
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
memcpy(&buf[nbuf+nbytes],pad,nbytesround-nbytes);
|
||||
nbuf += nbytesround;
|
||||
|
||||
fieldcount++;
|
||||
if (fieldcount == nfield) send_message();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::send_message()
|
||||
{
|
||||
// setup header message
|
||||
|
||||
int m = 0;
|
||||
header[m++] = msgID;
|
||||
header[m++] = nfield;
|
||||
for (int ifield = 0; ifield < nfield; ifield++) {
|
||||
header[m++] = fieldID[ifield];
|
||||
header[m++] = fieldtype[ifield];
|
||||
header[m++] = fieldlen[ifield];
|
||||
}
|
||||
|
||||
msg->send(nheader,header,nbuf,buf);
|
||||
nsend++;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int CSlib::recv(int &nfield_caller, int *&fieldID_caller,
|
||||
int *&fieldtype_caller, int *&fieldlen_caller)
|
||||
{
|
||||
msg->recv(maxheader,header,maxbuf,buf);
|
||||
nrecv++;
|
||||
|
||||
// unpack header message
|
||||
|
||||
int m = 0;
|
||||
msgID = header[m++];
|
||||
nfield = header[m++];
|
||||
allocate_fields();
|
||||
|
||||
int nbytes,nbytesround;
|
||||
|
||||
nbuf = 0;
|
||||
for (int ifield = 0; ifield < nfield; ifield++) {
|
||||
fieldID[ifield] = header[m++];
|
||||
fieldtype[ifield] = header[m++];
|
||||
fieldlen[ifield] = header[m++];
|
||||
fieldoffset[ifield] = nbuf;
|
||||
onefield(fieldtype[ifield],fieldlen[ifield],nbytes,nbytesround);
|
||||
nbuf += nbytesround;
|
||||
}
|
||||
|
||||
// return message parameters
|
||||
|
||||
nfield_caller = nfield;
|
||||
fieldID_caller = fieldID;
|
||||
fieldtype_caller = fieldtype;
|
||||
fieldlen_caller = fieldlen;
|
||||
|
||||
return msgID;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int CSlib::unpack_int(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_int(): Unknown field ID");
|
||||
if (fieldtype[ifield] != 1) error_all("unpack_int(): Mis-match of ftype");
|
||||
if (fieldlen[ifield] != 1) error_all("unpack_int(): Flen is not 1");
|
||||
|
||||
int *ptr = (int *) unpack(id);
|
||||
return *ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int64_t CSlib::unpack_int64(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_int64(): Unknown field ID");
|
||||
if (fieldtype[ifield] != 2) error_all("unpack_int64(): Mis-match of ftype");
|
||||
if (fieldlen[ifield] != 1) error_all("unpack_int64(): Flen is not 1");
|
||||
|
||||
int64_t *ptr = (int64_t *) unpack(id);
|
||||
return *ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
float CSlib::unpack_float(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_float(): Unknown field ID");
|
||||
if (fieldtype[ifield] != 3) error_all("unpack_float(): Mis-match of ftype");
|
||||
if (fieldlen[ifield] != 1) error_all("unpack_float(): Flen is not 1");
|
||||
|
||||
float *ptr = (float *) unpack(id);
|
||||
return *ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double CSlib::unpack_double(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_double(): Unknown field ID");
|
||||
if (fieldtype[ifield] != 4) error_all("unpack_double(): Mis-match of ftype");
|
||||
if (fieldlen[ifield] != 1) error_all("unpack_double(): Flen is not 1");
|
||||
|
||||
double *ptr = (double *) unpack(id);
|
||||
return *ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
char *CSlib::unpack_string(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_string(): Unknown field ID");
|
||||
if (fieldtype[ifield] != 5) error_all("unpack_string(): Mis-match of ftype");
|
||||
|
||||
char *ptr = (char *) unpack(id);
|
||||
return ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *CSlib::unpack(int id)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack(): Unknown field ID");
|
||||
return &buf[fieldoffset[ifield]];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::unpack(int id, void *data)
|
||||
{
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack(): Unknown field ID");
|
||||
|
||||
int ftype = fieldtype[ifield];
|
||||
int nbytes = fieldlen[ifield];
|
||||
if (ftype == 1) nbytes *= sizeof(int);
|
||||
else if (ftype == 2) nbytes *= sizeof(int64_t);
|
||||
else if (ftype == 3) nbytes *= sizeof(float);
|
||||
else if (ftype == 4) nbytes *= sizeof(double);
|
||||
memcpy(data,&buf[fieldoffset[ifield]],nbytes);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::unpack_parallel(int id, int nlocal, int *ids, int nper, void *data)
|
||||
{
|
||||
int i,j,k,m;
|
||||
|
||||
int ifield = find_field(id,nfield);
|
