dated example files
This commit is contained in:
Steve Plimpton
@ -19,7 +19,8 @@ LAMMPS supports operating in all these MDI modes. It can be an engine
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operating either as a stand-alone code or as a plugin. It can also be
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operating either as a stand-alone code or as a plugin. It can also be
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a driver and couple to an engine that is either a stand-alone code or
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a 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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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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The Run.sh file shows how run in all the modes. Type "sh Run.sh"
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to try them all out.
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To use LAMMPS as a plugin engine, you must build it as a shared
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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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library. Something like this with make, which also builds the normal
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@ -33,10 +34,7 @@ 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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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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using same the same version of MPI.
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5 use-case examples are explained below.
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5 example use-cases 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. Type "sh Run.sh" to run them all.
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In the first 3 examples, results running with MDI should be identical
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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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to running without MDI (alone log files). Example #4 has no non-MDI
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@ -47,43 +45,52 @@ run. Example #5 results should match the non-MDI run of example #1.
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* Example #1 = run ab initio MD (AIMD)
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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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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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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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You can compare the thermo output in log.aimd.alone.1 to the thermo output in
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have an option for running in NVE vs NPT mode. Comment in/out
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any of the log.aimd.driver* files. It should be identical.
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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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Note that the "alone" and "driver" input scripts have options for
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running in NVE vs NPT Comment in/out the appropriate line to make
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change. Nothing needs to be changed in the "engine" scripts.
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
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* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
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See the log snapshot and dump snapshot files.
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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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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LAMMPS is a surrogate for a quantum code
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You can compare the thermo output in log.snapshot.alone.1 to the
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thermo output in any of the log.snapshot.driver* files. It should be
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identical.
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You can compare the dumped forces in dump.snapshot.alone.1 to the
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forces in any of the dump.snapshot.* files. They should be identical,
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although at step 0 the forces are "zero" and may be epsilon different.
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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* Example #3 = run LAMMPS, compute QM forces on series of independent systems
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* Example #3 = run LAMMPS, compute QM forces on series of independent systems
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files See the log series and dump series files.
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Two instances of LAMMPS operate as a driver and engine. As an engine,
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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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LAMMPS is a surrogate for a quantum code
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You can compare the thermo output in log.series.alone.1 to the thermo
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output in any of the log.series.driver* files. It should be
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identical.
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You can compare the dumped forces in dump.series.alone.1 to the forces
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in any of the dump.series.* files. They should be identical,
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
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* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
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See the log sequence files.
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Each calculation can be a single-point evaluation, MD run, or
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Each calculation can be a single-point evaluation, MD run, or
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minimization
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minimization
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@ -114,13 +121,14 @@ copied here:
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# -seed 12345
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# -seed 12345
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# random number seed > 0, default = 12345
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# random number seed > 0, default = 12345
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You can compare the thermo output in any of the log.sequence.engine.*
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files. It should be identical.
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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-------------------------------------------------
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* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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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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First LAMMPS instance performs the MD timestepping. Second LAMMPS
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instance is surrogate QM to compute forces.
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instance is surrogate QM to compute forces.
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@ -132,3 +140,12 @@ switch is also explained the top of the file; the info is copied here:
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# -nsteps 10
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# -nsteps 10
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# number of timesteps in dynamics runs, default = 10
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# number of timesteps in dynamics runs, default = 10
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This calculation is the same as Example #1 with a LAMMPS driver and a
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LAMMPS engine. Now there is a Python driver and two LAMMPS engines.
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You can compare the thermo output in log.aimd.alone.1 output to the
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thermo output is any of the log.sequence.engine.* files. It should be
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identical for the Total Energy printed out by the Python driver script.
