more example bug fixes
This commit is contained in:
Steve Plimpton
@ -21,9 +21,9 @@ 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 example commands below illustrate how to run all the variants.
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To use LAMMPS as a plugin engine, you must build it as a shared library.
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Something like this, which also builds the normal LAMMPS executable
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lmp_mpi:
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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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cd src
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make yes-mdi
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@ -33,189 +33,59 @@ To use the serial_driver.py example you will need Python 3 with Numpy
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and mpi4py available in your Python. Make sure LAMMPS and Python are
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using same the same version of MPI.
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5 use-case examples are explained below.
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See the Run.sh file for commands to run each of the examples
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in all the different modes.
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In the first 3 examples, results running with MDI should be identical
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to running without MDI (alone log files). Example #4 has no non-MDI
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run. Example #5 results should match the non-MDI run of example #1.
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-------------------------------------------------
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-------------------------------------------------
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* Example #1 = run ab inito MD (AIMD)
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #1 = run ab initio MD (AIMD)
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See the log aimd files.
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code.
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Note that the 2 input scripts in.aimd.alone and in.aimd.driver
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have an option for running in NVE vs NPT mode. Comment in/out
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the appropriate line to change modes. Nothing needs to be
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changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
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---
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-------------------------------------------------
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-------------------------------------------------
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
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% lmp_mpi -log log.aimd.alone < in.aimd.alone
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See the log snapshot and dump snapshot files.
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With MDI, the thermo output of the driver should match the thermo
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output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code
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-------------------------------------------------
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-------------------------------------------------
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* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #3 = run LAMMPS, compute QM forces on series of independent systems
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---
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files See the log series and dump series files.
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.snapshot.alone < in.snapshot.alone
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With MDI, the thermo output of the driver should match the thermo
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output of the in.snapshot.alone script. Likewise the dump file written
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by the driver should match dump.snapshot.alone.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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LAMMPS is a surrogate for a quantum code
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-------------------------------------------------
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-------------------------------------------------
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* Example #1c = run LAMMPS, compute QM forces on series of independent systems
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
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---
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See the log sequence files.
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.series.alone < in.series.alone
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With MDI, the thermo output of the driver should match the thermo
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output of the in.series.alone script. Likewise the dump files written
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by the driver should match dump.series.alone files.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
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% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
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-------------------------------------------------
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-------------------------------------------------
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* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
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Each calculation can be a single-point evaluation, MD run, or minimization
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Each calculation can be a single-point evaluation, MD run, or
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minimization
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The sequence_driver.py code allows for optional switches in addition
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to -mdi (required) and the -plugin and -plugin_args switches which are
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@ -244,101 +114,21 @@ copied here:
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# -seed 12345
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# random number seed > 0, default = 12345
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---
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Run with TCP: 1 proc each
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% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
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---
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Run with TCP: 2 proc + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence.python
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---
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Run with MPI: 2 procs + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence -in in.sequence.python
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---
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Run in plugin mode: 1 proc
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% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
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-------------------------------------------------
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-------------------------------------------------
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* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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First LAMMPS instance performs the MD timestepping
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Second LAMMPS instance is surrogate QM = computes forces
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* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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See the log aimdpy files.
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First LAMMPS instance performs the MD timestepping. Second LAMMPS
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instance is surrogate QM to compute forces.
