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more example bug fixes

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This commit is contained in:
Steve Plimpton
2022-06-15 17:08:54 -06:00
parent a5745d925a
commit 12d6983c9b
49 changed files with 389 additions and 2175 deletions
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288
examples/mdi/README
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@ -21,9 +21,9 @@ a driver and couple to an engine that is either a stand-alone code or
a plugin. Examples for all these use cases are in this directory.
The example commands below illustrate how to run all the variants.
To use LAMMPS as a plugin engine, you must build it as a shared library.
Something like this, which also builds the normal LAMMPS executable
lmp_mpi:
To use LAMMPS as a plugin engine, you must build it as a shared
library. Something like this with make, which also builds the normal
LAMMPS executable lmp_mpi:
cd src
make yes-mdi
@ -33,189 +33,59 @@ To use the serial_driver.py example you will need Python 3 with Numpy
and mpi4py available in your Python. Make sure LAMMPS and Python are
using same the same version of MPI.
5 use-case examples are explained below.
See the Run.sh file for commands to run each of the examples
in all the different modes.
In the first 3 examples, results running with MDI should be identical
to running without MDI (alone log files). Example #4 has no non-MDI
run. Example #5 results should match the non-MDI run of example #1.
-------------------------------------------------
-------------------------------------------------
* Example #1 = run ab inito MD (AIMD)
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
* Example #1 = run ab initio MD (AIMD)
See the log aimd files.
Two instances of LAMMPS operate as a driver and engine. As an engine,
LAMMPS is a surrogate for a quantum code.
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
have an option for running in NVE vs NPT mode. Comment in/out
the appropriate line to change modes. Nothing needs to be
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
---
-------------------------------------------------
-------------------------------------------------
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
% lmp_mpi -log log.aimd.alone < in.aimd.alone
See the log snapshot and dump snapshot files.
With MDI, the thermo output of the driver should match the thermo
output of the in.aimd.alone script.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver
% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
---
Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
Two instances of LAMMPS operate as a driver and engine. As an engine,
LAMMPS is a surrogate for a quantum code
-------------------------------------------------
-------------------------------------------------
* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
* Example #3 = run LAMMPS, compute QM forces on series of independent systems
---
files See the log series and dump series files.
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi -log log.snapshot.alone < in.snapshot.alone
With MDI, the thermo output of the driver should match the thermo
output of the in.snapshot.alone script. Likewise the dump file written
by the driver should match dump.snapshot.alone.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver
% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
---
Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin
Two instances of LAMMPS operate as a driver and engine. As an engine,
LAMMPS is a surrogate for a quantum code
-------------------------------------------------
-------------------------------------------------
* Example #1c = run LAMMPS, compute QM forces on series of independent systems
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
---
See the log sequence files.
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi -log log.series.alone < in.series.alone
With MDI, the thermo output of the driver should match the thermo
output of the in.series.alone script. Likewise the dump files written
by the driver should match dump.series.alone files.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver
% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
---
Run in plugin mode: 3 procs
% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin
-------------------------------------------------
-------------------------------------------------
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
Each calculation can be a single-point evaluation, MD run, or minimization
Each calculation can be a single-point evaluation, MD run, or
minimization
The sequence_driver.py code allows for optional switches in addition
to -mdi (required) and the -plugin and -plugin_args switches which are
@ -244,101 +114,21 @@ copied here:
# -seed 12345
# random number seed > 0, default = 12345
---
Run with TCP: 1 proc each
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
% lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
---
Run with TCP: 2 proc + 4 procs
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python
---
Run with MPI: 1 proc each
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence.python
---
Run with MPI: 2 procs + 4 procs
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence -in in.sequence.python
---
Run in plugin mode: 1 proc
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
---
Run in plugin mode: 3 procs
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python
-------------------------------------------------
-------------------------------------------------
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
First LAMMPS instance performs the MD timestepping
Second LAMMPS instance is surrogate QM = computes forces
* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
See the log aimdpy files.
First LAMMPS instance performs the MD timestepping. Second LAMMPS
instance is surrogate QM to compute forces.
The aimd_driver.py code allows for an optional switch in addition to
-mdi (required) and the -plugin and -plugin_args swiches which are
used to link to the 2 engines as a plugin libraries. The example run
commands below use the default values of the optional switch. The
switch is also explained the top of the file; the info is copied
here:
switch is also explained the top of the file; the info is copied here:
# -nsteps 5
# number of timesteps in dynamics runs, default = 5
---
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi -log log.aimd.alone < in.aimd.alone
With MDI, the driver prints the QM and Total energies. These should
match the PotEng and TotEng output of the in.aimd.alone script.
---
Run with TCP: 1 proc each
% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
---
Run with TCP: 2 procs + 2 procs + 3 procs
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
---
Run with MPI: 1 proc each
% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
---
Run with MPI: 2 procs + 2 procs + 3 procs
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm

