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new MESSAGE package for client/server/coupling

This commit is contained in:
Steven J. Plimpton 2018-07-23 15:58:33 -06:00
parent 5c21d2aff9
commit 2f55981224
97 changed files with 8885 additions and 104 deletions
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9
doc/src/Section_commands.txt
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@ -482,6 +482,7 @@ in the command's documentation.
"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,
@ -513,6 +514,7 @@ in the command's documentation.
"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,
@ -574,6 +576,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"client/md"_fix_client_md.html,
"cmap"_fix_cmap.html,
"controller"_fix_controller.html,
"deform (k)"_fix_deform.html,
@ -678,8 +681,6 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/body/polygon"_fix_wall_body_polygon.html,
"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/gran/region"_fix_wall_gran_region.html,
@ -932,9 +933,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"airebo (oi)"_pair_airebo.html,
"airebo/morse (oi)"_pair_airebo.html,
"beck (go)"_pair_beck.html,
"body/nparticle"_pair_body_nparticle.html,
"body/rounded/polygon"_pair_body_rounded/polygon.html,
"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
"born (go)"_pair_born.html,
"born/coul/dsf"_pair_born.html,

132
doc/src/Section_howto.txt
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@ -37,7 +37,8 @@ This section describes how to perform common tasks using LAMMPS.
6.25 "Polarizable models"_#howto_25
6.26 "Adiabatic core/shell model"_#howto_26
6.27 "Drude induced dipoles"_#howto_27
6.28 "Magnetic spins"_#howto_28 :all(b)
6.28 "Magnetic spins"_#howto_28
6.29 "Using LAMMPS in client/server mode"_#howto_29 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section 7"_Section_example.html also show how to
@ -663,7 +664,7 @@ 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.
@ -752,7 +753,8 @@ 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 in a separate "howto section"_#howto_29.
6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
@ -2955,6 +2957,130 @@ property/atom"_compute_property_atom.html. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
:line
6.29 Using LAMMPS in client/server mode :link(howto_29),h4
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 in "this
section"_#howto10.
LAMMPS support for client/server coupling is in its "MESSAGE
package"_Section_package.html#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, a socket, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. It has its own
"website"_http://cslib.sandia.gov (as of Aug 2018) 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 -mpi 2 -in in.message.client -log log.client : -np 4 lmp_mpi -mpi 2 -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 -mpi P
command-line option as their first option, where P is the number of
processors the first code in the mpirun command (client or server) is
running on.
:line
:line

47
doc/src/Section_packages.txt
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@ -100,6 +100,7 @@ Package, Description, Doc page, Example, Library
"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MESSAGE"_#MESSAGE, client/server messaging, "message"_message.html, message, int
"MISC"_#MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
@ -879,6 +880,52 @@ examples/meam :ul
:line
MESSAGE package :link(MESSAGE),h4
[Contents:]
Commands to use LAMMPS as either a client or server
and couple it to another application.
[Install or un-install:]
Before building LAMMPS with this package, you must first build the
CSlib library in lib/message. You can do this 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
open-source ZMQ library if requested in the build.
You can then install/un-install the package and build LAMMPS in the
usual manner:
make yes-message
make machine :pre
make no-message
make machine :pre
[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(MISC),h4
[Contents:]

19
doc/src/Section_start.txt
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@ -1204,6 +1204,7 @@ letter abbreviation can be used:
-i or -in
-k or -kokkos
-l or -log
-m or -mpi
-nc or -nocite
-pk or -package
-p or -partition
@ -1351,6 +1352,24 @@ specified file is "none", then no log files are created. Using a
"log"_log.html command in the input script will override this setting.
Option -plog will override the name of the partition log files file.N.
-mpi P :pre
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when running LAMMPS in client/server
mode with 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
In the mpi/one mode of messaging, both executables (the client and the
server) are launched by one mpirun command. P should be specified as
the number of processors (MPI tasks) the first executable is running
on (could be the client or the server code).
This information is required so that both codes can shrink the
MPI_COMM_WORLD communicator they are part of to the subset of
processors they are actually running on.
-nocite :pre
Disable writing the log.cite file which is normally written to list

105
doc/src/fix_client_md.txt Normal file
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@ -0,0 +1,105 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
: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.
"This section"_Section_howto.html#howto_29 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 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 in this mode, 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"_Section_howto.html#howto_15. 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 "Making
LAMMPS"_Section_start.html#start_3 section 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

12
doc/src/lammps.book
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@ -67,6 +67,7 @@ label.html
lattice.html
log.html
mass.html
message.html
min_modify.html
min_style.html
minimize.html
@ -94,6 +95,9 @@ 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
@ -140,7 +144,8 @@ fix_bond_break.html
fix_bond_create.html
fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
fix_box_relax.htmlf
fix_client_md.html
fix_cmap.html
fix_colvars.html
fix_controller.html
@ -283,8 +288,6 @@ fix_vector.html
fix_viscosity.html
fix_viscous.html
fix_wall.html
fix_wall_body_polygon.html
fix_wall_body_polyhedron.html
fix_wall_ees.html
fix_wall_gran.html
fix_wall_gran_region.html
@ -426,9 +429,8 @@ pair_agni.html
pair_airebo.html
pair_awpmd.html
pair_beck.html
pair_body_nparticle.html
pair_body.html
pair_body_rounded_polygon.html
pair_body_rounded_polyhedron.html
pair_bop.html
pair_born.html
pair_brownian.html

159
doc/src/message.txt Normal file
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@ -0,0 +1,159 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
: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.
"This section"_Section_howto.html#howto_29 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. 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 -mpi 2 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpi 2 -in in.server # LAMMPS is server :pre
Note the use of the "-mpi P" command-line argument with LAMMPS. See
the "command-line args"_Section_start.html#start_6 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 "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"server"_server.html, "fix client/md"_fix_client_md.html
[Default:] none

71
doc/src/server.txt Normal file
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@ -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,Section_commands.html#comm)
: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.
"This section"_Section_howto.html#howto_29 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 "Making
LAMMPS"_Section_start.html#start_3 section 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

112
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@ -0,0 +1,112 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
: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.
"This section"_Section_howto.html#howto_29 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.
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 (as of Aug 2018).
The "cs" object in this pseudo code is an instance of the CSlib that
both the client and server codes store.
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(1,1,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(1,1,flag) # 1st field = accept/reject flag :pre
cs.send(RUN,1) # msgID = 5 with 1 field
cs.pack(1,1,nsteps) # 1st field = # of timesteps to run MD :pre
[Server replies]:
cs.send(NATOMS,1) # msgID = 1 with 1 field
cs.pack(1,1,Natoms) # 1st field = number of atoms :pre
cs.send(EINIT,2) # msgID = 2 with 2 fields
cs.pack(1,1,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(1,1,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 "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"message"_message.html
[Default:] none

122
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@ -0,0 +1,122 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
: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.
"This section"_Section_howto.html#howto_29 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.
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 virial 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 virial
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 (as of Aug 2018).
The "cs" object in this pseudo code is an instance of the CSlib that
both the client and server codes store.
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 code uses these values, defined as enums in LAMMPS:
enum{SETUP=1,STEP};
enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL}; :pre
[Client sends 2 kinds of messages]:
# required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
# optional fields: others in 2nd enum above :pre
cs.send(SETUP,nfields) # msgID with nfields :pre
cs.pack_string(UNITS,units) # units = "lj", "real", "metal", etc
cs.pack_int(NATOMS,natoms) # total numer of atoms
cs.pack_int(NTYPES,ntypes) # number of atom types
cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
cs.pack(BOXHI,3,boxhi) # 3-vector of upper box bounds
cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes
cs.pack(TYPES,natoms,type) # vector of per-atom types
cs.pack(COORDS,3*natoms,x) # vector of 3N atom coords
cs.pack(CHARGE,natoms,q) # vector of per-atom charge :pre
# required fields: COORDS
# optional fields: BOXLO, BOXHI, BOXTILT :pre
cs.send(STEP,nfields) # msgID with nfields :pre
cs.pack_int(NATOMS,natoms) # total numer of atoms
cs.pack_int(NTYPES,ntypes) # number of atom types
cs.pack(BOXLO,3,boxlo) # 3-vector of lower box bounds
cs.pack(BOXTILT,3,boxtilt) # 3-vector of tilt factors for triclinic boxes :pre
[Server replies to either kind of message]:
cs.send(msgID,3) # msgID = 1 with 3 fields
cs.pack(FORCES,3*Natoms,f) # vector of 3N forces on atoms
cs.pack(ENERGY,1,poteng) # total potential energy of system
cs.pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
:line
[Restrictions:]
This command is part of the MESSAGE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"message"_message.html, "fix client/md"_fix_client_md.html
[Default:] none