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The aimd_driver.py code allows for an optional switch in addition to
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-mdi (required) and the -plugin and -plugin_args swiches which are
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used to link to the 2 engines as a plugin libraries. The example run
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commands below use the default values of the optional switch. The
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switch is also explained the top of the file; the info is copied
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here:
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switch is also explained the top of the file; the info is copied here:
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# -nsteps 5
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# number of timesteps in dynamics runs, default = 5
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---
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi -log log.aimd.alone < in.aimd.alone
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With MDI, the driver prints the QM and Total energies. These should
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match the PotEng and TotEng output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with TCP: 2 procs + 2 procs + 3 procs
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% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
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---
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Run with MPI: 2 procs + 2 procs + 3 procs
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% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
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256
examples/mdi/Run.sh
Normal file
256
examples/mdi/Run.sh
Normal file
@ -0,0 +1,256 @@
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# Run all the examples
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# -------------------------------------------------
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# -------------------------------------------------
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# Example 1
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# ---
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# Run without MDI
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lmp_mpi -log log.aimd.alone.1 < in.aimd.alone
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# ---
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# Run with TCP: 1 proc each
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lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver &
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lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine
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# ---
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# Run with TCP: 3 procs + 4 procs
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver &
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mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine
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# ---
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# Run with MPI: 1 proc each
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mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine
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# ---
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# Run with MPI: 3 procs + 4 procs
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine
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# ---
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# Run in plugin mode: 1 proc
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lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin
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mv log.aimd.engine.plugin log.aimd.engine.plugin.1
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# ---
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# Run in plugin mode: 3 procs
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin
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mv log.aimd.engine.plugin log.aimd.engine.plugin.3
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# -------------------------------------------------
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# -------------------------------------------------
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# Example 2
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# ---
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# Run without MDI
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lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone
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mv dump.snapshot.alone dump.snapshot.alone.1
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# ---
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# Run with TCP: 1 proc each
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lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver &
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||||
|
||||
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.tcp.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.tcp.3
