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more doc page updates

This commit is contained in:
Steven J. Plimpton 2018-08-22 11:42:41 -06:00
parent 4e13ce1d25
commit 03b880a31c
8 changed files with 67 additions and 55 deletions
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10
doc/src/Build_extras.txt
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@ -380,9 +380,13 @@ file.
MESSAGE package :h4,link(message)
This package can optionally include support for messaging via sockets,
using the open-source "ZeroMQ library"_http://zeromq.org, which must
be installed on your system.
[CMake build]:
No additional settings are needed besides "-D PKG_MESSAGE=yes".
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
[Traditional make]:
@ -398,8 +402,8 @@ 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.
existing Makefile.lammps.* and has settings to link with the ZeroMQ
library if requested in the build.
:line

2
doc/src/Howto_client_server.txt
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@ -40,7 +40,7 @@ package"_Packages_details.html#PKG-MESSAGE which implements several
commands that enable LAMMPS to act as a client or server, as discussed
below. The MESSAGE package also wraps a client/server library called
CSlib which enables two codes to exchange messages in different ways,
either via files, a socket, or MPI. The CSlib is provided with LAMMPS
either via files, sockets, or MPI. The CSlib is provided with LAMMPS
in the lib/message dir. The CSlib has its own
"website"_http://cslib.sandia.gov with documentation and test
programs.

22
doc/src/fix_client_md.txt
View File

@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html)
:line
@ -25,11 +25,11 @@ 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.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When using this fix, LAMMPS (as the client code) passes the current
coordinates of all particles to the server code each timestep, which
@ -80,9 +80,9 @@ 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".
"output commands"_Howto_output.html. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
@ -91,8 +91,8 @@ 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.
was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with

29
doc/src/message.txt
View File

@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Command_all.html)
:line
@ -44,11 +44,11 @@ message server md mpi/two tmp.couple :pre
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.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
:line
@ -82,9 +82,12 @@ 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.
code's machine. Support for socket messaging is provided by the
open-source "ZeroMQ library"_http://zeromq.org, which must be
installed on your system. The client specifies an IP address (IPv4
format) or the DNS name of the machine the server code is running on,
followed by a 4-digit port ID for the socket, separated by a colon.
E.g.
localhost:5555 # client and server running on same machine
192.168.1.1:5555 # server is 192.168.1.1
@ -106,8 +109,8 @@ mpirun -np 2 lmp_mpi -mpi 2 -in in.client -log log.client : -np 4 othercode args
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.
the "command-line args"_Run_options.html doc page for further
explanation.
For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
be 2 separate mpirun commands. The specified {filename} argument is a
@ -149,8 +152,8 @@ fix client or server command.
[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.
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]

16
doc/src/server.txt
View File

@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html)
:line
@ -26,11 +26,11 @@ 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.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@ -57,8 +57,8 @@ mc"_server_mc.html doc page for details on the protocol.
[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.
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with

20
doc/src/server_mc.txt
View File

@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html)
:line
@ -25,11 +25,11 @@ 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.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@ -101,8 +101,12 @@ cs->send(RUN,0) # msgID = 5 with no fields
[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.
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
A script that uses this command must also use the
"message"_message.html command to setup the messaging protocol with
the other client code.
[Related commands:]

16
doc/src/server_md.txt
View File

@ -2,7 +2,7 @@
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(lc,Commands_all.html)
:line
@ -25,11 +25,11 @@ 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.
The "Howto client/server"_Howto_client_server.html doc page gives an
overview of client/server coupling of LAMMPS with another code where
one code is the "client" and sends request messages to a "server"
code. The server responds to each request with a reply message. This
enables the two codes to work in tandem to perform a simulation.
When this command is invoked, LAMMPS will run in server mode in an
endless loop, waiting for messages from the client code. The client
@ -111,8 +111,8 @@ cs->pack(VIRIAL,6,virial) # global virial tensor (6-vector) :pre
[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.
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
[Related commands:]

7
examples/message/README
View File

@ -11,9 +11,10 @@ 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.
See the doc pages for the "MESSAGE package"
(Package_details.html#PKG-MESSAGE) and "Howto client/server"
(Howto_client_server.html) for more details on how client/server
coupling works in LAMMPS.
--------------