256
examples/mdi/Run.sh Normal file
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@ -0,0 +1,256 @@
# Run all the examples
# -------------------------------------------------
# -------------------------------------------------
# Example 1
# ---
# Run without MDI
lmp_mpi -log log.aimd.alone.1 < in.aimd.alone
# ---
# Run with TCP: 1 proc each
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver &
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine
# ---
# Run with TCP: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver &
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine
# ---
# Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine
# ---
# Run with MPI: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine
# ---
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin
mv log.aimd.engine.plugin log.aimd.engine.plugin.1
# ---
# Run in plugin mode: 3 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin
mv log.aimd.engine.plugin log.aimd.engine.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 2
# ---
# Run without MDI
lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone
mv dump.snapshot.alone dump.snapshot.alone.1
# ---
# Run with TCP: 1 proc each
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver &
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine
mv dump.snapshot.driver dump.snapshot.driver.tcp.1
# ---
# Run with TCP: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver &
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine
mv dump.snapshot.driver dump.snapshot.driver.tcp.3
# ---
# Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine
mv dump.snapshot.driver dump.snapshot.driver.mpi.1
# ---
# Run with MPI: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine
mv dump.snapshot.driver dump.snapshot.driver.mpi.3
# ---
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1
# ---
# Run in plugin mode: 3 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 3
# ---
# Run without MDI
lmp_mpi -log log.series.alone.1 < in.series.alone
mv dump.series.alone dump.series.alone.1
# ---
# Run with TCP: 1 proc each
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver &
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine
mv dump.series.driver dump.series.driver.tcp.1
# ---
# Run with TCP: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver &
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine
mv dump.series.driver dump.series.driver.tcp.3
# ---
# Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine
mv dump.series.driver dump.series.driver.mpi.1
# ---
# Run with MPI: 3 procs + 4 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine
mv dump.series.driver dump.series.driver.mpi.3
# ---
# Run in plugin mode: 1 proc
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin
mv log.series.engine.plugin log.series.engine.plugin.1
mv dump.series.driver.plugin dump.series.driver.plugin.1
# ---
# Run in plugin mode: 3 procs
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin
mv log.series.engine.plugin log.series.engine.plugin.3
mv dump.series.driver.plugin dump.series.driver.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 4
# ---
# Run with TCP: 1 proc each
python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python
# ---
# Run with TCP: 2 proc + 4 procs
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python
# ---
# Run with MPI: 1 proc each
mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python
# ---
# Run with MPI: 2 procs + 4 procs
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python
# ---
# Run in plugin mode: 1 proc
python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python
# ---
# Run in plugin mode: 3 procs
mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python
# -------------------------------------------------
# -------------------------------------------------
# Example 5
# ---
# Run with TCP: 1 proc each
python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" &
lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimd.mm &
lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimd.qm
# ---
# Run with TCP: 2 procs + 2 procs + 3 procs
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" &
mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm.tcp.2 -in in.aimd.mm &
mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm.tcp.3 -in in.aimd.qm
# ---
# Run with MPI: 1 proc each
mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.1 -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.qm.1 -in in.aimd.qm
# ---
# Run with MPI: 2 procs + 2 procs + 3 procs
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.2 -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.mpi.3 -in in.aimd.qm

1
examples/mdi/in.sequence.python
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@ -19,3 +19,4 @@ fix 1 all nve
thermo 10
mdi engine

6
examples/mdi/in.series.alone
View File

@ -4,7 +4,6 @@ variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
label LOOP
@ -32,12 +31,11 @@ label LOOP
run 0
write_dump all custom dump.series.alone.${ifile} &
id type x y z fx fy fz modify sort id
write_dump all custom dump.series.alone &
id type x y z fx fy fz modify sort id append yes
clear
next ifile
next rho
jump SELF LOOP

15
examples/mdi/in.series.driver
View File

@ -4,10 +4,9 @@ variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
mdi start
mdi connect
label LOOP
@ -25,24 +24,20 @@ label LOOP
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes external yes
fix 1 all mdi/qm add no virial yes connect no
variable epress equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3]
run 0
write_dump all custom dump.series.driver.${ifile} &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
write_dump all custom dump.series.driver &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
# cannot do "clear" b/c will shutdown MDI engine
# have to
clear
next ifile
next rho
jump SELF LOOP
mdi stop
mdi exit