||||
if (ifield < 0) error_all("unpack_parallel(): Unknown field ID");
|
||||
if (nlocal < 0) error_all("unpack_parallel(): Invalid nlocal");
|
||||
if (nper < 1) error_all("pack_parallel(): Invalid nper");
|
||||
|
||||
MPI_Comm world = (MPI_Comm) myworld;
|
||||
|
||||
int upto;
|
||||
if (!ids) {
|
||||
MPI_Scan(&nlocal,&upto,1,MPI_INT,MPI_SUM,world);
|
||||
upto -= nlocal;
|
||||
}
|
||||
|
||||
if (fieldtype[ifield] == 1) {
|
||||
int *local = (int *) data;
|
||||
int *global = (int *) &buf[fieldoffset[ifield]];
|
||||
if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int));
|
||||
else {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
j = (ids[i]-1) * nper;
|
||||
if (nper == 1) local[m++] = global[j];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
local[m++] = global[j++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (fieldtype[ifield] == 2) {
|
||||
int64_t *local = (int64_t *) data;
|
||||
int64_t *global = (int64_t *) &buf[fieldoffset[ifield]];
|
||||
if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(int64_t));
|
||||
else {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
j = (ids[i]-1) * nper;
|
||||
if (nper == 1) local[m++] = global[j];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
local[m++] = global[j++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (fieldtype[ifield] == 3) {
|
||||
float *local = (float *) data;
|
||||
float *global = (float *) &buf[fieldoffset[ifield]];
|
||||
if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(float));
|
||||
else {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
j = (ids[i]-1) * nper;
|
||||
if (nper == 1) local[m++] = global[j];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
local[m++] = global[j++];
|
||||
}
|
||||
}
|
||||
|
||||
} else if (fieldtype[ifield] == 4) {
|
||||
double *local = (double *) data;
|
||||
double *global = (double *) &buf[fieldoffset[ifield]];
|
||||
if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(double));
|
||||
else {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
j = (ids[i]-1) * nper;
|
||||
if (nper == 1) local[m++] = global[j];
|
||||
else
|
||||
for (k = 0; k < nper; k++)
|
||||
local[m++] = global[j++];
|
||||
}
|
||||
}
|
||||
|
||||
/* eventually ftype = BYTE, but not yet
|
||||
} else if (fieldtype[ifield] == 5) {
|
||||
char *local = (char *) data;
|
||||
char *global = (char *) &buf[fieldoffset[ifield]];
|
||||
if (!ids) memcpy(local,&global[nper*upto],nper*nlocal*sizeof(char));
|
||||
else {
|
||||
m = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
j = (ids[i]-1) * nper;
|
||||
memcpy(&local[m],&global[j],nper);
|
||||
m += nper;
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int CSlib::extract(int flag)
|
||||
{
|
||||
if (flag == 1) return nsend;
|
||||
if (flag == 2) return nrecv;
|
||||
error_all("extract(): Invalid flag");
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::onefield(int ftype, int flen, int &nbytes, int &nbytesround)
|
||||
{
|
||||
int64_t bigbytes,bigbytesround;
|
||||
int64_t biglen = flen;
|
||||
|
||||
if (ftype == 1) bigbytes = biglen * sizeof(int);
|
||||
else if (ftype == 2) bigbytes = biglen * sizeof(int64_t);
|
||||
else if (ftype == 3) bigbytes = biglen * sizeof(float);
|
||||
else if (ftype == 4) bigbytes = biglen * sizeof(double);
|
||||
else if (ftype == 5) bigbytes = biglen * sizeof(char);
|
||||
bigbytesround = roundup(bigbytes,8);
|
||||
|
||||
if (nbuf + bigbytesround > INT_MAX)
|
||||
error_all("pack(): Message size exceeds 32-bit integer limit");
|
||||
|
||||
nbytes = (int) bigbytes;
|
||||
nbytesround = (int) bigbytesround;
|
||||
if (nbuf + nbytesround > maxbuf) {
|
||||
maxbuf = nbuf + nbytesround;
|
||||
buf = (char *) srealloc(buf,maxbuf);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int CSlib::find_field(int id, int n)
|
||||
{
|
||||
int ifield;
|
||||
for (ifield = 0; ifield < n; ifield++)
|
||||
if (id == fieldID[ifield]) return ifield;
|
||||
return -1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::allocate_fields()
|
||||
{
|
||||
int64_t bigbytes = (2 + 3*((int64_t) nfield)) * sizeof(int);
|
||||
if (bigbytes > INT_MAX)
|
||||
error_all("send(): Message header size exceeds 32-bit integer limit");
|
||||
|
||||
nheader = 2;
|
||||
nheader += 3 * nfield;
|
||||
|
||||
if (nfield > maxfield) {
|
||||
deallocate_fields();
|
||||
maxfield = nfield;
|
||||
fieldID = new int[maxfield];