3
examples/COUPLE/README
View File

@ -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 +34,11 @@ 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 Monte Carlo with LAMMPS MD
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 LAMMPS MD with VASP quantum DFT
library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran

34
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# 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)
# this line if built the CSlib within lib/message with ZMQ support
# note this is using the serial (no-mpi) version of the CSlib
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
# this line if built the CSlib without ZMQ support
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
clean:
@rm -f *.o mc
# rules
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<

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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 and the MC client code
First, build LAMMPS with its MESSAGE package installed:
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.
Next build the MC client code:
First edit the Makefile in this dir. The CSLIB variable should be the
path to where the LAMMPS lib/message dir is on your system. If you
built the CSlib without ZMQ support you will also need to
comment/uncomment two lines. 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

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# MC params
500 nsteps
100 ndynamics
0.1 delta
1.0 temperature
12345 seed

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@ -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

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LAMMPS (16 Jul 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 = 0.000633001 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 2.14577e-06 on 1 procs for 0 steps with 500 atoms
46.6% 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 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
314.6% 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
314.6% 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: 0:00:02

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LAMMPS (16 Jul 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 = 0.000604868 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 3.09944e-06 on 4 procs for 0 steps with 500 atoms
72.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 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 | | 3.099e-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 3.33786e-06 on 4 procs for 0 steps with 500 atoms
119.8% 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 | | 3.338e-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 3.51667e-06 on 4 procs for 0 steps with 500 atoms
113.7% 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 | | 3.517e-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 2.92063e-06 on 4 procs for 0 steps with 500 atoms
119.8% 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 | | 2.921e-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 3.39746e-06 on 4 procs for 0 steps with 500 atoms
117.7% 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 | | 3.397e-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 3.39746e-06 on 4 procs for 0 steps with 500 atoms
117.7% 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 | | 3.397e-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
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LAMMPS (16 Jul 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 = 0.000612974 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
46.6% 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 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: 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 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: 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 0 on 1 procs for 0 steps with 500 atoms
0.0% 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 | 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 | | 0 | | | 0.00
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 0 on 1 procs for 0 steps with 500 atoms
0.0% 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 | 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 | | 0 | | | 0.00
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.23Jul18.zmq.g++.4 Normal file
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LAMMPS (16 Jul 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 = 0.000566006 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 4.29153e-06 on 4 procs for 0 steps with 500 atoms
99.0% 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 | | 4.292e-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 3.57628e-06 on 4 procs for 0 steps with 500 atoms
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 | 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 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 3.09944e-06 on 4 procs for 0 steps with 500 atoms
121.0% 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 | | 3.099e-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 2.14577e-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 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 1.90735e-06 on 4 procs for 0 steps with 500 atoms
157.3% 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 | | 1.907e-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
151.5% 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 | | 2.146e-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

261
examples/COUPLE/lammps_mc/mc.cpp Normal file
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/* ----------------------------------------------------------------------
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 <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "cslib.h"
using namespace CSLIB_NS;
#include "mc.h"
#include "random_park.h"
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, CSlib *cs_caller)
{
cs = 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};
// 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
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/* ----------------------------------------------------------------------
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 *, class CSlib *);
~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;
class CSlib *cs; // messaging library
void options(char *);
};
#endif

72
examples/COUPLE/lammps_mc/random_park.cpp Normal file
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/* ----------------------------------------------------------------------
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
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/* ----------------------------------------------------------------------
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
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# 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
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K-Points
0
Monkhorst Pack
15 15 15
0 0 0

11
examples/COUPLE/lammps_vasp/POSCAR_W Normal file
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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

90
examples/COUPLE/lammps_vasp/README Normal file
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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_warp.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:
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.
----------------
To run in client/server mode:
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
--------------
The provided data.W file (for LAMMPS) and POSCAR_W file (for VASP) are
for a simple 2-atom unit cell of bcc tungsten (W). You could
replicate this with LAMMPS to create a larger system. The
vasp_wrap.py script needs to be generalized to create an appropriate
POSCAR_W file for a larger box.
VASP input file include the sample INCAR and KPOINTS files provided.
A POTCAR file is also needed, which should come from your VASP package
installation.

15
examples/COUPLE/lammps_vasp/data.W Normal file
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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
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# 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

63
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LAMMPS (20 Apr 2018)
# small W unit cell for use with VASP
#message client aimd file tmp.couple
message client aimd zmq localhost:5555
#message client aimd mpi/two tmp.couple
#message client aimd mpi/one tmp.couple
units real
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 1 MPI processor grid
reading atoms ...
2 atoms
mass 1 1.0
#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 message/aimd
fix_modify 2 energy yes
thermo 1
run 2
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 -48.069571 -172694.2
1 0.063865861 0 0 -48.069381 -172693.93
2 0.25546344 0 0 -48.06881 -172693.1
Loop time of 0.281842 on 1 procs for 2 steps with 2 atoms
Performance: 0.613 ns/day, 39.145 hours/ns, 7.096 timesteps/s
0.0% 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 | 0 | 0 | 0.0 | 0.00
Comm | 3.0994e-06 | 3.0994e-06 | 3.0994e-06 | 0.0 | 0.00
Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.03
Modify | 0.28174 | 0.28174 | 0.28174 | 0.0 | 99.97
Other | | 5.96e-06 | | | 0.00
Nlocal: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7 ave 7 max 7 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 = 0
Dangerous builds not checked
Total wall time: 0:00:06

234
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#!/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, virial to client
# NOTES:
# check to insure basic VASP input files are in place?
# worry about archiving VASP input/output in special filenames or dirs?
# how to get ordering (by type) of VASP atoms vs LAMMPS atoms
# create one initial permutation vector?
# could make syntax for launching VASP more flexible
# e.g. command-line arg for # of procs
import sys
import commands
import xml.etree.ElementTree as ET
from cslib import CSlib
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
# enums matching FixClientMD class in LAMMPS
SETUP,STEP = range(1,2+1)
UNITS,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE = range(1,10+1)
FORCES,ENERGY,VIRIAL = range(1,3+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
print >>psnew,psold[0],
print >>psnew,psold[1],
print >>psnew,"%g 0.0 0.0" % box[0]
print >>psnew,"0.0 %g 0.0" % box[1]
print >>psnew,"0.0 0.0 %g" % box[2]
print >>psnew,psold[5],
print >>psnew,psold[6],
# per-atom coords
# grouped by types
print >>psnew,"Cartesian"
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" % (x,y,z)
print >>psnew,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]
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
# could generalize this to be more like ServerMD class
# allow for box size, atom types, natoms, etc
# unpack coords from client
# create VASP input
# NOTE: generalize this for general list of atom types
coords = cs.unpack(COORDS,1)
#types = cs.unpack(2);
types = 2*[1]
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
# invoke VASP
print "Launching VASP ..."
print vaspcmd
out = commands.getoutput(vaspcmd)
print out
# process VASP output
energy,forces,virial = vasprun_read()
# return forces, energy, virial 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

1
examples/README
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@ -82,6 +82,7 @@ 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

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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 MESSAGE package (doc/Section_messages.html#MESSAGE)
and Section_howto.html#howto10 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
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
--------------
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.
--------------
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
--------------
Mpi/one mode of messaging:
Launch LAMMPS twice in a single mpirun command:
mpirun -np 2 lmp_mpi -mpi 2 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpi 2 -in in.message.server -v mode mpione -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 -mpi P
command-line option as their first option, where P is the number of
processors the first code in the mpirun command (client or server) is
running on.

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# 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
thermo 10
run 50

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# 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
fix 2 all client/md
fix_modify 2 energy yes
thermo 10
run 50

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# 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

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LAMMPS (16 Jul 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 = 0.00067687 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
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 5.12413 on 1 procs for 50 steps with 500 atoms
Performance: 4215.352 tau/day, 9.758 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 | 0.0001719 | 0.0001719 | 0.0001719 | 0.0 | 0.00
Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00
Modify | 5.1232 | 5.1232 | 5.1232 | 0.0 | 99.98
Other | | 0.0004876 | | | 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: 0:00:19

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LAMMPS (16 Jul 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 = 0.000554085 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
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 5.07392 on 2 procs for 50 steps with 500 atoms
Performance: 4257.065 tau/day, 9.854 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 | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.00
Comm | 0.00022864 | 0.00023806 | 0.00024748 | 0.0 | 0.00
Output | 0.00020814 | 0.00051165 | 0.00081515 | 0.0 | 0.01
Modify | 5.0659 | 5.0695 | 5.073 | 0.2 | 99.91
Other | | 0.003713 | | | 0.07
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: 0:00:07

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LAMMPS (16 Jul 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 = 0.000674009 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
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 0.0424271 on 1 procs for 50 steps with 500 atoms
Performance: 509109.009 tau/day, 1178.493 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 | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.02
Comm | 8.2016e-05 | 8.2016e-05 | 8.2016e-05 | 0.0 | 0.19
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.26
Modify | 0.042014 | 0.042014 | 0.042014 | 0.0 | 99.03
Other | | 0.0002129 | | | 0.50
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