6
examples/mdi/in.series.driver.plugin
View File

@ -4,7 +4,6 @@ variable x index 5
variable y index 5
variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9
label LOOP
@ -33,12 +32,11 @@ label LOOP
extra "-log log.series.engine.plugin" &
command "run 0"
write_dump all custom dump.series.driver.${ifile} &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id
write_dump all custom dump.series.driver.plugin &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next ifile
next rho
jump SELF LOOP

2
examples/mdi/in.snapshot.driver.plugin
View File

@ -32,7 +32,7 @@ thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 500 dump.snapshot.driver &
dump 1 all custom 500 dump.snapshot.driver.plugin &
id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id

90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
View File

@ -1,90 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
Performance: 505739.085 tau/day, 1170.692 timesteps/s
73.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
Other | | 6.054e-05 | | | 1.42
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19500 ave 19500 max 19500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1
View File

@ -1,79 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms
Performance: 731582.413 tau/day, 1693.478 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43
Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58
Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98
Other | | 3e-05 | | | 1.02
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 166 ave 166 max 166 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = -1
Ave neighs/atom = -0.002
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3
View File

@ -1,79 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms
Performance: 684416.574 tau/day, 1584.298 timesteps/s
99.5% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17
Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92
Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88
Other | | 0.0001272 | | | 4.03
Nlocal: 166.667 ave 200 max 150 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Nghost: 55.3333 ave 92 max 32 min
Histogram: 1 1 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = -3
Ave neighs/atom = -0.006
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1
View File

@ -1,80 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd plugin
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms
Performance: 544685.246 tau/day, 1260.845 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40
Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91
Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89
Other | | 3.184e-05 | | | 0.80
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 166 ave 166 max 166 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = -1
Ave neighs/atom = -0.002
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3
View File

@ -1,80 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd plugin
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms
Performance: 752045.581 tau/day, 1740.846 timesteps/s
99.1% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36
Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21
Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42
Other | | 8.637e-05 | | | 3.01
Nlocal: 166.667 ave 200 max 150 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Nghost: 55.3333 ave 92 max 32 min
Histogram: 1 1 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = -3
Ave neighs/atom = -0.006
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1
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@ -1,79 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms
Performance: 1792.736 tau/day, 4.150 timesteps/s
0.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00
Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02
Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97
Other | | 6.184e-05 | | | 0.01
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 166 ave 166 max 166 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = -1
Ave neighs/atom = -0.002
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08

79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3
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@ -1,79 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/aimd
fix_modify 2 energy yes virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms
Performance: 1800.259 tau/day, 4.167 timesteps/s
66.7% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.604e-06 | 4.8462e-05 | 7.527e-05 | 0.0 | 0.00
Output | 0.00015266 | 0.00020593 | 0.00031177 | 0.0 | 0.02
Modify | 1.1993 | 1.1994 | 1.1994 | 0.0 | 99.96
Other | | 0.0002123 | | | 0.02
Nlocal: 166.667 ave 200 max 150 min
Histogram: 2 0 0 0 0 0 0 0 0 1
Nghost: 55.3333 ave 92 max 32 min
Histogram: 1 1 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = -3
Ave neighs/atom = -0.006
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08

55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1
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LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:01

55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - MDI engine script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:01

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1
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@ -1,5 +0,0 @@
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2
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@ -1,5 +0,0 @@
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1
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@ -1,6 +0,0 @@
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2
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@ -1,6 +0,0 @@
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1
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@ -1,44 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
Total wall time: 0:00:00

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2
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@ -1,44 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
Total wall time: 0:00:00

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1
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@ -1,44 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
Total wall time: 0:00:11

44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2
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@ -1,44 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
Total wall time: 0:00:11

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:00

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:01

55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3
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@ -1,55 +0,0 @@
LAMMPS (17 Feb 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
Total wall time: 0:00:01

3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1
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@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16

3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2
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@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16

3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1
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@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16

3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3
View File

@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16

3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1
View File

@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16

3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2
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@ -1,3 +0,0 @@
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16

89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1
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@ -1,89 +0,0 @@
LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4
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@ -1,89 +0,0 @@
LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1
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@ -1,89 +0,0 @@
LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3
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@ -1,89 +0,0 @@
LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 3 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 3 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 3 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
3 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1
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LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4
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LAMMPS (17 Feb 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00