mirror of https://github.com/lammps/lammps.git
fix URLs to documentation files
This commit is contained in:
Axel Kohlmeyer
parent
0a30398d1f
commit
2ed11f55d6
|
|
@ -11,11 +11,11 @@ library.
|
|||
|
||||
See these sections of the LAMMPS manual for details:
|
||||
|
||||
Build LAMMPS as a library (doc/Build_basics.html)
|
||||
Link LAMMPS as a library to another code (doc/Build_link.html)
|
||||
Coupling LAMMPS to other codes (doc/Howto_couple.html)
|
||||
Using LAMMPS in client/server mode (doc/Howto_client_server.html)
|
||||
Library interface to LAMMPS (doc/Howto_library.html)
|
||||
Build LAMMPS as a library (doc/html/Build_basics.html)
|
||||
Link LAMMPS as a library to another code (doc/html/Build_link.html)
|
||||
Coupling LAMMPS to other codes (doc/html/Howto_couple.html)
|
||||
Using LAMMPS in client/server mode (doc/html/Howto_client_server.html)
|
||||
Library interface to LAMMPS (doc/html/Howto_library.html)
|
||||
|
||||
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
|
||||
|
|
@ -25,23 +25,23 @@ LAMMPS tasks desired.
|
|||
|
||||
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
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
plugin example for loading LAMMPS at runtime from a shared library
|
||||
lammps_mc client/server coupling of Monte Carlo client
|
||||
with LAMMPS server for energy evaluation
|
||||
lammps_nwchem client/server coupling of LAMMPS client with
|
||||
NWChem quantum DFT as server for quantum forces
|
||||
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_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
lammps_vasp client/server coupling of LAMMPS client with
|
||||
VASP quantum DFT as server for quantum forces
|
||||
library collection of useful inter-code communication routines
|
||||
library collection of useful inter-code communication routines
|
||||
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
|
||||
can be called from Fortran
|
||||
can be called from Fortran
|
||||
fortran_dftb wrapper written by Nir Goldman (LLNL), as an
|
||||
extension to fortran2, used for calling LAMMPS
|
||||
from Fortran DFTB+ tight-binding code
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
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.
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message 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
|
||||
|
|
@ -94,18 +94,18 @@ 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 lmp_mpi -v mode file -in in.mc.server
|
||||
|
||||
% 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:
|
||||
|
||||
% 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 4 lmp_mpi -v mode zmq < in.mc.server
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -in in.mc.server
|
||||
|
||||
--------------
|
||||
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
Sample LAMMPS MD wrapper on NWChem 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
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
|
||||
|
|
@ -182,16 +182,16 @@ background.
|
|||
|
||||
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
|
||||
|
||||
% 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
|
||||
|
||||
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
|
||||
|
||||
% 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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
grains).
|
||||
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
|
||||
After editing the Makefile, lmppath.h, and spkpath.h to make them
|
||||
suitable for your box, type:
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
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
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
|
||||
|
|
@ -134,16 +134,16 @@ background.
|
|||
|
||||
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
|
||||
|
||||
% 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
|
||||
|
||||
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
|
||||
|
||||
% 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
|
||||
|
|
|
|||
|
|
@ -179,7 +179,7 @@ the same simulation in different unit systems.
|
|||
|
||||
The USER directory contains subdirectories of user-provided example
|
||||
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.
|
||||
|
||||
The VISCOSITY directory has example scripts for computing the
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ In a separate terminal, then, you should run LAMMPS compiled to provide
|
|||
fix_ipi functionalities.
|
||||
|
||||
```bash
|
||||
$LAMMPS < in.graphene
|
||||
$LAMMPS -in in.graphene
|
||||
```
|
||||
|
||||
You can run multiple instances of LAMMPS if you want to exploit the
|
||||
|
|
|
|||
|
|
@ -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
|
||||
examples/COUPLE/lammps_vasp.
|
||||
|
||||
See the doc pages for the "MESSAGE package"
|
||||
(Package_details.html#PKG-MESSAGE) and "Howto client/server"
|
||||
(Howto_client_server.html) for more details on how client/server
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
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.
|
||||
|
||||
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.
|
||||
|
||||
--------------
|
||||
|
|
@ -38,8 +37,8 @@ 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
|
||||
% lmp_serial -in in.message
|
||||
% mpirun -np 4 lmp_mpi -in in.message
|
||||
|
||||
Or run with in.message.tilt.
|
||||
|
||||
|
|
@ -87,14 +86,14 @@ runs listed below.
|
|||
|
||||
File or ZMQ or mpi/two modes of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
|
||||
% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
|
||||
% mpirun -np 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 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 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 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
|
||||
% 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 in.message.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
Don't run the tilt files with the "file" mode; they run too slow.
|
||||
|
|
|
|||
Loading…
Reference in New Issue