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.mpi.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine
|
||||
mv dump.snapshot.driver dump.snapshot.driver.mpi.3
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin
|
||||
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1
|
||||
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin
|
||||
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3
|
||||
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 3
|
||||
|
||||
# ---
|
||||
|
||||
# Run without MDI
|
||||
|
||||
lmp_mpi -log log.series.alone.1 < in.series.alone
|
||||
mv dump.series.alone dump.series.alone.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver &
|
||||
|
||||
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.tcp.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.tcp.3
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.mpi.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 3 procs + 4 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine
|
||||
mv dump.series.driver dump.series.driver.mpi.3
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin
|
||||
mv log.series.engine.plugin log.series.engine.plugin.1
|
||||
mv dump.series.driver.plugin dump.series.driver.plugin.1
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin
|
||||
mv log.series.engine.plugin log.series.engine.plugin.3
|
||||
mv dump.series.driver.plugin dump.series.driver.plugin.3
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 4
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 2 proc + 4 procs
|
||||
|
||||
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||
|
||||
mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 2 procs + 4 procs
|
||||
|
||||
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 1 proc
|
||||
|
||||
python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python
|
||||
|
||||
# ---
|
||||
|
||||
# Run in plugin mode: 3 procs
|
||||
|
||||
mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python
|
||||
|
||||
# -------------------------------------------------
|
||||
# -------------------------------------------------
|
||||
|
||||
# Example 5
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 1 proc each
|
||||
|
||||
python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimd.mm &
|
||||
|
||||
lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimd.qm
|
||||
|
||||
# ---
|
||||
|
||||
# Run with TCP: 2 procs + 2 procs + 3 procs
|
||||
|
||||
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" &
|
||||
|
||||
mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm.tcp.2 -in in.aimd.mm &
|
||||
|
||||
mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm.tcp.3 -in in.aimd.qm
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.1 -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.qm.1 -in in.aimd.qm
|
||||
|
||||
# ---
|
||||
|
||||
# Run with MPI: 2 procs + 2 procs + 3 procs
|
||||
|
||||
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.2 -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.mpi.3 -in in.aimd.qm
|
||||
@ -19,3 +19,4 @@ fix 1 all nve
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
|
||||
|
||||
@ -4,7 +4,6 @@ variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable ifile loop 3
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
@ -32,12 +31,11 @@ label LOOP
|
||||
|
||||
run 0
|
||||
|
||||
write_dump all custom dump.series.alone.${ifile} &
|
||||
id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.alone &
|
||||
id type x y z fx fy fz modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next ifile
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
@ -4,10 +4,9 @@ variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable ifile loop 3
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
mdi start
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
@ -25,24 +24,20 @@ label LOOP
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm add no virial yes external yes
|
||||
fix 1 all mdi/qm add no virial yes connect no
|
||||
variable epress equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||
|
||||
thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3]
|
||||
|
||||
run 0
|
||||
|
||||
write_dump all custom dump.series.driver.${ifile} &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
|
||||
write_dump all custom dump.series.driver &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
# cannot do "clear" b/c will shutdown MDI engine
|
||||
# have to
|
||||
|
||||
clear
|
||||
|
||||
next ifile
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi stop
|
||||
mdi exit
|
||||
|
||||
@ -4,7 +4,6 @@ variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
variable ifile loop 3
|
||||
variable rho index 0.7 0.8 0.9
|
||||
|
||||
label LOOP
|
||||
@ -33,12 +32,11 @@ label LOOP
|
||||
extra "-log log.series.engine.plugin" &
|
||||
command "run 0"
|
||||
|
||||
write_dump all custom dump.series.driver.${ifile} &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
|
||||
write_dump all custom dump.series.driver.plugin &
|
||||
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||
|
||||
clear
|
||||
|
||||
next ifile
|
||||
next rho
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
@ -32,7 +32,7 @@ thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all custom 500 dump.snapshot.driver &
|
||||
dump 1 all custom 500 dump.snapshot.driver.plugin &