|
||||
fieldtype = new int[maxfield];
|
||||
fieldlen = new int[maxfield];
|
||||
fieldoffset = new int[maxfield];
|
||||
}
|
||||
|
||||
if (nheader > maxheader) {
|
||||
sfree(header);
|
||||
maxheader = nheader;
|
||||
header = (int *) smalloc(maxheader*sizeof(int));
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::deallocate_fields()
|
||||
{
|
||||
delete [] fieldID;
|
||||
delete [] fieldtype;
|
||||
delete [] fieldlen;
|
||||
delete [] fieldoffset;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *CSlib::smalloc(int nbytes)
|
||||
{
|
||||
if (nbytes == 0) return NULL;
|
||||
void *ptr = malloc(nbytes);
|
||||
if (ptr == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"malloc(): Failed to allocate %d bytes",nbytes);
|
||||
error_one(str);
|
||||
}
|
||||
return ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *CSlib::srealloc(void *ptr, int nbytes)
|
||||
{
|
||||
if (nbytes == 0) {
|
||||
sfree(ptr);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
ptr = realloc(ptr,nbytes);
|
||||
if (ptr == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"realloc(): Failed to reallocate %d bytes",nbytes);
|
||||
error_one(str);
|
||||
}
|
||||
return ptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::sfree(void *ptr)
|
||||
{
|
||||
if (ptr == NULL) return;
|
||||
free(ptr);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::error_all(const char *str)
|
||||
{
|
||||
if (me == 0) printf("CSlib ERROR: %s\n",str);
|
||||
MPI_Comm world = (MPI_Comm) myworld;
|
||||
MPI_Abort(world,1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void CSlib::error_one(const char *str)
|
||||
{
|
||||
printf("CSlib ERROR: %s\n",str);
|
||||
MPI_Comm world = (MPI_Comm) myworld;
|
||||
MPI_Abort(world,1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
round N up to multiple of nalign and return it
|
||||
NOTE: see mapreduce/src/keyvalue.cpp for doing this as uint64_t
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int64_t CSlib::roundup(int64_t n, int nalign)
|
||||
{
|
||||
if (n % nalign == 0) return n;
|
||||
n = (n/nalign + 1) * nalign;
|
||||
return n;
|
||||
}
|
||||
87
lib/message/cslib/src/cslib.h
Normal file
87
lib/message/cslib/src/cslib.h
Normal file
@ -0,0 +1,87 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef CSLIB_H
|
||||
#define CSLIB_H
|
||||
|
||||
#include <stdint.h>
|
||||
|
||||
namespace CSLIB_NS {
|
||||
|
||||
class CSlib {
|
||||
public:
|
||||
int nsend,nrecv;
|
||||
|
||||
CSlib(int, const char *, const void *, const void *);
|
||||
~CSlib();
|
||||
|
||||
void send(int, int);
|
||||
|
||||
void pack_int(int, int);
|
||||
void pack_int64(int, int64_t);
|
||||
void pack_float(int, float);
|
||||
void pack_double(int, double);
|
||||
void pack_string(int, char *);
|
||||
void pack(int, int, int, void *);
|
||||
void pack_parallel(int, int, int, int *, int, void *);
|
||||
|
||||
int recv(int &, int *&, int *&, int *&);
|
||||
|
||||
int unpack_int(int);
|
||||
int64_t unpack_int64(int);
|
||||
float unpack_float(int);
|
||||
double unpack_double(int);
|
||||
char *unpack_string(int);
|
||||
void *unpack(int);
|
||||
void unpack(int, void *);
|
||||
void unpack_parallel(int, int, int *, int, void *);
|
||||
|
||||
int extract(int);
|
||||
|
||||
private:
|
||||
uint64_t myworld; // really MPI_Comm, but avoids use of mpi.h in this file
|
||||
// so apps can include this file w/ no MPI on system
|
||||
int me,nprocs;
|
||||
int client,server;
|
||||
int nfield,maxfield;
|
||||
int msgID,fieldcount;
|
||||
int nheader,maxheader;
|
||||
int nbuf,maxbuf;
|
||||
int maxglobal,maxfieldbytes;
|
||||
int *fieldID,*fieldtype,*fieldlen,*fieldoffset;
|
||||
int *header;
|
||||
int *recvcounts,*displs; // nprocs size for Allgathers
|
||||
int *allids; // nglobal size for pack_parallel()
|
||||
char *buf; // maxbuf size for msg with all fields
|
||||
char *fielddata; // maxfieldbytes size for one global field
|
||||
const char *pad;
|
||||
|
||||
class Msg *msg;
|
||||
|
||||
void send_message();
|
||||
void onefield(int, int, int &, int &);
|
||||
int find_field(int, int);
|
||||
void allocate_fields();
|
||||
void deallocate_fields();
|
||||
int64_t roundup(int64_t, int);
|
||||
void *smalloc(int);
|
||||
void *srealloc(void *, int);
|
||||
void sfree(void *);
|
||||
void error_all(const char *);
|
||||
void error_one(const char *);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