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LAMMPS (16 Jul 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 = 0.000527859 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
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 0.027467 on 2 procs for 50 steps with 500 atoms
Performance: 786397.868 tau/day, 1820.365 timesteps/s
99.9% 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 | 4.0531e-06 | 4.1723e-06 | 4.2915e-06 | 0.0 | 0.02
Comm | 0.00017691 | 0.00018024 | 0.00018358 | 0.0 | 0.66
Output | 9.3222e-05 | 0.00012612 | 0.00015903 | 0.0 | 0.46
Modify | 0.026678 | 0.02676 | 0.026841 | 0.0 | 97.42
Other | | 0.0003968 | | | 1.44
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

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LAMMPS (16 Jul 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 = 0.000490904 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
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 0.0624809 on 1 procs for 50 steps with 500 atoms
Performance: 345705.501 tau/day, 800.244 timesteps/s
40.4% 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 | 7.391e-06 | 7.391e-06 | 7.391e-06 | 0.0 | 0.01
Comm | 8.5831e-05 | 8.5831e-05 | 8.5831e-05 | 0.0 | 0.14
Output | 0.00011873 | 0.00011873 | 0.00011873 | 0.0 | 0.19
Modify | 0.062024 | 0.062024 | 0.062024 | 0.0 | 99.27
Other | | 0.0002449 | | | 0.39
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: 0:00:07

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LAMMPS (16 Jul 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 = 0.000692129 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
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 0.0186305 on 2 procs for 50 steps with 500 atoms
Performance: 1159388.887 tau/day, 2683.771 timesteps/s
50.7% 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 | 3.8147e-06 | 4.7684e-06 | 0.0 | 0.02
Comm | 0.00017023 | 0.00017631 | 0.00018239 | 0.0 | 0.95
Output | 0.00010896 | 0.00013852 | 0.00016809 | 0.0 | 0.74
Modify | 0.017709 | 0.017821 | 0.017933 | 0.1 | 95.66
Other | | 0.0004908 | | | 2.63
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

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LAMMPS (16 Jul 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 = 0.000747919 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
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 0.0769799 on 1 procs for 50 steps with 500 atoms
Performance: 280592.815 tau/day, 649.520 timesteps/s
12.9% 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 | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.01
Comm | 9.5129e-05 | 9.5129e-05 | 9.5129e-05 | 0.0 | 0.12
Output | 0.00011516 | 0.00011516 | 0.00011516 | 0.0 | 0.15
Modify | 0.076471 | 0.076471 | 0.076471 | 0.0 | 99.34
Other | | 0.0002928 | | | 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: 0:00:08

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LAMMPS (16 Jul 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 = 0.000608921 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
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 0.0453095 on 2 procs for 50 steps with 500 atoms
Performance: 476720.759 tau/day, 1103.520 timesteps/s
55.6% 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 | 2.1458e-06 | 4.0531e-06 | 5.9605e-06 | 0.0 | 0.01
Comm | 0.0001595 | 0.00015998 | 0.00016046 | 0.0 | 0.35
Output | 8.893e-05 | 0.00011587 | 0.00014281 | 0.0 | 0.26
Modify | 0.044439 | 0.044582 | 0.044724 | 0.1 | 98.39
Other | | 0.0004481 | | | 0.99
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: 0:00:04

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LAMMPS (16 Jul 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 = 0.000540972 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
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 0.037292 on 1 procs for 50 steps with 500 atoms
Performance: 579212.643 tau/day, 1340.770 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 | 0.028156 | 0.028156 | 0.028156 | 0.0 | 75.50
Neigh | 0.0069656 | 0.0069656 | 0.0069656 | 0.0 | 18.68
Comm | 0.0011504 | 0.0011504 | 0.0011504 | 0.0 | 3.08
Output | 0.00013399 | 0.00013399 | 0.00013399 | 0.0 | 0.36
Modify | 0.00049257 | 0.00049257 | 0.00049257 | 0.0 | 1.32
Other | | 0.0003934 | | | 1.05
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

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LAMMPS (16 Jul 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 = 0.000635862 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
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 0.0152688 on 4 procs for 50 steps with 500 atoms
Performance: 1414649.236 tau/day, 3274.651 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.006639 | 0.007916 | 0.0083909 | 0.8 | 51.84
Neigh | 0.0015991 | 0.0018443 | 0.0019469 | 0.3 | 12.08
Comm | 0.0041771 | 0.0047471 | 0.0063298 | 1.3 | 31.09
Output | 9.6798e-05 | 0.00012475 | 0.00019407 | 0.0 | 0.82
Modify | 0.00015974 | 0.0001967 | 0.00023103 | 0.0 | 1.29
Other | | 0.0004399 | | | 2.88
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

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LAMMPS (16 Jul 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

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LAMMPS (16 Jul 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

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LAMMPS (16 Jul 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

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LAMMPS (16 Jul 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

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LAMMPS (16 Jul 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.23Jul18.message.server.mpitwo.g++.4 Normal file
View File

@ -0,0 +1,44 @@
LAMMPS (16 Jul 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.23Jul18.message.server.zmq.g++.1 Normal file
View File

@ -0,0 +1,44 @@
LAMMPS (16 Jul 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.23Jul18.message.server.zmq.g++.4 Normal file
View File

@ -0,0 +1,44 @@
LAMMPS (16 Jul 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

2
lib/README
View File

@ -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
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@ -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
View 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
View 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
View 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 (by Aug 2018) and 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 this website: 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.

501
lib/message/cslib/LICENSE Normal file
View File

@ -0,0 +1,501 @@
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
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That's all there is to it!

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This is the July 2018 version of 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 GNU LGPL
license. See the accompanying LICENSE file.
This directory contains the following:
README this file
LICENSE GNU LGPL license
src source files for library

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# 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 $<

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// 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

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// 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

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
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
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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
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
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# ------------------------------------------------------------------------
# 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 GNU Lesser General Public
# License (LGPL).
#
# 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)

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
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);
}

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! 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

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
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

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "msg.h"
using namespace CSLIB_NS;
/* ---------------------------------------------------------------------- */
Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld)
{
world = cworld;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
init(csflag);
}
/* ---------------------------------------------------------------------- */
Msg::Msg(int csflag, const void *ptr)
{
world = 0;
me = 0;
nprocs = 1;
init(csflag);
}
/* ---------------------------------------------------------------------- */
void Msg::init(int csflag)
{
client = server = 0;
if (csflag == 0) client = 1;
else if (csflag == 1) server = 1;
nsend = nrecv = 0;
}
/* ---------------------------------------------------------------------- */
void Msg::allocate(int nheader, int &maxheader, int *&header,
int nbuf, int &maxbuf, char *&buf)
{
if (nheader > maxheader) {
sfree(header);
maxheader = nheader;
header = (int *) smalloc(maxheader*sizeof(int));
}
if (nbuf > maxbuf) {
sfree(buf);
maxbuf = nbuf;
buf = (char *) smalloc(maxbuf*sizeof(char));
}
}
/* ---------------------------------------------------------------------- */
void *Msg::smalloc(int nbytes)
{
if (nbytes == 0) return NULL;
void *ptr = (void *) malloc(nbytes);
if (ptr == NULL) {
char str[128];
sprintf(str,"Failed to allocate %d bytes",nbytes);
}
return ptr;
}
/* ---------------------------------------------------------------------- */
void Msg::sfree(void *ptr)
{
if (ptr == NULL) return;
free(ptr);
}
/* ---------------------------------------------------------------------- */
void Msg::error_all(const char *str)
{
if (me == 0) printf("CSlib ERROR: %s\n",str);
MPI_Abort(world,1);
}
/* ---------------------------------------------------------------------- */
void Msg::error_one(const char *str)
{
printf("CSlib ERROR: %s\n",str);
MPI_Abort(world,1);
}

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifndef MSG_H
#define MSG_H
#include <mpi.h>
namespace CSLIB_NS {
class Msg {
public:
int nsend,nrecv;
MPI_Comm world;
Msg(int, const void *, MPI_Comm);
Msg(int, const void *);
virtual ~Msg() {}
virtual void send(int, int *, int, char *) = 0;
virtual void recv(int &, int *&, int &, char *&) = 0;
protected:
int me,nprocs;
int client,server;
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int lengths[2];
void init(int);
void allocate(int, int &, int *&, int, int &, char *&);
void *smalloc(int);
void sfree(void *);
void error_all(const char *);
void error_one(const char *);
};
}
#endif