|
||||
id type x y z f_2[1] f_2[2] f_2[3]
|
||||
dump_modify 1 sort id
|
||||
|
||||
|
||||
@ -1,90 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 505739.085 tau/day, 1170.692 timesteps/s
|
||||
73.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
|
||||
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
|
||||
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
|
||||
Other | | 6.054e-05 | | | 1.42
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 731582.413 tau/day, 1693.478 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43
|
||||
Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58
|
||||
Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98
|
||||
Other | | 3e-05 | | | 1.02
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 684416.574 tau/day, 1584.298 timesteps/s
|
||||
99.5% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17
|
||||
Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92
|
||||
Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88
|
||||
Other | | 0.0001272 | | | 4.03
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,80 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 544685.246 tau/day, 1260.845 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40
|
||||
Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91
|
||||
Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89
|
||||
Other | | 3.184e-05 | | | 0.80
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,80 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 752045.581 tau/day, 1740.846 timesteps/s
|
||||
99.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36
|
||||
Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21
|
||||
Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42
|
||||
Other | | 8.637e-05 | | | 3.01
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1792.736 tau/day, 4.150 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00
|
||||
Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02
|
||||
Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97
|
||||
Other | | 6.184e-05 | | | 0.01
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1800.259 tau/day, 4.167 timesteps/s
|
||||
66.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.604e-06 | 4.8462e-05 | 7.527e-05 | 0.0 | 0.00
|
||||
Output | 0.00015266 | 0.00020593 | 0.00031177 | 0.0 | 0.02
|
||||
Modify | 1.1993 | 1.1994 | 1.1994 | 0.0 | 99.96
|
||||
Other | | 0.0002123 | | | 0.02
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
@ -1,5 +0,0 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
@ -1,5 +0,0 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
@ -1,6 +0,0 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
@ -1,6 +0,0 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
@ -1,55 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
@ -1,3 +0,0 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
3 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -1,89 +0,0 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
@ -48,7 +48,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
virialflag = 0;
|
||||
addflag = 1;
|
||||
every = 1;
|
||||
extflag = 0;
|
||||
connectflag = 1;
|
||||
|
||||
int iarg = 3;
|
||||
while (iarg < narg) {
|
||||
@ -69,10 +69,10 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
every = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||
if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"external") == 0) {
|
||||
} else if (strcmp(arg[iarg],"connect") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) extflag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) extflag = 0;
|
||||
if (strcmp(arg[iarg+1],"yes") == 0) connectflag = 1;
|
||||
else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0;
|
||||
else error->all(FLERR,"Illegal fix mdi/qm command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal fix mdi/qm command");
|
||||
@ -100,8 +100,8 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
thermo_energy = thermo_virial = 1;
|
||||
}
|
||||
|
||||
// mdicomm will be one-time initialized in init()
|
||||
// cannot be done here for a plugin library, b/c mdi plugin command is later
|
||||
// mdicomm will be initialized in init()
|
||||
// cannot do here for a plugin library, b/c mdi plugin command comes later
|
||||
|
||||
mdicomm = MDI_COMM_NULL;
|
||||
|
||||
@ -143,10 +143,11 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
|
||||
FixMDIQM::~FixMDIQM()
|
||||
{
|
||||
// send exit command to engine if it is a stand-alone code
|
||||
// for plugin, this happens in MDIPlugin::plugin_wrapper()
|
||||
// send exit command to stand-alone engine code
|
||||
// for connnectflag = 0, this is done via "mdi exit" command
|
||||
// for plugin, this is done in MDIPlugin::plugin_wrapper()
|
||||
|
||||
if (!plugin && !extflag) {
|
||||
if (mdicomm != MDI_COMM_NULL && connectflag && !plugin) {
|
||||
int ierr = MDI_Send_command("EXIT", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: EXIT command");
|
||||
}
|
||||
@ -176,31 +177,47 @@ int FixMDIQM::setmask()
|
||||
|
||||
void FixMDIQM::init()
|
||||
{
|
||||
// one-time auto-detect whether engine is stand-alone code or plugin library
|
||||
// also initializes mdicomm
|
||||
// set plugin = 0/1 for engine = stand-alone code vs plugin library
|
||||
|
||||
if (!extflag) {
|
||||