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E.g. Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
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@ -81,7 +81,7 @@ mv dump.snapshot.driver dump.snapshot.driver.tcp.1
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver &
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -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.4 -in in.snapshot.engine
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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.4 -in in.snapshot.engine
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mv dump.snapshot.driver dump.snapshot.driver.tcp.3
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mv dump.snapshot.driver dump.snapshot.driver.tcp.4
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# ---
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# ---
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@ -95,7 +95,7 @@ mv dump.snapshot.driver dump.snapshot.driver.mpi.1
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# Run with MPI: 3 procs + 4 procs
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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.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
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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
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mv dump.snapshot.driver dump.snapshot.driver.mpi.3
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mv dump.snapshot.driver dump.snapshot.driver.mpi.4
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# ---
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# ---
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@ -141,7 +141,7 @@ mv dump.series.driver dump.series.driver.tcp.1
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver &
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mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -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.4 -in in.series.engine
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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.4 -in in.series.engine
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mv dump.series.driver dump.series.driver.tcp.3
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mv dump.series.driver dump.series.driver.tcp.4
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# ---
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# ---
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@ -155,7 +155,7 @@ mv dump.series.driver dump.series.driver.mpi.1
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# Run with MPI: 3 procs + 4 procs
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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.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
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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
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mv dump.series.driver dump.series.driver.mpi.3
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mv dump.series.driver dump.series.driver.mpi.4
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# ---
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# ---
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1527
examples/mdi/dump.17Jun22.series.alone.1
Normal file
1527
examples/mdi/dump.17Jun22.series.alone.1
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
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1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.1
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examples/mdi/dump.17Jun22.series.driver.plugin.1
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
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1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
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1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
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File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
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1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.alone.1
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2036
examples/mdi/dump.17Jun22.snapshot.alone.1
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
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2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
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2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
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2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
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2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
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2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
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File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
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File diff suppressed because it is too large
Load Diff
95
examples/mdi/log.17Jun22.aimd.alone.1
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95
examples/mdi/log.17Jun22.aimd.alone.1
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@ -0,0 +1,95 @@
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LAMMPS (2 Jun 2022)
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# 3d Lennard-Jones melt - MDI driver script
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 $x 0 $y 0 $z
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region box block 0 5 0 $y 0 $z
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region box block 0 5 0 5 0 $z
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region box block 0 5 0 5 0 5
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create_box 1 box
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Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 500 atoms
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using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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# NVE
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fix 1 all nve
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# NPT
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#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
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thermo_style custom step temp pe etotal press vol
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thermo 1
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run 10
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
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Step Temp PotEng TotEng Press Volume
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0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
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1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
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2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
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3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
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4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
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5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
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6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
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7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
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8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
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9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