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <stdint.h>
#include <unistd.h>
#include "msg_file.h"
using namespace CSLIB_NS;
#define MAXLINE 256
#define SLEEP 0.1 // delay in CPU secs to check for message file
/* ---------------------------------------------------------------------- */
MsgFile::MsgFile(int csflag, const void *ptr, MPI_Comm cworld) :
Msg(csflag, ptr, cworld)
{
char *filename = (char *) ptr;
init(filename);
}
/* ---------------------------------------------------------------------- */
MsgFile::MsgFile(int csflag, const void *ptr) : Msg(csflag, ptr)
{
char *filename = (char *) ptr;
init(filename);
}
/* ---------------------------------------------------------------------- */
MsgFile::~MsgFile()
{
delete [] fileroot;
}
/* ---------------------------------------------------------------------- */
void MsgFile::init(char *filename)
{
int n = strlen(filename) + 1;
fileroot = new char[n];
strcpy(fileroot,filename);
}
/* ---------------------------------------------------------------------- */
void MsgFile::send(int nheader, int *header, int nbuf, char *buf)
{
char filename[MAXLINE];
lengths[0] = nheader;
lengths[1] = nbuf;
if (me == 0) {
if (client) sprintf(filename,"%s.%s",fileroot,"client");
else if (server) sprintf(filename,"%s.%s",fileroot,"server");
fp = fopen(filename,"wb");
if (!fp) error_one("send(): Could not open send message file");
fwrite(lengths,sizeof(int),2,fp);
fwrite(header,sizeof(int),nheader,fp);
fwrite(buf,1,nbuf,fp);
fclose(fp);
}
// create empty signal file
if (me == 0) {
if (client) sprintf(filename,"%s.%s",fileroot,"client.signal");
else if (server) sprintf(filename,"%s.%s",fileroot,"server.signal");
fp = fopen(filename,"w");
fclose(fp);
}
}
/* ---------------------------------------------------------------------- */
void MsgFile::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
{
char filename[MAXLINE];
// wait until signal file exists to open message file
if (me == 0) {
if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
int delay = (int) (1000000 * SLEEP);
while (1) {
fp = fopen(filename,"r");
if (fp) break;
usleep(delay);
}
fclose(fp);
if (client) sprintf(filename,"%s.%s",fileroot,"server");
else if (server) sprintf(filename,"%s.%s",fileroot,"client");
fp = fopen(filename,"rb");
if (!fp) error_one("recv(): Could not open recv message file");
}
// read and broadcast data
if (me == 0) fread(lengths,sizeof(int),2,fp);
if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
int nheader = lengths[0];
int nbuf = lengths[1];
allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
if (me == 0) fread(header,sizeof(int),nheader,fp);
if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
if (me == 0) fread(buf,1,nbuf,fp);
if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
// delete both message and signal file
if (me == 0) {
fclose(fp);
unlink(filename);
if (client) sprintf(filename,"%s.%s",fileroot,"server.signal");
else if (server) sprintf(filename,"%s.%s",fileroot,"client.signal");
unlink(filename);
}
}

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifndef MSG_FILE_H
#define MSG_FILE_H
#include <stdio.h>
#include "msg.h"
namespace CSLIB_NS {
class MsgFile : public Msg {
public:
MsgFile(int, const void *, MPI_Comm);
MsgFile(int, const void *);
~MsgFile();
void send(int, int *, int, char *);
void recv(int &, int *&, int &, char *&);
private:
char *fileroot;
FILE *fp;
void init(char *);
};
}
#endif

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include <stdint.h>
#include <stdio.h>
#include <unistd.h>
#include "msg_mpi_one.h"
using namespace CSLIB_NS;
/* ---------------------------------------------------------------------- */
MsgMPIOne::MsgMPIOne(int csflag, const void *ptr, MPI_Comm cworld) :
Msg(csflag, ptr, cworld)
{
// NOTE: ideally would skip this call if mpi/two
init(ptr);
}
/* ---------------------------------------------------------------------- */
void MsgMPIOne::init(const void *ptr)
{
MPI_Comm *pbothcomm = (MPI_Comm *) ptr;
bothcomm = *pbothcomm;
if (client) {
MPI_Comm_size(world,&nprocs);
otherroot = nprocs;
} else if (server) {
otherroot = 0;
}
}
/* ---------------------------------------------------------------------- */
void MsgMPIOne::send(int nheader, int *header, int nbuf, char *buf)
{
lengths[0] = nheader;
lengths[1] = nbuf;
if (me == 0) {
MPI_Send(lengths,2,MPI_INT,otherroot,0,bothcomm);
MPI_Send(header,nheader,MPI_INT,otherroot,0,bothcomm);
MPI_Send(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm);
}
}
/* ---------------------------------------------------------------------- */
void MsgMPIOne::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
{
MPI_Status status;
if (me == 0) MPI_Recv(lengths,2,MPI_INT,otherroot,0,bothcomm,&status);
if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
int nheader = lengths[0];
int nbuf = lengths[1];
allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
if (me == 0) MPI_Recv(header,nheader,MPI_INT,otherroot,0,bothcomm,&status);
if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
if (me == 0) MPI_Recv(buf,nbuf,MPI_CHAR,otherroot,0,bothcomm,&status);
if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
}

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifndef MSG_MPI_ONE_H
#define MSG_MPI_ONE_H
#include "msg.h"
namespace CSLIB_NS {
class MsgMPIOne : public Msg {
public:
MsgMPIOne(int, const void *, MPI_Comm);
virtual ~MsgMPIOne() {}
void send(int, int *, int, char *);
void recv(int &, int *&, int &, char *&);
protected:
MPI_Comm bothcomm;
int otherroot;
void init(const void *);
};
}
#endif

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include <stdint.h>
#include <stdio.h>
#include <unistd.h>
#include "msg_mpi_two.h"
using namespace CSLIB_NS;
/* ---------------------------------------------------------------------- */
MsgMPITwo::MsgMPITwo(int csflag, const void *ptr, MPI_Comm cworld) :
MsgMPIOne(csflag, ptr, cworld)
{
char *filename = (char *) ptr;
init(filename);
}
/* ---------------------------------------------------------------------- */
MsgMPITwo::~MsgMPITwo()
{
// free the inter comm that spans both client and server
MPI_Comm_free(&bothcomm);
MPI_Close_port(port);
}
/* ---------------------------------------------------------------------- */
void MsgMPITwo::init(char *filename)
{
if (client) {
if (me == 0) {
FILE *fp = NULL;
while (!fp) {
fp = fopen(filename,"r");
if (!fp) sleep(1);
}
fgets(port,MPI_MAX_PORT_NAME,fp);
//printf("Client port: %s\n",port);
fclose(fp);
}
MPI_Bcast(port,MPI_MAX_PORT_NAME,MPI_CHAR,0,world);
MPI_Comm_connect(port,MPI_INFO_NULL,0,world,&bothcomm);
//if (me == 0) printf("CLIENT comm connect\n");
if (me == 0) unlink(filename);
} else if (server) {
MPI_Open_port(MPI_INFO_NULL,port);
if (me == 0) {
//printf("Server name: %s\n",port);
FILE *fp = fopen(filename,"w");
fprintf(fp,"%s",port);
fclose(fp);
}
MPI_Comm_accept(port,MPI_INFO_NULL,0,world,&bothcomm);
//if (me == 0) printf("SERVER comm accept\n");
}
otherroot = 0;
}

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifndef MSG_MPI_TWO_H
#define MSG_MPI_TWO_H
#include "msg_mpi_one.h"
namespace CSLIB_NS {
class MsgMPITwo : public MsgMPIOne {
public:
MsgMPITwo(int, const void *, MPI_Comm);
~MsgMPITwo();
private:
char port[MPI_MAX_PORT_NAME];
void init(char *);
};
}
#endif

