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couple/README
175
couple/README
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@ -1,10 +1,10 @@
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This directory has examples of how to use LAMMPS as a library, either
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by itself or in tandem with another code or library.
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This directory is meant to illustrate what is possible when coupling
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codes or calling LAMMPS as a library. All of the examples provided
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are just for demonstration purposes. The physics they calculate is
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too simple for modeling a realistic problem.
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These examples is meant to illustrate what is possible when coupling
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codes or calling LAMMPS as a library. The examples are provided for
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demonstration purposes. The physics they calculate is too simple to
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model a realistic problem.
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See these sections of the LAMMPS manaul for details:
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@ -23,7 +23,7 @@ The library interface to LAMMPS is in src/library.cpp. Routines can
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be easily added to this file so an external program can perform the
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LAMMPS tasks desired.
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--------------------------------
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-------------------------------------------------------------------
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These are the sub-directories included in this directory:
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@ -33,167 +33,4 @@ lammps_spparks grain-growth Monte Carlo with strain via MD,
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library collection of useful inter-code communication routines
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simple simple example of driver code calling LAMMPS as library
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--------------------------------
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The "simple" directory has its own README on how to proceed. The
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driver code is provided both in C++ and in C. It simply runs a LAMMPS
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simulation, extracts atom coordinates, changes a coordinate, passes
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the coordinates back to LAMMPS, and runs some more.
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--------------------------------
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The "library" directory has a small collection of routines, useful for
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exchanging data between 2 codes being run together as a coupled
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application. It is used by the LAMMPS <-> Quest and LAMMPS <->
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SPPARKS applications in the other 2 directories.
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The library dir has a Makefile (which you may need to edit for your
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box). If you type
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g++ -f Makefile.g++
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you should create libcouple.a, which the other coupled applications
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link to.
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Note that the library uses MPI, so the Makefile you use needs to
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include a path to the MPI include file, if it is not someplace
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the compiler will find it.
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--------------------------------
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The "lammps_quest" directory has an application that runs classical MD
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via LAMMPS, but uses quantum forces calculated by the Quest DFT
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(density functional) code in place of the usual classical MD forces
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calculated by a pair style in LAMMPS.
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lmpqst.cpp main program
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it links LAMMPS as a library
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it invokes Quest as an executable
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in.lammps LAMMPS input script, without the run command
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si_111.in Quest input script for an 8-atom Si unit cell
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lmppath.h contains path to LAMMPS home directory
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qstexe.h contains full pathname to Quest executable
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After editing the Makefile, lmppath.h, and qstexe.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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and you should get the lmpqst executable.
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NOTE: To run this coupled application, you must of course, have Quest
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built on your system. It's WWW site is http://dft.sandia.gov/Quest.
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It is not an open-source code, buy you can contact its authors to
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obtain a copy.
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You can run lmpqst in serial or parallel as:
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% lmpqst Niter in.lammps in.quest
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% mpirun -np 4 lmpqst Niter in.lammps in.quest
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where
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Niter = # of MD iterations
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in.lammps = LAMMPS input script
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in.quest = Quest input script
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The log files are for this run:
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% lmpqst 10 in.lammps si_111.in
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This application is an example of a coupling where the driver code
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(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
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calling the other code (Quest) as an inner code. Specifically, the
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driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
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loop, and grabs information from the other code (Quest) during its
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timestep. This is done in LAMMPS using the fix external command,
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which makes a "callback" to the driver application (lmpqst), which in
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turn invokes Quest with new atom coordinates, lets Quest compute
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forces, and returns those forces to the LAMMPS fix external.
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The driver code launches LAMMPS in parallel. But Quest is only run on
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a single processor. It would be possible to change this by using a
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parallel build of Quest.
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Since Quest does not currently have a library interface, the driver
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code interfaces with Quest via input and output files.
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Note that essentially 100% of the run time for this coupled
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application is spent in Quest, as the quantum calculation of forces
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dominates the calculation.
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You can look at the log files in the directory to see sample LAMMPS
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output for this simulation. Dump files produced by LAMMPS are stored
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as dump.md.