362
lib/message/cslib/src/cslib.py
Normal file
362
lib/message/cslib/src/cslib.py
Normal file
@ -0,0 +1,362 @@
|
||||
# ------------------------------------------------------------------------
|
||||
# CSlib - Client/server library for code coupling
|
||||
# http://cslib.sandia.gov, Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
#
|
||||
# Copyright 2018 National Technology & Engineering Solutions of
|
||||
# Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
# NTESS, the U.S. Government retains certain rights in this software.
|
||||
# This software is distributed under the modified Berkeley Software
|
||||
# Distribution (BSD) License.
|
||||
#
|
||||
# See the README file in the top-level CSlib directory.
|
||||
# -------------------------------------------------------------------------
|
||||
|
||||
# Python wrapper on CSlib library via ctypes
|
||||
|
||||
# ctypes and Numpy data types:
|
||||
# 32-bit int = c_int = np.intc = np.int32
|
||||
# 64-bit int = c_longlong = np.int64
|
||||
# 32-bit floating point = c_float = np.float32
|
||||
# 64-bit floating point = c_double = np.float = np.float64
|
||||
|
||||
import sys,traceback
|
||||
from ctypes import *
|
||||
|
||||
# Numpy and mpi4py packages may not exist
|
||||
|
||||
try:
|
||||
import numpy as np
|
||||
numpyflag = 1
|
||||
except:
|
||||
numpyflag = 0
|
||||
|
||||
try:
|
||||
from mpi4py import MPI
|
||||
mpi4pyflag = 1
|
||||
except:
|
||||
mpi4pyflag = 0
|
||||
|
||||
# wrapper class
|
||||
|
||||
class CSlib:
|
||||
|
||||
# instantiate CSlib thru its C-interface
|
||||
|
||||
def __init__(self,csflag,mode,ptr,comm):
|
||||
|
||||
# load libcslib.so
|
||||
|
||||
try:
|
||||
if comm: self.lib = CDLL("libcsmpi.so",RTLD_GLOBAL)
|
||||
else: self.lib = CDLL("libcsnompi.so",RTLD_GLOBAL)
|
||||
except:
|
||||
etype,value,tb = sys.exc_info()
|
||||
traceback.print_exception(etype,value,tb)
|
||||
raise OSError,"Could not load CSlib dynamic library"
|
||||
|
||||
# define ctypes API for each library method
|
||||
|
||||
self.lib.cslib_open.argtypes = [c_int,c_char_p,c_void_p,c_void_p,
|
||||
POINTER(c_void_p)]
|
||||
self.lib.cslib_open.restype = None
|
||||
|
||||
self.lib.cslib_close.argtypes = [c_void_p]
|
||||
self.lib.cslib_close.restype = None
|
||||
|
||||
self.lib.cslib_send.argtypes = [c_void_p,c_int,c_int]
|
||||
self.lib.cslib_send.restype = None
|
||||
|
||||
self.lib.cslib_pack_int.argtypes = [c_void_p,c_int,c_int]
|
||||
self.lib.cslib_pack_int.restype = None
|
||||
|
||||
self.lib.cslib_pack_int64.argtypes = [c_void_p,c_int,c_longlong]
|
||||
self.lib.cslib_pack_int64.restype = None
|
||||
|
||||
self.lib.cslib_pack_float.argtypes = [c_void_p,c_int,c_float]
|
||||
self.lib.cslib_pack_float.restype = None
|
||||
|
||||
self.lib.cslib_pack_double.argtypes = [c_void_p,c_int,c_double]
|
||||
self.lib.cslib_pack_double.restype = None
|
||||
|
||||
self.lib.cslib_pack_string.argtypes = [c_void_p,c_int,c_char_p]
|
||||
self.lib.cslib_pack_string.restype = None
|
||||
|
||||
self.lib.cslib_pack.argtypes = [c_void_p,c_int,c_int,c_int,c_void_p]
|
||||
self.lib.cslib_pack.restype = None
|
||||
|
||||
self.lib.cslib_pack_parallel.argtypes = [c_void_p,c_int,c_int,c_int,
|
||||
POINTER(c_int),c_int,c_void_p]
|
||||
self.lib.cslib_pack_parallel.restype = None
|
||||
|
||||
self.lib.cslib_recv.argtypes = [c_void_p,POINTER(c_int),
|
||||
POINTER(POINTER(c_int)),
|
||||
POINTER(POINTER(c_int)),
|
||||
POINTER(POINTER(c_int))]
|
||||
self.lib.cslib_recv.restype = c_int
|
||||
|
||||
self.lib.cslib_unpack_int.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack_int.restype = c_int
|
||||
|
||||
self.lib.cslib_unpack_int64.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack_int64.restype = c_longlong
|
||||
|
||||
self.lib.cslib_unpack_float.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack_float.restype = c_float
|
||||
|
||||
self.lib.cslib_unpack_double.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack_double.restype = c_double
|
||||
|
||||
self.lib.cslib_unpack_string.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack_string.restype = c_char_p
|
||||
|
||||
# override return in unpack()
|
||||