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <zmq.h>
#include <string.h>
#include <stdlib.h>
#include <stdint.h>
#include <stdio.h>
#include "msg_zmq.h"
using namespace CSLIB_NS;
/* ---------------------------------------------------------------------- */
MsgZMQ::MsgZMQ(int csflag, const void *ptr, MPI_Comm cworld) :
Msg(csflag, ptr, cworld)
{
char *port = (char *) ptr;
init(port);
}
MsgZMQ::MsgZMQ(int csflag, const void *ptr) : Msg(csflag, ptr)
{
char *port = (char *) ptr;
init(port);
}
/* ---------------------------------------------------------------------- */
MsgZMQ::~MsgZMQ()
{
if (me == 0) {
zmq_close(socket);
zmq_ctx_destroy(context);
}
}
/* ---------------------------------------------------------------------- */
void MsgZMQ::init(char *port)
{
#ifdef ZMQ_NO
error_all("constructor(): Library not built with ZMQ support");
#endif
if (me == 0) {
int n = strlen(port) + 8;
char *socket_name = new char[n];
strcpy(socket_name,"tcp://");
strcat(socket_name,port);
if (client) {
context = zmq_ctx_new();
socket = zmq_socket(context,ZMQ_REQ);
zmq_connect(socket,socket_name);
} else if (server) {
context = zmq_ctx_new();
socket = zmq_socket(context,ZMQ_REP);
int rc = zmq_bind(socket,socket_name);
if (rc) error_one("constructor(): Server could not make socket connection");
}
delete [] socket_name;
}
}
/* ----------------------------------------------------------------------
client/server sockets (REQ/REP) must follow this protocol:
client sends request (REQ) which server receives
server sends response (REP) which client receives
every exchange is of this form, server cannot initiate a send
thus each ZMQ send below has a following ZMQ recv, except last one
if client calls send(), it will next call recv()
if server calls send(), it will next call recv() from its wait loop
in either case, recv() issues a ZMQ recv to match last ZMQ send here
------------------------------------------------------------------------- */
void MsgZMQ::send(int nheader, int *header, int nbuf, char *buf)
{
lengths[0] = nheader;
lengths[1] = nbuf;
if (me == 0) {
zmq_send(socket,lengths,2*sizeof(int),0);
zmq_recv(socket,NULL,0,0);
}
if (me == 0) {
zmq_send(socket,header,nheader*sizeof(int),0);
zmq_recv(socket,NULL,0,0);
}
if (me == 0) zmq_send(socket,buf,nbuf,0);
}
/* ----------------------------------------------------------------------
client/server sockets (REQ/REP) must follow this protocol:
client sends request (REQ) which server receives
server sends response (REP) which client receives
every exchange is of this form, server cannot initiate a send
thus each ZMQ recv below has a following ZMQ send, except last one
if client calls recv(), it will next call send() to ping server again,
if server calls recv(), it will next call send() to respond to client
in either case, send() issues a ZMQ send to match last ZMQ recv here
------------------------------------------------------------------------- */
void MsgZMQ::recv(int &maxheader, int *&header, int &maxbuf, char *&buf)
{
if (me == 0) {
zmq_recv(socket,lengths,2*sizeof(int),0);
zmq_send(socket,NULL,0,0);
}
if (nprocs > 1) MPI_Bcast(lengths,2,MPI_INT,0,world);
int nheader = lengths[0];
int nbuf = lengths[1];
allocate(nheader,maxheader,header,nbuf,maxbuf,buf);
if (me == 0) {
zmq_recv(socket,header,nheader*sizeof(int),0);
zmq_send(socket,NULL,0,0);
}
if (nprocs > 1) MPI_Bcast(header,nheader,MPI_INT,0,world);
if (me == 0) zmq_recv(socket,buf,nbuf,0);
if (nprocs > 1) MPI_Bcast(buf,nbuf,MPI_CHAR,0,world);
}

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/* ----------------------------------------------------------------------
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 GNU Lesser General Public
License (LGPL).
See the README file in the top-level CSlib directory.
------------------------------------------------------------------------- */
#ifndef MSG_ZMQ_H
#define MSG_ZMQ_H
#include "msg.h"
namespace CSLIB_NS {
class MsgZMQ : public Msg {
public:
MsgZMQ(int, const void *, MPI_Comm);
MsgZMQ(int, const void *);
~MsgZMQ();
void send(int, int *, int, char *);
void recv(int &, int *&, int &, char *&);
private:
void *context,*socket;
void init(char *);
};
}
#endif

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# Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# arg1 = file, arg2 = file it depends on
# enforce using portable C locale
LC_ALL=C
export LC_ALL
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../$2) then
cp $1 ..
if (test $mode = 2) then
echo " updating src/$1"
fi
fi
elif (test -n "$2") then
if (test ! -e ../$2) then
rm -f ../$1
fi
fi
}
# all package files with no dependencies
for file in *.cpp *.h; do
test -f ${file} && action $file
done
# edit 2 Makefile.package files to include/exclude package info
if (test $1 = 1) then
if (test -e ../Makefile.package) then
sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/message/cslib/src |' ../Makefile.package
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/message/cslib/src |' ../Makefile.package
sed -i -e 's|^PKG_LIB =[ \t]*|&-lmessage |' ../Makefile.package
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(message_SYSINC) |' ../Makefile.package
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(message_SYSLIB) |' ../Makefile.package
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(message_SYSPATH) |' ../Makefile.package
fi
if (test -e ../Makefile.package.settings) then
sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
# multiline form needed for BSD sed on Macs
sed -i -e '4 i \
include ..\/..\/lib\/message\/Makefile.lammps
' ../Makefile.package.settings
fi
elif (test $1 = 0) then
if (test -e ../Makefile.package) then
sed -i -e 's/[^ \t]*message[^ \t]* //' ../Makefile.package
fi
if (test -e ../Makefile.package.settings) then
sed -i -e '/^include.*message.*$/d' ../Makefile.package.settings
fi
fi

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <cstdio>
#include <cstring>
#include "fix_client_md.h"
#include "cslib.h"
#include "atom.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
using namespace FixConst;
enum{SETUP=1,STEP};
enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
/* ---------------------------------------------------------------------- */
FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->clientserver != 1)
error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map");
if (sizeof(tagint) != 4)
error->all(FLERR,"Fix client/md requires 4-byte atom IDs");
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
virial_flag = 1;
thermo_virial = 1;
maxatom = 0;
xpbc = NULL;
}
/* ---------------------------------------------------------------------- */
FixClientMD::~FixClientMD()
{
memory->destroy(xpbc);
CSlib *cs = (CSlib *) lmp->cslib;
// all-done message to server
cs->send(-1,0);
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
// clean-up
delete cs;
lmp->cslib = NULL;
}
/* ---------------------------------------------------------------------- */
int FixClientMD::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixClientMD::init()
{
if (3*atom->natoms > INT_MAX)
error->all(FLERR,"Fix client/md max atoms is 1/3 of 2^31");
}
/* ---------------------------------------------------------------------- */
void FixClientMD::setup(int vflag)
{
CSlib *cs = (CSlib *) lmp->cslib;
// required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
// optional fields: others in enum above
int nfields = 6;
if (domain->dimension == 2) nfields++;
if (domain->triclinic) nfields++;
if (atom->q_flag) nfields++;
cs->send(SETUP,nfields);
cs->pack_int(NATOMS,atom->natoms);
cs->pack_int(NTYPES,atom->ntypes);
cs->pack(BOXLO,4,3,domain->boxlo);
cs->pack(BOXHI,4,3,domain->boxhi);
cs->pack_parallel(TYPES,1,atom->nlocal,atom->tag,1,atom->type);
pack_coords();
cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
if (domain->dimension == 2) cs->pack_int(DIM,domain->dimension);
if (domain->triclinic) {
double boxtilt[3];
boxtilt[0] = domain->xy;
if (domain->dimension == 3) {
boxtilt[1] = domain->xz;
boxtilt[2] = domain->yz;
} else boxtilt[1] = boxtilt[2] = 0.0;
cs->pack(BOXTILT,4,3,boxtilt);
}
if (atom->q_flag)
cs->pack_parallel(CHARGE,4,atom->nlocal,atom->tag,1,atom->q);
// receive initial forces, energy, virial
receive_fev(vflag);
}
/* ---------------------------------------------------------------------- */
void FixClientMD::min_setup(int vflag)
{
setup(vflag);
}
/* ---------------------------------------------------------------------- */
void FixClientMD::post_force(int vflag)
{
int i,j,m;
// energy and virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
// required fields: COORDS
// optional fields: BOXLO, BOXHI, BOXTILT
// send coords
CSlib *cs = (CSlib *) lmp->cslib;
int nfields = 1;
if (domain->box_change) nfields += 2;
if (domain->box_change && domain->triclinic) nfields++;;
cs->send(STEP,nfields);
pack_coords();
cs->pack_parallel(COORDS,4,atom->nlocal,atom->tag,3,xpbc);
if (domain->box_change) {
cs->pack(BOXLO,4,3,domain->boxlo);
cs->pack(BOXHI,4,3,domain->boxhi);
if (domain->triclinic) {
double boxtilt[3];
boxtilt[0] = domain->xy;
if (domain->dimension == 3) {
boxtilt[1] = domain->xz;
boxtilt[2] = domain->yz;
} else boxtilt[1] = boxtilt[2] = 0.0;
cs->pack(BOXTILT,4,3,boxtilt);
}
}
// recv forces, energy, virial
receive_fev(vflag);
}
/* ---------------------------------------------------------------------- */
void FixClientMD::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
potential energy from QM code
------------------------------------------------------------------------- */
double FixClientMD::compute_scalar()
{
return eng;
}
/* ----------------------------------------------------------------------
pack local coords into xpbc, enforcing PBC
------------------------------------------------------------------------- */
void FixClientMD::pack_coords()
{
double **x = atom->x;
int nlocal = atom->nlocal;
if (nlocal > maxatom) {
memory->destroy(xpbc);
maxatom = atom->nmax;
memory->create(xpbc,3*maxatom,"message:xpbc");
}
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
int j = 0;
for (int i = 0; i < nlocal; i++) {
domain->remap(&xpbc[j]);
j += 3;
}
}
/* ----------------------------------------------------------------------
receive message from server with forces, energy, virial
------------------------------------------------------------------------- */
void FixClientMD::receive_fev(int vflag)
{
CSlib *cs = (CSlib *) lmp->cslib;
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
double *forces = (double *) cs->unpack(FORCES);
double **f = atom->f;
int nlocal = atom->nlocal;
bigint natoms = atom->natoms;
int m;
int j = 0;
for (tagint id = 1; id <= natoms; id++) {
m = atom->map(id);
if (m < 0 || m >= nlocal) j += 3;
else {
f[m][0] += forces[j++];
f[m][1] += forces[j++];
f[m][2] += forces[j++];
}
}
eng = cs->unpack_double(ENERGY);
if (vflag) {
double *v = (double *) cs->unpack(VIRIAL);
double invnprocs = 1.0 / comm->nprocs;
for (int i = 0; i < 6; i++)
virial[i] = invnprocs*v[i];
}
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(client/md,FixClientMD)
#else
#ifndef LMP_FIX_CLIENT_MD_H
#define LMP_FIX_CLIENT_MD_H
#include "fix.h"
namespace LAMMPS_NS {
class FixClientMD : public Fix {
public:
FixClientMD(class LAMMPS *, int, char **);
~FixClientMD();
int setmask();
void init();
void setup(int);
void min_setup(int);
void post_force(int);
void min_post_force(int);
double compute_scalar();
private:
void *cslib;
int maxatom;
double eng;
double *xpbc;
void pack_coords();
void receive_fev(int );
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/

