more docs, less debug
This commit is contained in:
Steve Plimpton
78
examples/mdi/LATTE/README
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78
examples/mdi/LATTE/README
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Examples in this directoy use LAMMPS as an MDI driver code and the
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LATTE tight-binding code as an MDI engine to perform ab initio MD and
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evaluate the energy/forces/virial for a series of MD snapshots or
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conformations with LATTE.
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Talk about LATTE package and fix latte command
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---------
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Build LAMMPS with MDI support via the MDI package:
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% cd lammps/lib/mdi
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% python Install.py -m mpi # creates libmdi.a (not shared)
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% cd lammps/src
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% make yes-mdi
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% make mpi # builds LAMMPS with MDI
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---------
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Build LATTE in its own Git repo:
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cd latte/git
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cp makefiles/makefile.CHOICES.mdi makefile.CHOICES
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toggle settings:
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MAKELIB = OFF
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SHARED = ON
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MDI = ON
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for MDI, also need to set MDI_PATH to mdi/git/build/MDI_Library
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also commented out some LIB lines for Cuda
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then just type "make"
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produces exe = LATTE_DOUBLE and libfile = liblatte_mdi.so
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the exe is not the non-MDI LATTE main, but a new one that goes into engine mode
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---------
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copy lmp_mpi and LATTE_DOUBLE into this dir
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set LD_LIB_PATH to ~/latte/git for liblatte_mdi.so file in plugin mode
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LATTE always uses in.latte as input file, contains no element info
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LATTE always uses latte.in
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this version of LATTE does not use MPI, only OpenMP or GPU
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run LATTE with OpenMP: setenv OMP_NUM_THREADS max-core-count
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---------
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Run AIMD test problem:
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build LAMMPS with molecule package
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LAMMPS uses in.mdi.aimd or in.mdi.aimd.plugin
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++ Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
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-log log.aimd.driver.mpi.1 -in in.mdi.aimd : \
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-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
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++ Run in plugin mode: 1 proc
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lmp_mpi -mdi \
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"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
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-log log.aimd.driver.plugin.1 -in in.mdi.aimd.plugin
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---------
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Run sequence of configs:
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++ Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
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-log log.series.driver.mpi.1 -in in.series.driver : \
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-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
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++ Run in plugin mode: 1 proc
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lmp_mpi -mdi \
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"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
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-log log.series.driver.plugin.1 -in in.series.driver.plugin
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@ -2,15 +2,14 @@ These are examples that work the MDI package in LAMMPS which uses the
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MolSSI MDI library for coupling codes together and communicating
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between them with MDI messages.
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Within the MDI context, one code is the driver and another code is
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the engine. The 2 codes can be written in any language; C++ (LAMMPS)
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and Python are illustrated here. The 2 codes can each be stand-alone
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codes, in which case they can be run on different numbers of processors.
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The 2
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codes can communicate either via TCP (sockets) or via MPI. For the
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TCP case, the driver and engine need to be launched separately,
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e.g. in 2 windows on your desktop machine. For the MPI case, a single
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mpirun command launches both codes.
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Within the MDI context, one code is the driver and another code is the
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engine. The 2 codes can be written in any language; C++ (LAMMPS) and
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Python are illustrated here. The 2 codes can each be stand-alone
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codes, in which case they can be run on different numbers of
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processors. The 2 codes can communicate either via TCP (sockets) or
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via MPI. For the TCP case, the driver and engine need to be launched
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separately, e.g. in 2 windows on your desktop machine. For the MPI
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case, a single mpirun command launches both codes.
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Alternatively the engine code can be a plugin library which the driver
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code loads, in which case the driver and engine run on the same
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@ -19,13 +18,19 @@ processors.
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LAMMPS supports operating in all these MDI modes. It can be an engine
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operating either as a stand-alone code or as a plugin. It can also be
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a driver and couple to an engine that is either a stand-alone code or
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a plugin. Examples for all these use cases are in this directory.
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The Run.sh file shows how run in all the modes. Type "sh Run.sh"
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to try them all out.
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a plugin.
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To use LAMMPS as a plugin engine, you must build it as a shared
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library. Something like this with make, which also builds the normal
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LAMMPS executable lmp_mpi:
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Examples for all these use cases, using LAMMPS as a driver and as an
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engine are in this directory. The Run.sh file shows how run in all
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the modes. Type "sh Run.sh" to try them all out.
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Examples for using LAMMPS as a driver with the tight-binding code LATTE
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are in the LATTE sub-directory. See its README file for more info.
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Note that to use LAMMPS as a plugin engine for some the examples in
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this dir, you must build it as a shared library. Something like this
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with traditional make, which also builds the normal LAMMPS executable
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lmp_mpi:
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cd src
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make yes-mdi
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@ -39,9 +44,9 @@ Python/mpi4py are using same the same version of MPI.
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You will also need MDI installed in your Python. You cannot use the
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LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a
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static library, not shared, which Python requires.
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static library, while Python requires a shared library.
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You can install MDI in your Python via conda:
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Instead you can install MDI in your Python via conda:
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% conda install -c conda-forge pymdi=1.4.1
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