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10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
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Loop time of 0.00919691 on 1 procs for 10 steps with 500 atoms
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Performance: 469723.136 tau/day, 1087.322 timesteps/s
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98.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0066536 | 0.0066536 | 0.0066536 | 0.0 | 72.35
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Neigh | 0.0017906 | 0.0017906 | 0.0017906 | 0.0 | 19.47
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Comm | 0.0002554 | 0.0002554 | 0.0002554 | 0.0 | 2.78
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Output | 0.00029976 | 0.00029976 | 0.00029976 | 0.0 | 3.26
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Modify | 9.8718e-05 | 9.8718e-05 | 9.8718e-05 | 0.0 | 1.07
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Other | | 9.887e-05 | | | 1.08
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Nlocal: 500 ave 500 max 500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1956 ave 1956 max 1956 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 19396 ave 19396 max 19396 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 19396
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Ave neighs/atom = 38.792
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:00
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83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
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@ -0,0 +1,83 @@
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LAMMPS (2 Jun 2022)
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# 3d Lennard-Jones melt - MDI driver script
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variable x index 5
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variable y index 5
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variable z index 5
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units lj
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atom_style atomic
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lattice fcc 0.8442
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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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.0078442 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 550725.026 tau/day, 1274.826 timesteps/s
|
||||||
|
99.4% 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 | 1.592e-06 | 1.592e-06 | 1.592e-06 | 0.0 | 0.02
|
||||||
|
Comm | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.34
|
||||||
|
Output | 0.00021168 | 0.00021168 | 0.00021168 | 0.0 | 2.70
|
||||||
|
Modify | 0.0075488 | 0.0075488 | 0.0075488 | 0.0 | 96.23
|
||||||
|
Other | | 5.544e-05 | | | 0.71
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00523112 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 825827.658 tau/day, 1911.638 timesteps/s
|
||||||
|
98.8% 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 | 5.95e-07 | 1.7073e-06 | 3.907e-06 | 0.0 | 0.03
|
||||||
|
Comm | 3.8259e-05 | 6.2707e-05 | 7.5974e-05 | 0.0 | 1.20
|
||||||
|
Output | 0.00017543 | 0.00021238 | 0.00028075 | 0.0 | 4.06
|
||||||
|
Modify | 0.004815 | 0.0048289 | 0.0048521 | 0.0 | 92.31
|
||||||
|
Other | | 0.0001254 | | | 2.40
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
LAMMPS (2 Jun 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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00940117 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 459517.175 tau/day, 1063.697 timesteps/s
|
||||||
|
96.1% 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 | 1.9e-06 | 1.9e-06 | 1.9e-06 | 0.0 | 0.02
|
||||||
|
Comm | 3.0131e-05 | 3.0131e-05 | 3.0131e-05 | 0.0 | 0.32
|
||||||
|
Output | 0.00030359 | 0.00030359 | 0.00030359 | 0.0 | 3.23
|
||||||
|
Modify | 0.0090041 | 0.0090041 | 0.0090041 | 0.0 | 95.78
|
||||||
|
Other | | 6.144e-05 | | | 0.65
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
LAMMPS (2 Jun 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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00613177 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 704527.327 tau/day, 1630.850 timesteps/s
|
||||||
|
99.2% 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 | 7.93e-07 | 1.8723e-06 | 3.996e-06 | 0.0 | 0.03
|
||||||
|
Comm | 4.4254e-05 | 7.4628e-05 | 9.321e-05 | 0.0 | 1.22
|
||||||
|
Output | 0.00019476 | 0.00024309 | 0.00032745 | 0.0 | 3.96
|
||||||
|
Modify | 0.005637 | 0.0056559 | 0.0056903 | 0.0 | 92.24
|
||||||
|
Other | | 0.0001563 | | | 2.55
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 2.41182 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1791.180 tau/day, 4.146 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 | 2.596e-06 | 2.596e-06 | 2.596e-06 | 0.0 | 0.00
|
||||||
|
Comm | 4.9627e-05 | 4.9627e-05 | 4.9627e-05 | 0.0 | 0.00
|
||||||
|
Output | 0.00063707 | 0.00063707 | 0.00063707 | 0.0 | 0.03
|
||||||
|
Modify | 2.411 | 2.411 | 2.411 | 0.0 | 99.97
|
||||||
|
Other | | 0.0001146 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 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/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 2.39983 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1800.127 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 | 3.75e-07 | 1.3583e-06 | 2.574e-06 | 0.0 | 0.00
|
||||||
|
Comm | 5.4167e-05 | 0.00010938 | 0.00015338 | 0.0 | 0.00
|
||||||
|
Output | 0.00030885 | 0.00042099 | 0.00064497 | 0.0 | 0.02
|
||||||
|
Modify | 2.3988 | 2.3989 | 2.3989 | 0.0 | 99.96
|
||||||
|
Other | | 0.0004276 | | | 0.02
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:02
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:02
|
||||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
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
|
||||||
|
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||||
|
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 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
|
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
|
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 2 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
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
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
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
|
||||||
|
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||||
|
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 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
|
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
|
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
Total wall time: 0:00:00
|
||||||
11
examples/mdi/log.17Jun22.aimdpy.driver.tcp.1
Normal file
11
examples/mdi/log.17Jun22.aimdpy.driver.tcp.1
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
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
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
11
examples/mdi/log.17Jun22.aimdpy.driver.tcp.2
Normal file
11
examples/mdi/log.17Jun22.aimdpy.driver.tcp.2
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
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
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 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:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 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 = 0.000 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:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 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:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:02
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 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:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
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
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:02
