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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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26
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
@ -25,23 +25,23 @@ LAMMPS tasks desired.
These are the sub-directories included in this directory: These are the sub-directories included in this directory:
simple simple example of driver code calling LAMMPS as a lib simple simple example of driver code calling LAMMPS as a lib
multiple example of driver code calling multiple instances of LAMMPS multiple example of driver code calling multiple instances of LAMMPS
plugin example for loading LAMMPS at runtime from a shared library plugin example for loading LAMMPS at runtime from a shared library
lammps_mc client/server coupling of Monte Carlo client lammps_mc client/server coupling of Monte Carlo client
with LAMMPS server for energy evaluation with LAMMPS server for energy evaluation
lammps_nwchem client/server coupling of LAMMPS client with lammps_nwchem client/server coupling of LAMMPS client with
NWChem quantum DFT as server for quantum forces NWChem quantum DFT as server for quantum forces
lammps_quest MD with quantum forces, coupling to Quest DFT code lammps_quest MD with quantum forces, coupling to Quest DFT code
lammps_spparks grain-growth Monte Carlo with strain via MD, lammps_spparks grain-growth Monte Carlo with strain via MD,
coupling to SPPARKS kinetic MC code coupling to SPPARKS kinetic MC code
lammps_vasp client/server coupling of LAMMPS client with lammps_vasp client/server coupling of LAMMPS client with
VASP quantum DFT as server for quantum forces VASP quantum DFT as server for quantum forces
library collection of useful inter-code communication routines library collection of useful inter-code communication routines
fortran a simple wrapper on the LAMMPS library API that fortran a simple wrapper on the LAMMPS library API that
can be called from Fortran can be called from Fortran
fortran2 a more sophisticated wrapper on the LAMMPS library API that fortran2 a more sophisticated wrapper on the LAMMPS library API that
can be called from Fortran can be called from Fortran
fortran_dftb wrapper written by Nir Goldman (LLNL), as an fortran_dftb wrapper written by Nir Goldman (LLNL), as an
extension to fortran2, used for calling LAMMPS extension to fortran2, used for calling LAMMPS
from Fortran DFTB+ tight-binding code from Fortran DFTB+ tight-binding code

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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

10
examples/COUPLE/lammps_spparks/README
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@ -16,11 +16,11 @@ Lennard-Jones sigma between particles of different types that is
larger than the sigma between particles of the same type (interior to larger than the sigma between particles of the same type (interior to
grains). grains).
lmpspk.cpp main program lmpspk.cpp main program
it links LAMMPS and SPPARKS as libraries it links LAMMPS and SPPARKS as libraries
in.spparks SPPARKS input script, without the run command in.spparks SPPARKS input script, without the run command
lmppath.h contains path to LAMMPS home directory lmppath.h contains path to LAMMPS home directory
spkpath.h contains path to SPPARKS home directory spkpath.h contains path to SPPARKS home directory
After editing the Makefile, lmppath.h, and spkpath.h to make them After editing the Makefile, lmppath.h, and spkpath.h to make them
suitable for your box, type: suitable for your box, type:

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

23
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.
-------------- --------------
@ -30,7 +29,7 @@ You can also run the in.message scripts with an NPT integrator
instead of NVE, if you comment/uncomment the correct lines. instead of NVE, if you comment/uncomment the correct lines.
The client and server script define a "mode" variable The client and server script define a "mode" variable
which can be set to file, zmq, mpi/one, or mpi/two, which can be set to file, zmq, mpi/one, or mpi/two,
as illustrated below. as illustrated below.
-------------- --------------
@ -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.