self.lib.cslib_unpack.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_unpack.restype = c_void_p
|
||||
|
||||
self.lib.cslib_unpack_data.argtypes = [c_void_p,c_int,c_void_p]
|
||||
self.lib.cslib_unpack_data.restype = None
|
||||
|
||||
# override last arg in unpack_parallel()
|
||||
self.lib.cslib_unpack_parallel.argtypes = [c_void_p,c_int,c_int,
|
||||
POINTER(c_int),c_int,c_void_p]
|
||||
self.lib.cslib_unpack_parallel.restype = None
|
||||
|
||||
self.lib.cslib_extract.argtypes = [c_void_p,c_int]
|
||||
self.lib.cslib_extract.restype = c_int
|
||||
|
||||
# create an instance of CSlib with or w/out MPI communicator
|
||||
|
||||
self.cs = c_void_p()
|
||||
|
||||
if not comm:
|
||||
self.lib.cslib_open(csflag,mode,ptr,None,byref(self.cs))
|
||||
elif not mpi4pyflag:
|
||||
print "Cannot pass MPI communicator to CSlib w/out mpi4py package"
|
||||
sys.exit()
|
||||
else:
|
||||
address = MPI._addressof(comm)
|
||||
comm_ptr = c_void_p(address)
|
||||
if mode == "mpi/one":
|
||||
address = MPI._addressof(ptr)
|
||||
ptrcopy = c_void_p(address)
|
||||
else: ptrcopy = ptr
|
||||
self.lib.cslib_open(csflag,mode,ptrcopy,comm_ptr,byref(self.cs))
|
||||
|
||||
# destroy instance of CSlib
|
||||
|
||||
def __del__(self):
|
||||
if self.cs: self.lib.cslib_close(self.cs)
|
||||
|
||||
def close(self):
|
||||
self.lib.cslib_close(self.cs)
|
||||
self.lib = None
|
||||
|
||||
# send a message
|
||||
|
||||
def send(self,msgID,nfield):
|
||||
self.nfield = nfield
|
||||
self.lib.cslib_send(self.cs,msgID,nfield)
|
||||
|
||||
# pack one field of message
|
||||
|
||||
def pack_int(self,id,value):
|
||||
self.lib.cslib_pack_int(self.cs,id,value)
|
||||
|
||||
def pack_int64(self,id,value):
|
||||
self.lib.cslib_pack_int64(self.cs,id,value)
|
||||
|
||||
def pack_float(self,id,value):
|
||||
self.lib.cslib_pack_float(self.cs,id,value)
|
||||
|
||||
def pack_double(self,id,value):
|
||||
self.lib.cslib_pack_double(self.cs,id,value)
|
||||
|
||||
def pack_string(self,id,value):
|
||||
self.lib.cslib_pack_string(self.cs,id,value)
|
||||
|
||||
def pack(self,id,ftype,flen,data):
|
||||
cdata = self.data_convert(ftype,flen,data)
|
||||
self.lib.cslib_pack(self.cs,id,ftype,flen,cdata)
|
||||
|
||||
def pack_parallel(self,id,ftype,nlocal,ids,nper,data):
|
||||
cids = self.data_convert(1,nlocal,ids)
|
||||
cdata = self.data_convert(ftype,nper*nlocal,data)
|
||||
self.lib.cslib_pack_parallel(self.cs,id,ftype,nlocal,cids,nper,cdata)
|
||||
|
||||
# convert input data to a ctypes vector to pass to CSlib
|
||||
|
||||
def data_convert(self,ftype,flen,data):
|
||||
|
||||
# tflag = type of data
|
||||
# tflag = 1 if data is list or tuple
|
||||
# tflag = 2 if data is Numpy array
|
||||
# tflag = 3 if data is ctypes vector
|
||||
# same usage of tflag as in unpack function
|
||||
|
||||
txttype = str(type(data))
|
||||
if "numpy" in txttype: tflag = 2
|
||||
elif "c_" in txttype: tflag = 3
|
||||
else: tflag = 1
|
||||
|
||||
# create ctypes vector out of data to pass to lib
|
||||
# cdata = ctypes vector to return
|
||||
# NOTE: error check on ftype and tflag everywhere, also flen
|
||||
|
||||
if ftype == 1:
|
||||
if tflag == 1: cdata = (flen * c_int)(*data)
|
||||
elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_int))
|
||||
elif tflag == 3: cdata = data
|
||||
elif ftype == 2:
|
||||
if tflag == 1: cdata = (flen * c_longlong)(*data)
|
||||
elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_longlong))
|
||||
elif tflag == 3: cdata = data
|
||||
elif ftype == 3:
|
||||
if tflag == 1: cdata = (flen * c_float)(*data)
|
||||
elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_float))
|
||||
elif tflag == 3: cdata = data
|
||||
elif ftype == 4:
|
||||
if tflag == 1: cdata = (flen * c_double)(*data)
|
||||
elif tflag == 2: cdata = data.ctypes.data_as(POINTER(c_double))
|
||||
elif tflag == 3: cdata = data
|
||||
|
||||
return cdata
|
||||
|
||||
# receive a message
|
||||
|
||||
def recv(self):
|
||||
self.lib.cslib_recv.restype = c_int
|
||||
nfield = c_int()
|
||||
fieldID = POINTER(c_int)()
|
||||
fieldtype = POINTER(c_int)()
|
||||
fieldlen = POINTER(c_int)()
|
||||
msgID = self.lib.cslib_recv(self.cs,byref(nfield),
|
||||
byref(fieldID),byref(fieldtype),byref(fieldlen))
|
||||
|
||||