90
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <string.h>
#include "message.h"
#include "error.h"
// CSlib interface
#include "cslib.h"
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
// customize by adding a new server protocol enum
enum{MD,MC};
/* ---------------------------------------------------------------------- */
void Message::command(int narg, char **arg)
{
if (narg < 3) error->all(FLERR,"Illegal message command");
int clientserver;
if (strcmp(arg[0],"client") == 0) clientserver = 1;
else if (strcmp(arg[0],"server") == 0) clientserver = 2;
else error->all(FLERR,"Illegal message command");
lmp->clientserver = clientserver;
// customize by adding a new server protocol
int protocol;
if (strcmp(arg[1],"md") == 0) protocol = MD;
else if (strcmp(arg[1],"mc") == 0) protocol = MC;
else error->all(FLERR,"Unknown message protocol");
// instantiate CSlib with chosen communication mode
if (strcmp(arg[2],"file") == 0 || strcmp(arg[2],"zmq") == 0 ||
strcmp(arg[2],"mpi/two") == 0) {
if (narg != 4) error->all(FLERR,"Illegal message command");
lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world);
} else if (strcmp(arg[2],"mpi/one") == 0) {
if (narg != 3) error->all(FLERR,"Illegal message command");
if (!lmp->cscomm)
error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used");
lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world);
} else error->all(FLERR,"Illegal message command");
// perform initial handshake between client and server
// other code being coupled to must perform similar operation
// client sends protocol with msgID = 0
// server matches it and replies
CSlib *cs = (CSlib *) lmp->cslib;
if (clientserver == 1) {
cs->send(0,1);
cs->pack_string(1,arg[1]);
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
} else {
int nfield;
int *fieldID,*fieldtype,*fieldlen;
int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake");
char *pstr = cs->unpack_string(1);
if (strcmp(pstr,arg[1]) != 0)
error->one(FLERR,"Mismatch in client/server protocol");
cs->send(0,0);
}
}

40
src/MESSAGE/message.h Normal file
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@ -0,0 +1,40 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(message,Message)
#else
#ifndef LMP_MESSAGE_H
#define LMP_MESSAGE_H
#include "pointers.h"
namespace LAMMPS_NS {
class Message : protected Pointers {
public:
Message(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

50
src/MESSAGE/server.cpp Normal file
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@ -0,0 +1,50 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <string.h>
#include "server.h"
#include "error.h"
// customize by adding a new server protocol include and enum
#include "server_md.h"
#include "server_mc.h"
using namespace LAMMPS_NS;
enum{MD,MC};
/* ---------------------------------------------------------------------- */
void Server::command(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal server command");
if (lmp->clientserver != 2)
error->all(FLERR,"Message command not used to setup LAMMPS as a server");
// customize by adding a new server protocol
int protocol;
if (strcmp(arg[0],"md") == 0) protocol = MD;
else if (strcmp(arg[0],"mc") == 0) protocol = MC;
else error->all(FLERR,"Unknown message protocol");
if (protocol == MD) {
ServerMD *server = new ServerMD(lmp);
server->loop();
} else if (protocol == MC) {
ServerMC *server = new ServerMC(lmp);
server->loop();
}
}

40
src/MESSAGE/server.h Normal file
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@ -0,0 +1,40 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(server,Server)
#else
#ifndef LMP_SERVER_H
#define LMP_SERVER_H
#include "pointers.h"
namespace LAMMPS_NS {
class Server : protected Pointers {
public:
Server(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

148
src/MESSAGE/server_mc.cpp Normal file
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@ -0,0 +1,148 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "server_mc.h"
#include "atom.h"
#include "update.h"
#include "integrate.h"
#include "input.h"
#include "output.h"
#include "thermo.h"
#include "error.h"
// CSlib interface
#include "cslib.h"
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
/* ---------------------------------------------------------------------- */
ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void ServerMC::loop()
{
int i,j,m;
double xold[3],xnew[3];
tagint atomid;
CSlib *cs = (CSlib *) lmp->cslib;
// require atom map
if (!atom->map_style) error->all(FLERR,"Server mode requires atom map");
// initialize LAMMPS for dynamics
input->one("run 0");
//update->whichflag = 1;
//lmp->init();
// loop on messages
// receive a message, process it, send return message if necessary
int msgID,nfield;
int *fieldID,*fieldtype,*fieldlen;
while (1) {
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID < 0) break;
if (msgID == NATOMS) {
cs->send(msgID,1);
cs->pack_int(1,atom->natoms);
} else if (msgID == EINIT) {
double dval;
output->thermo->evaluate_keyword((char *) "pe",&dval);
cs->send(msgID,2);
cs->pack_double(1,dval);
double *coords = NULL;
if (atom->nlocal) coords = &atom->x[0][0];
cs->pack_parallel(2,4,atom->nlocal,atom->tag,3,coords);
} else if (msgID == DISPLACE) {
atomid = cs->unpack_int(1);
double *xnew = (double *) cs->unpack(2);
double **x = atom->x;
m = atom->map(atomid);
if (m >= 0 && m < atom->nlocal) {
xold[0] = x[m][0];
xold[1] = x[m][1];
xold[2] = x[m][2];
x[m][0] = xnew[0];
x[m][1] = xnew[1];
x[m][2] = xnew[2];
}
input->one("run 0");
double dval;
output->thermo->evaluate_keyword((char *) "pe",&dval);
cs->send(msgID,1);
cs->pack_double(1,dval);
} else if (msgID == ACCEPT) {
int accept = cs->unpack_int(1);
double **x = atom->x;
if (!accept) {
m = atom->map(atomid);
if (m >= 0 && m < atom->nlocal) {
x[m][0] = xold[0];
x[m][1] = xold[1];
x[m][2] = xold[2];
}
}
cs->send(msgID,0);
} else if (msgID == RUN) {
int nsteps = cs->unpack_int(1);
//input->one("run 100");
update->nsteps = nsteps;
update->firststep = update->ntimestep;
update->laststep = update->ntimestep + nsteps;
update->integrate->setup(1);
update->integrate->run(nsteps);
cs->send(msgID,0);
} else error->all(FLERR,"Server received unrecognized message");
}
// final reply to client
cs->send(0,0);
// clean up
delete cs;
lmp->cslib = NULL;
}

29
src/MESSAGE/server_mc.h Normal file
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@ -0,0 +1,29 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_SERVER_MC_H
#define LMP_SERVER_MC_H
#include "pointers.h"
namespace LAMMPS_NS {
class ServerMC : protected Pointers {
public:
ServerMC(class LAMMPS *);
void loop();
};
}
#endif

