diff --git a/examples/COUPLE/README b/examples/COUPLE/README index 5a9f297b0f..a7053ade2f 100644 --- a/examples/COUPLE/README +++ b/examples/COUPLE/README @@ -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 diff --git a/examples/COUPLE/lammps_mc/README b/examples/COUPLE/lammps_mc/README index c201a6351c..4aed39dc8e 100644 --- a/examples/COUPLE/lammps_mc/README +++ b/examples/COUPLE/lammps_mc/README @@ -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 -------------- diff --git a/examples/COUPLE/lammps_nwchem/README b/examples/COUPLE/lammps_nwchem/README index cb5c5b58cf..fc0f0cf868 100644 --- a/examples/COUPLE/lammps_nwchem/README +++ b/examples/COUPLE/lammps_nwchem/README @@ -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 diff --git a/examples/COUPLE/lammps_spparks/README b/examples/COUPLE/lammps_spparks/README index fc31de5f0b..c8365ae8e8 100644 --- a/examples/COUPLE/lammps_spparks/README +++ b/examples/COUPLE/lammps_spparks/README @@ -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: diff --git a/examples/COUPLE/lammps_vasp/README b/examples/COUPLE/lammps_vasp/README index e942d52535..d81a5326e6 100644 --- a/examples/COUPLE/lammps_vasp/README +++ b/examples/COUPLE/lammps_vasp/README @@ -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 diff --git a/examples/README b/examples/README index 2ec7dc7a82..7eaa63bbd1 100644 --- a/examples/README +++ b/examples/README @@ -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 diff --git a/examples/USER/misc/ipi/README b/examples/USER/misc/ipi/README index c3ecdea88d..d093cea4c5 100644 --- a/examples/USER/misc/ipi/README +++ b/examples/USER/misc/ipi/README @@ -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 diff --git a/examples/message/README b/examples/message/README index 6cd99d5c09..6db735803e 100644 --- a/examples/message/README +++ b/examples/message/README @@ -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.