# copy returned C args to native Python int and lists
|
||||
# store them in class so unpack() methods can access the info
|
||||
|
||||
self.nfield = nfield = nfield.value
|
||||
self.fieldID = fieldID[:nfield]
|
||||
self.fieldtype = fieldtype[:nfield]
|
||||
self.fieldlen = fieldlen[:nfield]
|
||||
|
||||
return msgID,self.nfield,self.fieldID,self.fieldtype,self.fieldlen
|
||||
|
||||
# unpack one field of message
|
||||
# tflag = type of data to return
|
||||
# 3 = ctypes vector is default, since no conversion required
|
||||
|
||||
def unpack_int(self,id):
|
||||
return self.lib.cslib_unpack_int(self.cs,id)
|
||||
|
||||
def unpack_int64(self,id):
|
||||
return self.lib.cslib_unpack_int64(self.cs,id)
|
||||
|
||||
def unpack_float(self,id):
|
||||
return self.lib.cslib_unpack_float(self.cs,id)
|
||||
|
||||
def unpack_double(self,id):
|
||||
return self.lib.cslib_unpack_double(self.cs,id)
|
||||
|
||||
def unpack_string(self,id):
|
||||
return self.lib.cslib_unpack_string(self.cs,id)
|
||||
|
||||
def unpack(self,id,tflag=3):
|
||||
index = self.fieldID.index(id)
|
||||
|
||||
# reset data type of return so can morph by tflag
|
||||
# cannot do this for the generic c_void_p returned by CSlib
|
||||
|
||||
if self.fieldtype[index] == 1:
|
||||
self.lib.cslib_unpack.restype = POINTER(c_int)
|
||||
elif self.fieldtype[index] == 2:
|
||||
self.lib.cslib_unpack.restype = POINTER(c_longlong)
|
||||
elif self.fieldtype[index] == 3:
|
||||
self.lib.cslib_unpack.restype = POINTER(c_float)
|
||||
elif self.fieldtype[index] == 4:
|
||||
self.lib.cslib_unpack.restype = POINTER(c_double)
|
||||
#elif self.fieldtype[index] == 5:
|
||||
# self.lib.cslib_unpack.restype = POINTER(c_char)
|
||||
|
||||
cdata = self.lib.cslib_unpack(self.cs,id)
|
||||
|
||||
# tflag = user-requested type of data to return
|
||||
# tflag = 1 to return data as list
|
||||
# tflag = 2 to return data as Numpy array
|
||||
# tflag = 3 to return data as ctypes vector
|
||||
# same usage of tflag as in pack functions
|
||||
# tflag = 2,3 should NOT perform a data copy
|
||||
|
||||
if tflag == 1:
|
||||
data = cdata[:self.fieldlen[index]]
|
||||
elif tflag == 2:
|
||||
if numpyflag == 0:
|
||||
print "Cannot return Numpy array w/out numpy package"
|
||||
sys.exit()
|
||||
data = np.ctypeslib.as_array(cdata,shape=(self.fieldlen[index],))
|
||||
elif tflag == 3:
|
||||
data = cdata
|
||||
|
||||
return data
|
||||
|
||||
# handle data array like pack() or unpack_parallel() ??
|
||||
|
||||
def unpack_data(self,id,tflag=3):
|
||||
index = self.fieldID.index(id)
|
||||
|
||||
# unpack one field of message in parallel
|
||||
# tflag = type of data to return
|
||||
# 3 = ctypes vector is default, since no conversion required
|
||||
# NOTE: allow direct use of user array (e.g. Numpy), if user provides data arg?
|
||||
# as opposed to creating this cdata
|
||||
# does that make any performance difference ?
|
||||
# e.g. should we allow CSlib to populate an existing Numpy array's memory
|
||||
|
||||
def unpack_parallel(self,id,nlocal,ids,nper,tflag=3):
|
||||
cids = self.data_convert(1,nlocal,ids)
|
||||
|
||||
# allocate memory for the returned data
|
||||
# pass cdata ptr to the memory to CSlib unpack_parallel()
|
||||
# this resets data type of last unpack_parallel() arg
|
||||
|
||||
index = self.fieldID.index(id)
|
||||
if self.fieldtype[index] == 1: cdata = (nper*nlocal * c_int)()
|
||||
elif self.fieldtype[index] == 2: cdata = (nlocal*nper * c_longlong)()
|
||||
elif self.fieldtype[index] == 3: cdata = (nlocal*nper * c_float)()
|
||||
elif self.fieldtype[index] == 4: cdata = (nlocal*nper * c_double)()
|
||||
#elif self.fieldtype[index] == 5: cdata = (nlocal*nper * c_char)()
|
||||
|
||||
self.lib.cslib_unpack_parallel(self.cs,id,nlocal,cids,nper,cdata)
|
||||
|
||||
# tflag = user-requested type of data to return
|
||||
# tflag = 1 to return data as list
|
||||
# tflag = 2 to return data as Numpy array
|
||||
# tflag = 3 to return data as ctypes vector
|
||||
# same usage of tflag as in pack functions
|
||||
|
||||
if tflag == 1:
|
||||
data = cdata[:nper*nlocal]
|
||||
elif tflag == 2:
|
||||
if numpyflag == 0:
|
||||
print "Cannot return Numpy array w/out numpy package"
|
||||
sys.exit()