|
||||||
60
examples/mdi/log.17Jun22.aimdpy.qm.mpi.1
Normal file
60
examples/mdi/log.17Jun22.aimdpy.qm.mpi.1
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
LAMMPS (2 Jun 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 = 0.000 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
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:00
|
||||||
60
examples/mdi/log.17Jun22.aimdpy.qm.mpi.3
Normal file
60
examples/mdi/log.17Jun22.aimdpy.qm.mpi.3
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:00
|
||||||
60
examples/mdi/log.17Jun22.aimdpy.qm.tcp.1
Normal file
60
examples/mdi/log.17Jun22.aimdpy.qm.tcp.1
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:02
|
||||||
60
examples/mdi/log.17Jun22.aimdpy.qm.tcp.3
Normal file
60
examples/mdi/log.17Jun22.aimdpy.qm.tcp.3
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:02
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
@ -0,0 +1,248 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 2.729e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
109.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.729e-06 | | |100.00
|
||||||
|
|
||||||
|
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: 15687 ave 15687 max 15687 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 15687
|
||||||
|
Ave neighs/atom = 31.374
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.135 | 3.135 | 3.135 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.434e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
139.5% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.434e-06 | | |100.00
|
||||||
|
|
||||||
|
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: 18734 ave 18734 max 18734 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18734
|
||||||
|
Ave neighs/atom = 37.468
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
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) = 3.134 | 3.134 | 3.134 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.483e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
134.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.483e-06 | | |100.00
|
||||||
|
|
||||||
|
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: 20023 ave 20023 max 20023 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 20023
|
||||||
|
Ave neighs/atom = 40.046
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 1.919e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
0.0% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.919e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.141e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
87.6% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.141e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.002 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.019e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
98.1% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.019e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 4.00933e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
91.5% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 4.009e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.11833e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
117.6% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.118e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.85467e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
140.1% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.855e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
@ -0,0 +1,212 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 2.359e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
127.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.359e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.468e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
204.4% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.468e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.378e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
145.1% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.378e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
@ -0,0 +1,212 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 3.50867e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
114.0% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.509e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.225e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
82.7% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.225e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.713e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
98.3% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.713e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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 rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 3.017e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
99.4% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.017e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.977e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
101.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.977e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.042e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
97.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.042e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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 = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 9.08933e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
95.3% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 9.089e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.63567e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
100.9% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.636e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 3.806e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
105.1% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.806e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
42
examples/mdi/log.17Jun22.series.engine.plugin.1
Normal file
42
examples/mdi/log.17Jun22.series.engine.plugin.1
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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) = 3.134 | 3.134 | 3.134 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
42
examples/mdi/log.17Jun22.series.engine.plugin.3
Normal file
42
examples/mdi/log.17Jun22.series.engine.plugin.3
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
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) = 3.104 | 3.105 | 3.107 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.tcp.1
Normal file
58
examples/mdi/log.17Jun22.series.engine.tcp.1
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.tcp.4
Normal file
58
examples/mdi/log.17Jun22.series.engine.tcp.4
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 = 7 7 7
|
||||||
|
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) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
82
examples/mdi/log.17Jun22.snapshot.alone.1
Normal file
82
examples/mdi/log.17Jun22.snapshot.alone.1
Normal file
@ -0,0 +1,82 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.alone id type x y z fx fy fz
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300
|
||||||
|
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) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.159268 on 1 procs for 300 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 813725.152 tau/day, 1883.623 timesteps/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.10659 | 0.10659 | 0.10659 | 0.0 | 66.93
|
||||||
|
Neigh | 0.038637 | 0.038637 | 0.038637 | 0.0 | 24.26
|
||||||
|
Comm | 0.0053144 | 0.0053144 | 0.0053144 | 0.0 | 3.34
|
||||||
|
Output | 0.0048583 | 0.0048583 | 0.0048583 | 0.0 | 3.05
|
||||||
|
Modify | 0.002043 | 0.002043 | 0.002043 | 0.0 | 1.28
|
||||||
|
Other | | 0.001821 | | | 1.14
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.1
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