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--------------------------------
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The "lammps_spparks" directory has an application that models grain
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growth in the presence of strain. The grain growth is simulated by a
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Potts model in a kinetic Monte Carlo code SPPARKS. Clusters of like
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spins on a lattice represent grains. The Hamiltonian for the energy
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due of a collection of spins includes a strain term and is described
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on this page in the SPPARKS documentation:
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http://www.sandia.gov/~sjplimp/spparks/doc/app_potts_strain.html. The
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strain is computed by LAMMPS as a particle displacement where pairs of
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atoms across a grain boundary are of different types and thus push off
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from each other due to a Lennard-Jones sigma between particles of
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different types that is larger than the sigma between particles of the
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same type (interior to grains).
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lmpspk.cpp main program
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it links LAMMPS and SPPARKS as libraries
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in.spparks SPPARKS input script, without the run command
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lmppath.h contains path to LAMMPS home directory
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spkpath.h contains path to SPPARKS home directory
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After editing the Makefile, lmppath.h, and spkpath.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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and you should get the lmpspk executable.
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NOTE: To build and run this coupled application, you must of course,
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have SPPARKS built on your system. It's WWW site is
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http://www.sandia.gov/~sjplimp/spparks.html. It is an open-source
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code, written by two of the LAMMPS authors.
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You can run lmpspk in serial or parallel as:
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% lmpspk Niter Ndelta Sfactor in.spparks
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% mpirun -np 4 lmpspk Niter Ndelta Sfactor in.spparks
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where
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Niter = # of outer iterations
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Ndelta = time to run MC in each iteration
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Sfactor = multiplier on strain effect
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in.spparks = SPPARKS input script
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The log files are for this run:
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% lmpspk 5 10.0 5 in.spparks
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This application is an example of a coupling where the driver code
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(lmpspk) alternates back and forth between the 2 applications (LAMMPS
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and SPPARKS). Each outer timestep in the driver code, the following
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tasks are performed. One code (SPPARKS) is invoked for a few Monte
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Carlo steps. Some of its output (spin state) is passed to the other
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code (LAMMPS) as input (atom type). The the other code (LAMMPS) is
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invoked for a few timesteps. Some of its output (atom coords) is
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massaged to become an input (per-atom strain) for the original code
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(SPPARKS).
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The driver code launches both SPPARKS and LAMMPS in parallel and they
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both decompose their spatial domains in the same manner. The datums
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in SPPARKS (lattice sites) are the same as the datums in LAMMPS
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(coarse-grained particles). If this were not the case, more
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sophisticated inter-code communication could be performed.
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You can look at the log files in the directory to see sample LAMMPS
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and SPPARKS output for this simulation. Dump files produced by the
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run are stored as dump.mc and dump.md. The image*.png files show
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snapshots from both the LAMMPS and SPPARKS output. Note that the
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in.lammps and data.lammps files are not inputs; they are generated by
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the lmpspk driver.
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Each sub-directory has its own README.
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@ -0,0 +1,64 @@
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This directory has an application that runs classical MD via LAMMPS,
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but uses quantum forces calculated by the Quest DFT (density
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functional) code in place of the usual classical MD forces calculated
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by a pair style in LAMMPS.
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lmpqst.cpp main program
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it links LAMMPS as a library
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it invokes Quest as an executable
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in.lammps LAMMPS input script, without the run command
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si_111.in Quest input script for an 8-atom Si unit cell
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lmppath.h contains path to LAMMPS home directory
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qstexe.h contains full pathname to Quest executable
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After editing the Makefile, lmppath.h, and qstexe.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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and you should get the lmpqst executable.
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NOTE: To run this coupled application, you must of course, have Quest
|
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built on your system. It's WWW site is http://dft.sandia.gov/Quest.
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It is not an open-source code, buy you can contact its authors to
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obtain a copy.
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You can run lmpqst in serial or parallel as:
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% lmpqst Niter in.lammps in.quest
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% mpirun -np 4 lmpqst Niter in.lammps in.quest
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where
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Niter = # of MD iterations
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in.lammps = LAMMPS input script
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in.quest = Quest input script
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The log files are for this run:
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% lmpqst 10 in.lammps si_111.in
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This application is an example of a coupling where the driver code
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(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
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calling the other code (Quest) as an inner code. Specifically, the
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driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
|
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loop, and grabs information from the other code (Quest) during its
|
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timestep. This is done in LAMMPS using the fix external command,
|
||||
which makes a "callback" to the driver application (lmpqst), which in
|
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turn invokes Quest with new atom coordinates, lets Quest compute
|
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forces, and returns those forces to the LAMMPS fix external.
|
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|
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The driver code launches LAMMPS in parallel. But Quest is only run on
|
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a single processor. It would be possible to change this by using a
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parallel build of Quest.
|
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|
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Since Quest does not currently have a library interface, the driver
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code interfaces with Quest via input and output files.
|
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|
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Note that essentially 100% of the run time for this coupled
|
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application is spent in Quest, as the quantum calculation of forces
|
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dominates the calculation.
|
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|
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You can look at the log files in the directory to see sample LAMMPS
|
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output for this simulation. Dump files produced by LAMMPS are stored
|
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as dump.md.