|
||||
# NOTE: next line gives ctypes warning for fieldtype = 2 = 64-bit int
|
||||
# not sure why, reported as bug between ctypes and Numpy here:
|
||||
# https://stackoverflow.com/questions/4964101/pep-3118-
|
||||
# warning-when-using-ctypes-array-as-numpy-array
|
||||
# but why not same warning when just using unpack() ??
|
||||
# in Python these lines give same warning:
|
||||
# >>> import ctypes,numpy
|
||||
# >>> a = (10 * ctypes.c_longlong)()
|
||||
# >>> b = numpy.ctypeslib.as_array(a)
|
||||
data = np.ctypeslib.as_array(cdata,shape=(nlocal*nper,))
|
||||
elif tflag == 3:
|
||||
data = cdata
|
||||
|
||||
return data
|
||||
|
||||
# extract a library value
|
||||
|
||||
def extract(self,flag):
|
||||
return self.lib.cslib_extract(self.cs,flag)
|
||||
239
lib/message/cslib/src/cslib_wrap.cpp
Normal file
239
lib/message/cslib/src/cslib_wrap.cpp
Normal file
@ -0,0 +1,239 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// C style library interface to CSlib class
|
||||
|
||||
#include <mpi.h>
|
||||
#include <string.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "cslib_wrap.h"
|
||||
#include "cslib.h"
|
||||
|
||||
using namespace CSLIB_NS;
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_open(int csflag, const char *mode, const void *ptr,
|
||||
const void *pcomm, void **csptr)
|
||||
{
|
||||
CSlib *cs = new CSlib(csflag,mode,ptr,pcomm);
|
||||
*csptr = (void *) cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_open_fortran(int csflag, const char *mode, const char *str,
|
||||
const void *pcomm, void **csptr)
|
||||
{
|
||||
MPI_Comm ccomm;
|
||||
void *pccomm = NULL;
|
||||
|
||||
if (pcomm) {
|
||||
MPI_Fint *fcomm = (MPI_Fint *) pcomm;
|
||||
ccomm = MPI_Comm_f2c(*fcomm);
|
||||
pccomm = &ccomm;
|
||||
}
|
||||
|
||||
CSlib *cs = new CSlib(csflag,mode,str,pccomm);
|
||||
*csptr = (void *) cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_open_fortran_mpi_one(int csflag, const char *mode,
|
||||
const void *pboth, const void *pcomm,
|
||||
void **csptr)
|
||||
{
|
||||
MPI_Comm ccomm,cboth;
|
||||
void *pccomm,*pcboth;
|
||||
|
||||
MPI_Fint *fcomm = (MPI_Fint *) pcomm;
|
||||
ccomm = MPI_Comm_f2c(*fcomm);
|
||||
pccomm = &ccomm;
|
||||
|
||||
MPI_Fint *fboth = (MPI_Fint *) pboth;
|
||||
cboth = MPI_Comm_f2c(*fboth);
|
||||
pcboth = &cboth;
|
||||
|
||||
CSlib *cs = new CSlib(csflag,mode,pcboth,pccomm);
|
||||
*csptr = (void *) cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_close(void *ptr)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
delete cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_send(void *ptr, int msgID, int nfield)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->send(msgID,nfield);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_int(void *ptr, int id, int value)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_int(id,value);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_int64(void *ptr, int id, int64_t value)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_int64(id,value);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_float(void *ptr, int id, float value)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_float(id,value);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_double(void *ptr, int id, double value)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_double(id,value);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_string(void *ptr, int id, char *value)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_string(id,value);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack(void *ptr, int id, int ftype, int flen, void *data)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack(id,ftype,flen,data);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_pack_parallel(void *ptr, int id, int ftype,
|
||||
int nlocal, int *ids, int nper, void *data)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->pack_parallel(id,ftype,nlocal,ids,nper,data);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
int cslib_recv(void *ptr, int *nfield_caller,
|
||||
int **fieldID_caller, int **fieldtype_caller,
|
||||
int **fieldlen_caller)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
|
||||
int nfield;
|
||||
int *fieldID,*fieldtype,*fieldlen;
|
||||
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
|
||||
*nfield_caller = nfield;
|
||||
*fieldID_caller = fieldID;
|
||||
*fieldtype_caller = fieldtype;
|
||||
*fieldlen_caller = fieldlen;
|
||||
|
||||
return msgID;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
int cslib_unpack_int(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack_int(id);
|
||||
}
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
int64_t cslib_unpack_int64(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack_int64(id);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
float cslib_unpack_float(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack_float(id);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
double cslib_unpack_double(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack_double(id);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
char *cslib_unpack_string(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack_string(id);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void *cslib_unpack(void *ptr, int id)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->unpack(id);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_unpack_data(void *ptr, int id, void *data)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->unpack(id,data);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
void cslib_unpack_parallel(void *ptr, int id, int nlocal, int *ids,
|
||||
int nper, void *data)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
cs->unpack_parallel(id,nlocal,ids,nper,data);
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
int cslib_extract(void *ptr, int flag)
|
||||
{
|
||||
CSlib *cs = (CSlib *) ptr;
|
||||
return cs->extract(flag);
|
||||
}
|
||||
147
lib/message/cslib/src/cslib_wrap.f90
Normal file
147
lib/message/cslib/src/cslib_wrap.f90
Normal file
@ -0,0 +1,147 @@
|
||||
! ISO_C_binding wrapper on CSlib C interface
|
||||
|
||||
module cslib_wrap
|
||||
|
||||
interface
|
||||
subroutine cslib_open_fortran(csflag,mode,str,pcomm,ptr) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int), value :: csflag