// set local mdicomm one-time only
|
||||
// also set plugin = 0/1 for engine = stand-alone code vs plugin library
|
||||
|
||||
if (mdicomm == MDI_COMM_NULL) {
|
||||
MDI_Get_communicator(&mdicomm, 0);
|
||||
if (mdicomm == MDI_COMM_NULL) {
|
||||
plugin = 0;
|
||||
MDI_Accept_communicator(&mdicomm);
|
||||
if (mdicomm == MDI_COMM_NULL)
|
||||
error->all(FLERR, "MDI unable to connect to stand-alone engine");
|
||||
} else {
|
||||
plugin = 1;
|
||||
int method;
|
||||
MDI_Get_method(&method, mdicomm);
|
||||
if (method != MDI_PLUGIN)
|
||||
error->all(FLERR, "MDI internal error for plugin engine");
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
plugin = 0;
|
||||
mdicomm = lmp->mdicomm;
|
||||
// this fix makes one-time connection to engine
|
||||
|
||||
if (connectflag) {
|
||||
|
||||
// if MDI's mdicomm not set, need to Accept_comm() with stand-alone engine
|
||||
// othewise are already connected to plugin engine
|
||||
|
||||
MDI_Get_communicator(&mdicomm, 0);
|
||||
|
||||
if (mdicomm == MDI_COMM_NULL) {
|
||||
plugin = 0;
|
||||
MDI_Accept_communicator(&mdicomm);
|
||||
if (mdicomm == MDI_COMM_NULL)
|
||||
error->all(FLERR, "MDI unable to connect to stand-alone engine");
|
||||
|
||||
} else {
|
||||
plugin = 1;
|
||||
int method;
|
||||
MDI_Get_method(&method, mdicomm);
|
||||
if (method != MDI_PLUGIN)
|
||||
error->all(FLERR, "MDI internal error for plugin engine");
|
||||
}
|
||||
|
||||
// connection should have been already made by "mdi connect" command
|
||||
// only works for stand-alone engines
|
||||
|
||||
} else {
|
||||
plugin = 0;
|
||||
|
||||
if (lmp->mdicomm == nullptr)
|
||||
error->all(FLERR,"Fix mdi/qm is not connected to engine via mdi connect");
|
||||
|
||||
int nbytes = sizeof(MDI_Comm);
|
||||
char *ptrcomm = (char *) lmp->mdicomm;
|
||||
memcpy(&mdicomm,ptrcomm,nbytes);
|
||||
}
|
||||
}
|
||||
|
||||
// send natoms, atom types, and simulation box to engine
|
||||
|
||||
@ -40,7 +40,7 @@ class FixMDIQM : public Fix {
|
||||
|
||||
private:
|
||||
int nprocs;
|
||||
int virialflag,addflag,extflag,every;
|
||||
int every,virialflag,addflag,connectflag;
|
||||
int plugin;
|
||||
int maxlocal;
|
||||
int sumflag;
|
||||
|
||||
@ -16,13 +16,19 @@
|
||||
#include "error.h"
|
||||
#include "mdi_engine.h"
|
||||
#include "mdi_plugin.h"
|
||||
#include "memory.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
mdi command: engine or plugin
|
||||
mdi command: engine or plugin or connect or exit
|
||||
engine is used when LAMMPS is an MDI engine, to start listening for requests
|
||||
plugin is used when LAMMPS is an MDI driver to load a plugin library
|
||||
connect and exit are used when LAMMPS is an MDI driver to
|
||||
(a) connect = setup comm with a stand-alone MDI engine
|
||||
(b) exit = terminate comm with a stand-alone MDI engine
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MDICommand::command(int narg, char **arg)
|
||||
@ -35,22 +41,41 @@ void MDICommand::command(int narg, char **arg)
|
||||
} else if (strcmp(arg[0], "plugin") == 0) {
|
||||
MDIPlugin(lmp, narg - 1, &arg[1]);
|
||||
|
||||
} else if (strcmp(arg[0], "start") == 0) {
|
||||
} else if (strcmp(arg[0], "connect") == 0) {
|
||||
|
||||
if (lmp->mdicomm != nullptr)
|
||||
error->all(FLERR,"MDI cannot connect to already connected engine");
|
||||
|
||||
MDI_Comm mdicomm;
|
||||
MDI_Get_communicator(&mdicomm, 0);
|
||||
|
||||
if (mdicomm == MDI_COMM_NULL) {
|
||||
MDI_Accept_communicator(&mdicomm);
|
||||
if (mdicomm == MDI_COMM_NULL)
|
||||
error->all(FLERR, "MDI unable to connect to stand-alone engine");
|
||||
} else error->all(FLERR, "Cannot use mdi start in plugin mode");
|
||||
lmp->mdicomm = mdicomm;
|
||||
} else error->all(FLERR, "Cannot use mdi connect with plugin engine");
|
||||
|
||||
} else if (strcmp(arg[0], "stop") == 0) {
|
||||
int nbytes = sizeof(MDI_Comm);
|
||||
char *ptrcomm = (char *) memory->smalloc(nbytes,"mdi:mdicomm");
|
||||
memcpy(ptrcomm,&mdicomm,nbytes);
|
||||
|
||||
lmp->mdicomm = (void *) ptrcomm;
|
||||
|
||||
} else if (strcmp(arg[0], "exit") == 0) {
|
||||
|
||||
if (lmp->mdicomm == nullptr)
|
||||
error->all(FLERR,"MDI cannot send exit to unconnected engine");
|
||||
|
||||
MDI_Comm mdicomm;
|
||||
int nbytes = sizeof(MDI_Comm);
|
||||
char *ptrcomm = (char *) lmp->mdicomm;
|
||||
memcpy(&mdicomm,ptrcomm,nbytes);
|
||||
|
||||
MDI_Comm mdicomm = lmp->mdicomm;
|
||||
int ierr = MDI_Send_command("EXIT", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: EXIT command");
|
||||
lmp->mdicomm = MDI_COMM_NULL;
|
||||
|
||||
memory->sfree(ptrcomm);
|
||||
lmp->mdicomm = nullptr;
|
||||
|
||||
} else error->all(FLERR, "Illegal mdi command");
|
||||
}
|
||||
|
||||
@ -130,7 +130,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
|
||||
num_ver = utils::date2num(version);
|
||||
|
||||
external_comm = 0;
|
||||
mdicomm = 0;
|
||||
mdicomm = nullptr;
|
||||
|
||||
skiprunflag = 0;
|
||||
|
||||
|
||||
@ -69,7 +69,7 @@ class LAMMPS {
|
||||
// when multiple programs launched by mpirun
|
||||
// set by -mpicolor command line arg
|
||||
|
||||
int mdicomm; // for use with MDI code coupling library
|
||||
void *mdicomm; // for use with MDI code coupling library
|
||||
|
||||
const char *match_style(const char *style, const char *name);
|
||||
static const char *installed_packages[];
|
||||
|
||||
Reference in New Issue
Block a user