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fix URLs to documentation files

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This commit is contained in:
Axel Kohlmeyer
2020-10-21 11:12:13 -04:00
parent 0a30398d1f
commit 2ed11f55d6
8 changed files with 50 additions and 51 deletions
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10
examples/COUPLE/README
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@ -11,11 +11,11 @@ library.
See these sections of the LAMMPS manual for details: See these sections of the LAMMPS manual for details:
Build LAMMPS as a library (doc/Build_basics.html) Build LAMMPS as a library (doc/html/Build_basics.html)
Link LAMMPS as a library to another code (doc/Build_link.html) Link LAMMPS as a library to another code (doc/html/Build_link.html)
Coupling LAMMPS to other codes (doc/Howto_couple.html) Coupling LAMMPS to other codes (doc/html/Howto_couple.html)
Using LAMMPS in client/server mode (doc/Howto_client_server.html) Using LAMMPS in client/server mode (doc/html/Howto_client_server.html)
Library interface to LAMMPS (doc/Howto_library.html) Library interface to LAMMPS (doc/html/Howto_library.html)
The library interface to LAMMPS is in src/library.cpp. Routines can The library interface to LAMMPS is in src/library.cpp. Routines can
be easily added to this file so an external program can perform the be easily added to this file so an external program can perform the

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examples/COUPLE/lammps_mc/README
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@ -1,8 +1,8 @@
Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) See the MESSAGE package documentation Build_extras.html#message
and Section_howto.html#howto10 for more details on how and Build_extras.html#message for more details on how client/server
client/server coupling works in LAMMPS. coupling works in LAMMPS.
In this dir, the mc.cpp/h files are a standalone "client" MC code. It 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 should be run on a single processor, though it could become a parallel
@ -94,18 +94,18 @@ background.
File mode of messaging: File mode of messaging:
% mpirun -np 1 mc in.mc file tmp.couple % mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 1 lmp_mpi -v mode file < in.mc.server % mpirun -np 1 lmp_mpi -v mode file -in in.mc.server
% mpirun -np 1 mc in.mc file tmp.couple % mpirun -np 1 mc in.mc file tmp.couple
% mpirun -np 4 lmp_mpi -v mode file < in.mc.server % mpirun -np 4 lmp_mpi -v mode file -in in.mc.server
ZMQ mode of messaging: ZMQ mode of messaging:
% mpirun -np 1 mc in.mc zmq localhost:5555 % mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server % mpirun -np 1 lmp_mpi -v mode zmq -in in.mc.server
% mpirun -np 1 mc in.mc zmq localhost:5555 % mpirun -np 1 mc in.mc zmq localhost:5555
% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server % mpirun -np 4 lmp_mpi -v mode zmq -in in.mc.server
-------------- --------------

12
examples/COUPLE/lammps_nwchem/README
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@ -1,7 +1,7 @@
Sample LAMMPS MD wrapper on NWChem via client/server coupling Sample LAMMPS MD wrapper on NWChem via client/server coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and See the MESSAGE package documentation Build_extras.html#message
Section_howto.html#howto10 for more details on how client/server and Build_extras.html#message for more details on how client/server
coupling works in LAMMPS. coupling works in LAMMPS.
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
@ -182,16 +182,16 @@ background.
File mode of messaging: File mode of messaging:
% mpirun -np 1 lmp_mpi -v mode file < in.client.W % mpirun -np 1 lmp_mpi -v mode file -in in.client.W
% python nwchem_wrap.py file pw w.nw % python nwchem_wrap.py file pw w.nw
% mpirun -np 2 lmp_mpi -v mode file < in.client.h2o % mpirun -np 2 lmp_mpi -v mode file -in in.client.h2o
% python nwchem_wrap.py file ao h2o.nw % python nwchem_wrap.py file ao h2o.nw
ZMQ mode of messaging: ZMQ mode of messaging:
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W % mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
% python nwchem_wrap.py zmq pw w.nw % python nwchem_wrap.py zmq pw w.nw
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.h2o % mpirun -np 2 lmp_mpi -v mode zmq -in in.client.h2o
% python nwchem_wrap.py zmq ao h2o.nw % python nwchem_wrap.py zmq ao h2o.nw