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|
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@ -0,0 +1,71 @@
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This directory has an application that models grain growth in the
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presence of strain. The grain growth is simulated by a Potts model in
|
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a kinetic Monte Carlo code SPPARKS. Clusters of like spins on a
|
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lattice represent grains. The Hamiltonian for the energy due of a
|
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collection of spins includes a strain term and is described on this
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page in the SPPARKS documentation:
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http://www.sandia.gov/~sjplimp/spparks/doc/app_potts_strain.html.
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The strain is computed by LAMMPS as a particle displacement where
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pairs of atoms across a grain boundary are of different types and thus
|
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push off from each other due to a Lennard-Jones sigma between
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particles of different types that is larger than the sigma between
|
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particles of the same type (interior to grains).
|
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|
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lmpspk.cpp main program
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it links LAMMPS and SPPARKS as libraries
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in.spparks SPPARKS input script, without the run command
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lmppath.h contains path to LAMMPS home directory
|
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spkpath.h contains path to SPPARKS home directory
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After editing the Makefile, lmppath.h, and spkpath.h to make them
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suitable for your box, type:
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g++ -f Makefile.g++
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and you should get the lmpspk executable.
|
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NOTE: To build and run this coupled application, you must of course,
|
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have SPPARKS built on your system. It's WWW site is
|
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http://www.sandia.gov/~sjplimp/spparks.html. It is an open-source
|
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code, written by two of the LAMMPS authors.
|
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|
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You can run lmpspk in serial or parallel as:
|
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% lmpspk Niter Ndelta Sfactor in.spparks
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% mpirun -np 4 lmpspk Niter Ndelta Sfactor in.spparks
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where
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Niter = # of outer iterations
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Ndelta = time to run MC in each iteration
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Sfactor = multiplier on strain effect
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in.spparks = SPPARKS input script
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The log files are for this run:
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% lmpspk 5 10.0 5 in.spparks
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This application is an example of a coupling where the driver code
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(lmpspk) alternates back and forth between the 2 applications (LAMMPS
|
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and SPPARKS). Each outer timestep in the driver code, the following
|
||||
tasks are performed. One code (SPPARKS) is invoked for a few Monte
|
||||
Carlo steps. Some of its output (spin state) is passed to the other
|
||||
code (LAMMPS) as input (atom type). The the other code (LAMMPS) is
|
||||
invoked for a few timesteps. Some of its output (atom coords) is
|
||||
massaged to become an input (per-atom strain) for the original code
|
||||
(SPPARKS).
|
||||
|
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The driver code launches both SPPARKS and LAMMPS in parallel and they
|
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both decompose their spatial domains in the same manner. The datums
|
||||
in SPPARKS (lattice sites) are the same as the datums in LAMMPS
|
||||
(coarse-grained particles). If this were not the case, more
|
||||
sophisticated inter-code communication could be performed.
|
||||
|
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You can look at the log files in the directory to see sample LAMMPS
|
||||
and SPPARKS output for this simulation. Dump files produced by the
|
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run are stored as dump.mc and dump.md. The image*.png files show
|
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snapshots from both the LAMMPS and SPPARKS output. Note that the
|
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in.lammps and data.lammps files are not inputs; they are generated by
|
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the lmpspk driver.
|
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|
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@ -0,0 +1,16 @@
|
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This directory has a small collection of routines, useful for
|
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exchanging data between 2 codes being run together as a coupled
|
||||
application. It is used by the LAMMPS <-> Quest and LAMMPS <->
|
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SPPARKS applications in 2 sister directories.
|
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|
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The library dir has a Makefile (which you may need to edit for your
|
||||
box). If you type
|
||||
|
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g++ -f Makefile.g++
|
||||
|
||||
you should create libcouple.a, which the other coupled applications
|
||||
link to.
|
||||
|
||||
Note that the library uses MPI, so the Makefile you use needs to
|
||||
include a path to the MPI include file, if it is not someplace
|
||||
the compiler will find it.
|
||||
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