333
src/MESSAGE/server_md.cpp Normal file
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@ -0,0 +1,333 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include <cstring>
#include "server_md.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "integrate.h"
#include "kspace.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
// CSlib interface
#include "cslib.h"
using namespace LAMMPS_NS;
using namespace CSLIB_NS;
enum{SETUP=1,STEP};
enum{UNITS=1,DIM,NATOMS,NTYPES,BOXLO,BOXHI,BOXTILT,TYPES,COORDS,CHARGE};
enum{FORCES=1,ENERGY,VIRIAL};
// NOTE: features that could be added to this interface
// allow client to set periodicity vs shrink-wrap
// currently just assume server is same as client
// test that triclinic boxes actually work
// send new box size/shape every step, for NPT client
// unit check between client/server with unit conversion if needed
// option for client to send other per-atom quantities, e.g. rmass
// more precise request of energy/virial (global or peratom) by client
// maybe Verlet should have a single(eflag,vflag) method to more easily comply
/* ---------------------------------------------------------------------- */
ServerMD::ServerMD(LAMMPS *lmp) : Pointers(lmp)
{
if (domain->box_exist == 0)
error->all(FLERR,"Server command before simulation box is defined");
if (!atom->map_style) error->all(FLERR,"Server md mode requires atom map");
if (atom->tag_enable == 0) error->all(FLERR,"Server md mode requires atom IDs");
if (sizeof(tagint) != 4) error->all(FLERR,"Server md requires 4-byte atom IDs");
}
/* ---------------------------------------------------------------------- */
void ServerMD::loop()
{
int i,j,m;
// cs = instance of CSlib
CSlib *cs = (CSlib *) lmp->cslib;
// counters
int forcecalls = 0;
int neighcalls = 0;
// loop on messages
// receive a message, process it, send return message
int msgID,nfield;
int *fieldID,*fieldtype,*fieldlen;
while (1) {
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
if (msgID < 0) break;
// SETUP call at beginning of each run
// required fields: NATOMS, NTYPES, BOXLO, BOXHI, TYPES, COORDS
// optional fields: others in enum above
if (msgID == SETUP) {
int natoms = -1;
int ntypes = -1;
double *boxlo = NULL;
double *boxhi = NULL;
double *boxtilt = NULL;
int *types = NULL;
double *coords = NULL;
double *charge = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
if (fieldID[ifield] == UNITS) {
char *units = cs->unpack_string(UNITS);
if (strcmp(units,update->unit_style) != 0)
error->all(FLERR,"Server md units mis-match with client");
} else if (fieldID[ifield] == DIM) {
int dim = cs->unpack_int(DIM);
if (dim != domain->dimension)
error->all(FLERR,"Server md dimension mis-match with client");
} else if (fieldID[ifield] == NATOMS) {
natoms = cs->unpack_int(NATOMS);
if (3*natoms > INT_MAX)
error->all(FLERR,"Server md max atoms is 1/3 of 2^31");
} else if (fieldID[ifield] == NTYPES) {
ntypes = cs->unpack_int(NTYPES);
if (ntypes != atom->ntypes)
error->all(FLERR,"Server md ntypes mis-match with client");
} else if (fieldID[ifield] == BOXLO) {
boxlo = (double *) cs->unpack(BOXLO);
} else if (fieldID[ifield] == BOXHI) {
boxhi = (double *) cs->unpack(BOXHI);
} else if (fieldID[ifield] == BOXTILT) {
boxtilt = (double *) cs->unpack(BOXTILT);
} else if (fieldID[ifield] == TYPES) {
types = (int *) cs->unpack(TYPES);
} else if (fieldID[ifield] == COORDS) {
coords = (double *) cs->unpack(COORDS);
} else if (fieldID[ifield] == CHARGE) {
charge = (double *) cs->unpack(CHARGE);
} else error->all(FLERR,"Server md setup field unknown");
}
if (natoms < 0 || ntypes < 0 || !boxlo || !boxhi || !types || !coords)
error->all(FLERR,"Required server md setup field not received");
if (charge && atom->q_flag == 0)
error->all(FLERR,"Server md does not define atom attribute q");
// reset box, global and local
// reset proc decomposition
box_change(boxlo,boxhi,boxtilt);
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
// clear all atoms
atom->nlocal = 0;
atom->nghost = 0;
// add atoms that are in my sub-box
int nlocal = 0;
for (int i = 0; i < natoms; i++) {
if (!domain->ownatom(i+1,&coords[3*i],NULL,0)) continue;
atom->avec->create_atom(types[i],&coords[3*i]);
atom->tag[nlocal] = i+1;
if (charge) atom->q[nlocal] = charge[i];
nlocal++;
}
int ntotal;
MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world);
if (ntotal != natoms)
error->all(FLERR,"Server md atom cound does not match client");
atom->map_init();
atom->map_set();
atom->natoms = natoms;
// perform system setup() for dynamics
// also OK for minimization, since client runs minimizer
// return forces, energy, virial to client
update->whichflag = 1;
lmp->init();
update->integrate->setup_minimal(1);
neighcalls++;
forcecalls++;
send_fev(msgID);
// STEP call at each timestep of run or minimization
// required fields: COORDS
// optional fields: BOXLO, BOXHI, BOXTILT
} else if (msgID == STEP) {
double *boxlo = NULL;
double *boxhi = NULL;
double *boxtilt = NULL;
double *coords = NULL;
for (int ifield = 0; ifield < nfield; ifield++) {
if (fieldID[ifield] == BOXLO) {
boxlo = (double *) cs->unpack(BOXLO);
} else if (fieldID[ifield] == BOXHI) {
boxhi = (double *) cs->unpack(BOXHI);
} else if (fieldID[ifield] == BOXTILT) {
boxtilt = (double *) cs->unpack(BOXTILT);
} else if (fieldID[ifield] == COORDS) {
coords = (double *) cs->unpack(COORDS);
} else error->all(FLERR,"Server md step field unknown");
}
if (!coords)
error->all(FLERR,"Required server md step field not received");
// change box size/shape, only if both box lo/hi received
if (boxlo && boxhi) box_change(boxlo,boxhi,boxtilt);
// assign received coords to owned atoms
// closest_image() insures xyz matches current server PBC
double **x = atom->x;
int nlocal = atom->nlocal;
int nall = atom->natoms;
j = 0;
for (tagint id = 1; id <= nall; id++) {
m = atom->map(id);
if (m < 0 || m >= nlocal) j += 3;
else {
domain->closest_image(x[m],&coords[j],x[m]);
j += 3;
}
}
// if no need to reneighbor, just ghost comm
// else setup_minimal(1) which includes reneigh
// setup_minimal computes forces for 0 or 1
int nflag = neighbor->decide();
if (nflag == 0) {
comm->forward_comm();
update->integrate->setup_minimal(0);
} else {
update->integrate->setup_minimal(1);
neighcalls++;
}
forcecalls++;
send_fev(msgID);
} else error->all(FLERR,"Server MD received unrecognized message");
}
// final reply to client
cs->send(0,0);
// stats
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Server MD calls = %d\n",forcecalls);
fprintf(screen,"Server MD reneighborings = %d\n",neighcalls);
}
if (logfile) {
fprintf(logfile,"Server MD calls = %d\n",forcecalls);
fprintf(logfile,"Server MD reneighborings %d\n",neighcalls);
}
}
// clean up
delete cs;
lmp->cslib = NULL;
}
/* ----------------------------------------------------------------------
box change due to received message
------------------------------------------------------------------------- */
void ServerMD::box_change(double *boxlo, double *boxhi, double *boxtilt)
{
domain->boxlo[0] = boxlo[0];
domain->boxhi[0] = boxhi[0];
domain->boxlo[1] = boxlo[1];
domain->boxhi[1] = boxhi[1];
if (domain->dimension == 3) {
domain->boxlo[2] = boxlo[2];
domain->boxhi[2] = boxhi[2];
}
if (boxtilt) {
if (!domain->triclinic)
error->all(FLERR,"Server md not setup for triclinic box");
domain->xy = boxtilt[0];
if (domain->dimension == 3) {
domain->xz = boxtilt[1];
domain->yz = boxtilt[2];
}
}
}
/* ----------------------------------------------------------------------
send return message with forces, energy, pressure tensor
pressure tensor should be just pair style virial
------------------------------------------------------------------------- */
void ServerMD::send_fev(int msgID)
{
CSlib *cs = (CSlib *) lmp->cslib;
cs->send(msgID,3);
double *forces = NULL;
if (atom->nlocal) forces = &atom->f[0][0];
cs->pack_parallel(FORCES,4,atom->nlocal,atom->tag,3,forces);
double eng = force->pair->eng_vdwl + force->pair->eng_coul;
double engall;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
cs->pack_double(ENERGY,engall);
double v[6],vall[6];
for (int i = 0; i < 6; i++)
v[i] = force->pair->virial[i];
if (force->kspace)
for (int i = 0; i < 6; i++)
v[i] += force->kspace->virial[i];
MPI_Allreduce(&v,&vall,6,MPI_DOUBLE,MPI_SUM,world);
cs->pack(VIRIAL,4,6,vall);
}