12
examples/COUPLE/lammps_vasp/README
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@ -1,8 +1,8 @@
Sample LAMMPS MD wrapper on VASP quantum DFT via client/server Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
coupling coupling
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and See the MESSAGE package documentation Build_extras.html#message
Section_howto.html#howto10 for more details on how client/server and Build_extras.html#message for more details on how client/server
coupling works in LAMMPS. coupling works in LAMMPS.
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
@ -134,16 +134,16 @@ background.
File mode of messaging: File mode of messaging:
% mpirun -np 1 lmp_mpi -v mode file < in.client.W % mpirun -np 1 lmp_mpi -v mode file -in in.client.W
% python vasp_wrap.py file POSCAR_W % python vasp_wrap.py file POSCAR_W
% mpirun -np 2 lmp_mpi -v mode file < in.client.W % mpirun -np 2 lmp_mpi -v mode file -in in.client.W
% python vasp_wrap.py file POSCAR_W % python vasp_wrap.py file POSCAR_W
ZMQ mode of messaging: ZMQ mode of messaging:
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W % mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
% python vasp_wrap.py zmq POSCAR_W % python vasp_wrap.py zmq POSCAR_W
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W % mpirun -np 2 lmp_mpi -v mode zmq -in in.client.W
% python vasp_wrap.py zmq POSCAR_W % python vasp_wrap.py zmq POSCAR_W

2
examples/README
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@ -179,7 +179,7 @@ the same simulation in different unit systems.
The USER directory contains subdirectories of user-provided example The USER directory contains subdirectories of user-provided example
scripts for ser packages. See the README files in those directories scripts for ser packages. See the README files in those directories
for more info. See the doc/Section_start.html file for more info for more info. See the doc/html/Build_package.html file for more info
about installing and building user packages. about installing and building user packages.
The VISCOSITY directory has example scripts for computing the The VISCOSITY directory has example scripts for computing the

2
examples/USER/misc/ipi/README
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@ -36,7 +36,7 @@ In a separate terminal, then, you should run LAMMPS compiled to provide
fix_ipi functionalities. fix_ipi functionalities.
```bash ```bash
$LAMMPS < in.graphene $LAMMPS -in in.graphene
``` ```
You can run multiple instances of LAMMPS if you want to exploit the You can run multiple instances of LAMMPS if you want to exploit the

21
examples/message/README
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@ -11,9 +11,8 @@ 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 that ab initio MD could be performed. See an example of the latter in
examples/COUPLE/lammps_vasp. examples/COUPLE/lammps_vasp.
See the doc pages for the "MESSAGE package" See the MESSAGE package documentation Build_extras.html#message
(Package_details.html#PKG-MESSAGE) and "Howto client/server" and Build_extras.html#message for more details on how client/server
(Howto_client_server.html) for more details on how client/server
coupling works in LAMMPS. coupling works in LAMMPS.
-------------- --------------
@ -38,8 +37,8 @@ as illustrated below.
To run this problem in the traditional way (no client/server coupling) To run this problem in the traditional way (no client/server coupling)
do one of these: do one of these:
% lmp_serial < in.message % lmp_serial -in in.message
% mpirun -np 4 lmp_mpi < in.message % mpirun -np 4 lmp_mpi -in in.message
Or run with in.message.tilt. Or run with in.message.tilt.
@ -87,14 +86,14 @@ runs listed below.
File or ZMQ or mpi/two modes of messaging: 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 1 lmp_mpi -v mode file -log log.client -in in.message.client &
% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server % mpirun -np 2 lmp_mpi -v mode file -log log.server -in in.message.server
% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client & % mpirun -np 4 lmp_mpi -v mode zmq -log log.client -in in.message.client &
% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server % mpirun -np 1 lmp_mpi -v mode zmq -log log.server -in in.message.server
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client & % mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client -in in.message.client &
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server % mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server -in in.message.server
Or run with in.message.tilt.client/server. Or run with in.message.tilt.client/server.
Don't run the tilt files with the "file" mode; they run too slow. Don't run the tilt files with the "file" mode; they run too slow.