|
||||
character(c_char) :: mode(*),str(*)
|
||||
type(c_ptr), value :: pcomm
|
||||
type(c_ptr) :: ptr
|
||||
end subroutine cslib_open_fortran
|
||||
|
||||
subroutine cslib_open_fortran_mpi_one(csflag,mode,pboth,pcomm,ptr) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int), value :: csflag
|
||||
character(c_char) :: mode(*)
|
||||
type(c_ptr), value :: pboth,pcomm
|
||||
type(c_ptr) :: ptr
|
||||
end subroutine cslib_open_fortran_mpi_one
|
||||
|
||||
subroutine cslib_close(ptr) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
end subroutine cslib_close
|
||||
|
||||
subroutine cslib_send(ptr,msgID,nfield) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: msgID,nfield
|
||||
end subroutine cslib_send
|
||||
|
||||
subroutine cslib_pack_int(ptr,id,value) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
integer(c_int), value :: value
|
||||
end subroutine cslib_pack_int
|
||||
|
||||
subroutine cslib_pack_int64(ptr,id,value) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
integer(c_int64_t), value :: value
|
||||
end subroutine cslib_pack_int64
|
||||
|
||||
subroutine cslib_pack_float(ptr,id,value) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
real(c_float), value :: value
|
||||
end subroutine cslib_pack_float
|
||||
|
||||
subroutine cslib_pack_double(ptr,id,value) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
real(c_double), value :: value
|
||||
end subroutine cslib_pack_double
|
||||
|
||||
subroutine cslib_pack_string(ptr,id,value) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
character(c_char) :: value(*)
|
||||
end subroutine cslib_pack_string
|
||||
|
||||
subroutine cslib_pack(ptr,id,ftype,flen,data) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id,ftype,flen
|
||||
type(c_ptr), value :: data
|
||||
end subroutine cslib_pack
|
||||
|
||||
subroutine cslib_pack_parallel(ptr,id,ftype,nlocal,ids,nper,data) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id,ftype,nlocal,nper
|
||||
type(c_ptr), value :: ids,data
|
||||
end subroutine cslib_pack_parallel
|
||||
|
||||
function cslib_recv(ptr,nfield,fieldID,fieldtype,fieldlen) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int) :: cslib_recv
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int) :: nfield
|
||||
type(c_ptr) :: fieldID,fieldtype,fieldlen
|
||||
end function cslib_recv
|
||||
|
||||
function cslib_unpack_int(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int) :: cslib_unpack_int
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack_int
|
||||
|
||||
function cslib_unpack_int64(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int64_t) :: cslib_unpack_int64
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack_int64
|
||||
|
||||
function cslib_unpack_float(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
real(c_float) :: cslib_unpack_float
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack_float
|
||||
|
||||
function cslib_unpack_double(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
real(c_double) :: cslib_unpack_double
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack_double
|
||||
|
||||
function cslib_unpack_string(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr) :: cslib_unpack_string
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack_string
|
||||
|
||||
function cslib_unpack(ptr,id) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr) :: cslib_unpack
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id
|
||||
end function cslib_unpack
|
||||
|
||||
subroutine cslib_unpack_parallel(ptr,id,nlocal,ids,nper,data) bind(c)
|
||||
use iso_c_binding
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: id,nlocal,nper
|
||||
type(c_ptr), value :: ids,data
|
||||
end subroutine cslib_unpack_parallel
|
||||
|
||||
function cslib_extract(ptr,flag) bind(c)
|
||||
use iso_c_binding
|
||||
integer(c_int) :: cslib_extract
|
||||
type(c_ptr), value :: ptr
|
||||
integer(c_int), value :: flag
|
||||
end function cslib_extract
|
||||
end interface
|
||||
|
||||
end module cslib_wrap
|
||||
54
lib/message/cslib/src/cslib_wrap.h
Normal file
54
lib/message/cslib/src/cslib_wrap.h
Normal file
@ -0,0 +1,54 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
CSlib - Client/server library for code coupling
|
||||
http://cslib.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright 2018 National Technology & Engineering Solutions of
|
||||
Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
|
||||
NTESS, the U.S. Government retains certain rights in this software.
|
||||
This software is distributed under the modified Berkeley Software
|
||||
Distribution (BSD) License.
|
||||
|
||||
See the README file in the top-level CSlib directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* C style library interface to CSlib class
|
||||
ifdefs allow this file to be included in a C program
|
||||
*/
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
void cslib_open(int, const char *, const void *, const void *, void **);
|
||||
void cslib_open_fortran(int, const char *, const char *, const void *, void **);
|
||||
void cslib_open_fortran_mpi_one(int, const char *, const void *,
|
||||
const void *, void **);
|
||||
void cslib_close(void *);
|
||||
|
||||
void cslib_send(void *, int, int);
|
||||
|
||||
void cslib_pack_int(void *, int, int);
|
||||
void cslib_pack_int64(void *, int, int64_t);
|
||||
void cslib_pack_float(void *, int, float);
|
||||
void cslib_pack_double(void *, int, double);
|
||||
void cslib_pack_string(void *, int, char *);
|
||||
void cslib_pack(void *, int, int, int, void *);
|
||||
void cslib_pack_parallel(void *, int, int, int, int *, int, void *);
|
||||
|
||||
int cslib_recv(void *, int *, int **, int **, int **);
|
||||
|
||||
int cslib_unpack_int(void *, int);
|
||||
int64_t cslib_unpack_int64(void *, int);
|
||||
float cslib_unpack_float(void *, int);
|
||||
double cslib_unpack_double(void *, int);
|
||||
char *cslib_unpack_string(void *, int);
|
||||
void *cslib_unpack(void *, int);
|
||||
void cslib_unpack_data(void *, int, void *);
|
||||
void cslib_unpack_parallel(void *, int, int, int *, int, void *);
|
||||
|
||||
int cslib_extract(void *, int);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user