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) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.052449 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0497171 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.0506296 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 853255.432 tau/day, 1975.128 timesteps/s
|
||||||
|
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.032111 | 0.032111 | 0.032111 | 0.0 | 63.42
|
||||||
|
Neigh | 0.012403 | 0.012403 | 0.012403 | 0.0 | 24.50
|
||||||
|
Comm | 0.0016352 | 0.0016352 | 0.0016352 | 0.0 | 3.23
|
||||||
|
Output | 0.001556 | 0.001556 | 0.001556 | 0.0 | 3.07
|
||||||
|
Modify | 0.0023767 | 0.0023767 | 0.0023767 | 0.0 | 4.69
|
||||||
|
Other | | 0.0005478 | | | 1.08
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.3
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.3
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
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) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0242313 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734558025
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0269411 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752864010326673494
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.022648 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1907449.463 tau/day, 4415.392 timesteps/s
|
||||||
|
100.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0091419 | 0.010422 | 0.011089 | 0.9 | 46.02
|
||||||
|
Neigh | 0.0036491 | 0.0040749 | 0.0043554 | 0.5 | 17.99
|
||||||
|
Comm | 0.004713 | 0.0056035 | 0.0073471 | 1.6 | 24.74
|
||||||
|
Output | 0.00062782 | 0.00063348 | 0.00064461 | 0.0 | 2.80
|
||||||
|
Modify | 0.0013385 | 0.0013655 | 0.0013943 | 0.1 | 6.03
|
||||||
|
Other | | 0.0005485 | | | 2.42
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752797469732716884
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
|
||||||
|
Total wall time: 0:00:00
|
||||||
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.1
Normal file
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.1
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
"""
|
||||||
|
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
|
||||||
|
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) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0623265 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0498825 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.050109 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 862120.560 tau/day, 1995.649 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.031747 | 0.031747 | 0.031747 | 0.0 | 63.36
|
||||||
|
Neigh | 0.012304 | 0.012304 | 0.012304 | 0.0 | 24.55
|
||||||
|
Comm | 0.0016113 | 0.0016113 | 0.0016113 | 0.0 | 3.22
|
||||||
|
Output | 0.0015529 | 0.0015529 | 0.0015529 | 0.0 | 3.10
|
||||||
|
Modify | 0.0023537 | 0.0023537 | 0.0023537 | 0.0 | 4.70
|
||||||
|
Other | | 0.0005398 | | | 1.08
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:00
|
||||||
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.3
Normal file
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.3
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (2 Jun 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
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
"""
|
||||||
|
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
|
||||||
|
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) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0245664 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734442562
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566498001 -0.48020228608205661747 -0.33571704057970125357 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0221302 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266690531
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305301251 -0.51524577748319111414 -0.27940441114042025017 -0.42108499009554783976
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.0224519 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1924114.069 tau/day, 4453.968 timesteps/s
|
||||||
|
100.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0096043 | 0.010493 | 0.011044 | 0.6 | 46.74
|
||||||
|
Neigh | 0.0037658 | 0.0041299 | 0.004422 | 0.4 | 18.39
|
||||||
|
Comm | 0.0048946 | 0.0055617 | 0.0068824 | 1.3 | 24.77
|
||||||
|
Output | 0.00063471 | 0.00063884 | 0.00064691 | 0.0 | 2.85
|
||||||
|
Modify | 0.0010632 | 0.0010754 | 0.0010895 | 0.0 | 4.79
|
||||||
|
Other | | 0.0005531 | | | 2.46
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327239895
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521697958 -0.24280603320323956851 -0.42189158691169470483 -0.59061971935071611028
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.1
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
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) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.276735 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.276667 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.278602 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 155060.058 tau/day, 358.935 timesteps/s
|
||||||
|
26.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.049067 | 0.049067 | 0.049067 | 0.0 | 17.61
|
||||||
|
Neigh | 0.01894 | 0.01894 | 0.01894 | 0.0 | 6.80
|
||||||
|
Comm | 0.0026936 | 0.0026936 | 0.0026936 | 0.0 | 0.97
|
||||||
|
Output | 0.002919 | 0.002919 | 0.002919 | 0.0 | 1.05
|
||||||
|
Modify | 0.20406 | 0.20406 | 0.20406 | 0.0 | 73.24
|
||||||
|
Other | | 0.0009253 | | | 0.33
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:01
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.3
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.3
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
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) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.271725 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734558025
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.275711 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752864010326673494
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.27674 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 156103.145 tau/day, 361.350 timesteps/s
|
||||||
|
71.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0086137 | 0.01236 | 0.019756 | 4.7 | 4.47
|
||||||
|
Neigh | 0.003253 | 0.0047355 | 0.0075676 | 2.9 | 1.71
|
||||||
|
Comm | 0.0065383 | 0.016521 | 0.021738 | 5.5 | 5.97
|
||||||
|
Output | 0.0011823 | 0.0011972 | 0.0012111 | 0.0 | 0.43
|
||||||
|
Modify | 0.24066 | 0.24076 | 0.24093 | 0.0 | 87.00
|
||||||
|
Other | | 0.001171 | | | 0.42
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752797469732716884
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
|
||||||
|
Total wall time: 0:00:01
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.1
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.1
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.3
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.3
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.1
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.1
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.3
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.3
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.tcp.1
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.tcp.1
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:01
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.tcp.4
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.tcp.4
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
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
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
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 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:01
|
||||||
Reference in New Issue
Block a user