33
src/MESSAGE/server_md.h Normal file
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@ -0,0 +1,33 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_SERVER_MD_H
#define LMP_SERVER_MD_H
#include "pointers.h"
namespace LAMMPS_NS {
class ServerMD : protected Pointers {
public:
ServerMD(class LAMMPS *);
void loop();
private:
void box_change(double *, double *, double *);
void send_fev(int);
};
}
#endif

6
src/Makefile
View File

@ -53,7 +53,7 @@ endif
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
granular kim kokkos kspace latte manybody mc meam misc \
granular kim kokkos kspace latte manybody mc meam message misc \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap spin srd voronoi
@ -65,14 +65,14 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
PACKLIB = compress gpu kim kokkos latte meam mpiio mscg poems \
PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-qmmm user-quip user-smd user-vtk
PACKSYS = compress mpiio python user-lb
PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
user-h5md user-molfile user-netcdf user-qmmm user-quip \

3
src/atom.cpp
View File

@ -1533,7 +1533,8 @@ void Atom::set_mass(const char *file, int line, int narg, char **arg)
}
/* ----------------------------------------------------------------------
set all masses as read in from restart file
set all masses
called from reading of restart file, also from ServerMD
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)

6
src/domain.cpp
View File

@ -1208,13 +1208,9 @@ int Domain::closest_image(double *pos, int j)
/* ----------------------------------------------------------------------
find and return Xj image = periodic image of Xj that is closest to Xi
for triclinic, add/subtract tilt factors in other dims as needed
not currently used (Jan 2017):
used to be called by pair TIP4P styles but no longer,
due to use of other closest_image() method
------------------------------------------------------------------------- */
void Domain::closest_image(const double * const xi, const double * const xj,
double * const xjimage)
void Domain::closest_image(double *xi, double *xj, double *xjimage)
{
double dx = xj[0] - xi[0];
double dy = xj[1] - xi[1];

3
src/domain.h
View File

@ -116,8 +116,7 @@ class Domain : protected Pointers {
void minimum_image_once(double *);
int closest_image(int, int);
int closest_image(double *, int);
void closest_image(const double * const, const double * const,
double * const);
void closest_image(double *, double *, double *);
void remap(double *, imageint &);
void remap(double *);
void remap_near(double *, double *);

229
src/lammps.cpp
View File

@ -47,8 +47,8 @@
#include "accelerator_omp.h"
#include "timer.h"
#include "python.h"
#include "memory.h"
#include "version.h"
#include "memory.h"
#include "error.h"
#include "lmpinstalledpkgs.h"
@ -73,12 +73,50 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
output = NULL;
python = NULL;
clientserver = 0;
cslib = NULL;
cscomm = 0;
screen = NULL;
logfile = NULL;
infile = NULL;
initclock = MPI_Wtime();
// check if -mpi is first arg
// if so, then 2 apps were launched with one mpirun command
// this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
// e.g. for client/server coupling with another code
// communicator needs to shrink to be just LAMMPS
// syntax: -mpi P1 means P1 procs for one app, P-P1 procs for second app
// LAMMPS could be either app, based on proc IDs
// do the following:
// perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
// NOTE: assuming other app is doing the same thing, else will hang!
// re-create universe with subcomm
// store full two-app comm in cscomm
// cscomm is used by CSLIB package to exchange messages w/ other app
// eventually should extend to N > 2 apps launched with one mpirun command
int iarg = 1;
if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
strcmp(arg[iarg],"-m") == 0)) {
int me,nprocs;
MPI_Comm_rank(communicator,&me);
MPI_Comm_size(communicator,&nprocs);
int p1 = atoi(arg[iarg+1]);
if (p1 <= 0 || p1 >= nprocs)
error->universe_all(FLERR,"Invalid command-line argument");
int which = 0;
if (me >= p1) which = 1;
MPI_Comm subcomm;
MPI_Comm_split(communicator,which,me,&subcomm);
cscomm = communicator;
communicator = subcomm;
delete universe;
universe = new Universe(this,communicator);
}
// parse input switches
int inflag = 0;
@ -107,59 +145,30 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
int *pfirst = NULL;
int *plast = NULL;
int iarg = 1;
iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"-partition") == 0 ||
strcmp(arg[iarg],"-p") == 0) {
universe->existflag = 1;
if (strcmp(arg[iarg],"-echo") == 0 ||
strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg++;
while (iarg < narg && arg[iarg][0] != '-') {
universe->add_world(arg[iarg]);
iarg++;
}
iarg += 2;
} else if (strcmp(arg[iarg],"-help") == 0 ||
strcmp(arg[iarg],"-h") == 0) {
if (iarg+1 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
helpflag = 1;
citeflag = 0;
iarg += 1;
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-screen") == 0 ||
strcmp(arg[iarg],"-sc") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
screenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-log") == 0 ||
strcmp(arg[iarg],"-l") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
logflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-var") == 0 ||
strcmp(arg[iarg],"-v") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 3;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
} else if (strcmp(arg[iarg],"-echo") == 0 ||
strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-pscreen") == 0 ||
strcmp(arg[iarg],"-ps") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partscreenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-plog") == 0 ||
strcmp(arg[iarg],"-pl") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partlogflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-kokkos") == 0 ||
strcmp(arg[iarg],"-k") == 0) {
if (iarg+2 > narg)
@ -172,6 +181,26 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
kkfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
kklast = iarg;
} else if (strcmp(arg[iarg],"-log") == 0 ||
strcmp(arg[iarg],"-l") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
logflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-mpi") == 0 ||
strcmp(arg[iarg],"-m") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-nocite") == 0 ||
strcmp(arg[iarg],"-nc") == 0) {
citeflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
@ -188,6 +217,69 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
else break;
}
plast[npack++] = iarg;
} else if (strcmp(arg[iarg],"-partition") == 0 ||
strcmp(arg[iarg],"-p") == 0) {
universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg++;
while (iarg < narg && arg[iarg][0] != '-') {
universe->add_world(arg[iarg]);
iarg++;
}
} else if (strcmp(arg[iarg],"-plog") == 0 ||
strcmp(arg[iarg],"-pl") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partlogflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-pscreen") == 0 ||
strcmp(arg[iarg],"-ps") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partscreenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (universe->existflag)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"-restart") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartflag = 1;
rfile = arg[iarg+1];
dfile = arg[iarg+2];
// check for restart remap flag
if (strcmp(dfile,"remap") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartremapflag = 1;
dfile = arg[iarg+3];
iarg++;
}
iarg += 3;
// delimit any extra args for the write_data command
wdfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wdlast = iarg;
} else if (strcmp(arg[iarg],"-screen") == 0 ||
strcmp(arg[iarg],"-sc") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
screenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-suffix") == 0 ||
strcmp(arg[iarg],"-sf") == 0) {
if (iarg+2 > narg)
@ -213,45 +305,14 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
strcpy(suffix,arg[iarg+1]);
iarg += 2;
}
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
} else if (strcmp(arg[iarg],"-var") == 0 ||
strcmp(arg[iarg],"-v") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (universe->existflag)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"-restart") == 0 ||
strcmp(arg[iarg],"-r") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartflag = 1;
rfile = arg[iarg+1];
dfile = arg[iarg+2];
// check for restart remap flag
if (strcmp(dfile,"remap") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartremapflag = 1;
dfile = arg[iarg+3];
iarg++;
}
iarg += 3;
// delimit any extra args for the write_data command
wdfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wdlast = iarg;
} else if (strcmp(arg[iarg],"-nocite") == 0 ||
strcmp(arg[iarg],"-nc") == 0) {
citeflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"-help") == 0 ||
strcmp(arg[iarg],"-h") == 0) {
if (iarg+1 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
helpflag = 1;
citeflag = 0;
iarg += 1;
} else error->universe_all(FLERR,"Invalid command-line argument");
}
@ -595,6 +656,14 @@ LAMMPS::~LAMMPS()
delete [] suffix;
delete [] suffix2;
// free the MPI comm created by -mpi command-line arg
// it was passed to universe as if origianl universe world
// may have been split later by partitions, universe will free the splits
// free a copy of uorig here, so check in universe destructor will still work
MPI_Comm copy = universe->uorig;
if (cscomm) MPI_Comm_free(&copy);
delete input;
delete universe;
delete error;

4
src/lammps.h
View File

@ -51,6 +51,10 @@ class LAMMPS {
int num_package; // number of cmdline package commands
int cite_enable; // 1 if generating log.cite, 0 if disabled
int clientserver; // 0 = neither, 1 = client, 2 = server
void *cslib; // client/server messaging via CSlib
MPI_Comm cscomm; // MPI comm for client+server in mpi/one mode
class KokkosLMP *kokkos; // KOKKOS accelerator class
class AtomKokkos *atomKK; // KOKKOS version of Atom class
class MemoryKokkos *memoryKK; // KOKKOS version of Memory class