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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. a plugin. Examples for all these use cases are in this directory.
The example commands below illustrate how to run all the variants. 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. To use LAMMPS as a plugin engine, you must build it as a shared
Something like this, which also builds the normal LAMMPS executable library. Something like this with make, which also builds the normal
lmp_mpi: LAMMPS executable lmp_mpi:
cd src cd src
make yes-mdi 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 and mpi4py available in your Python. Make sure LAMMPS and Python are
using same the same version of MPI. 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) * Example #1 = run ab initio MD (AIMD)
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code 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 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 have an option for running in NVE vs NPT mode. Comment in/out
the appropriate line to change modes. Nothing needs to be the appropriate line to change modes. Nothing needs to be
changed in the in.aimd.engine or in.aimd.engine.plugin scripts. changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
--- -------------------------------------------------
-------------------------------------------------
Run the entire calculation with a single instance of LAMMPS by itself * Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
results should be identical to running this example with MDI
% 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 Two instances of LAMMPS operate as a driver and engine. As an engine,
output of the in.aimd.alone script. LAMMPS is a surrogate for a quantum code
---
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
------------------------------------------------- -------------------------------------------------
------------------------------------------------- -------------------------------------------------
* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run * Example #3 = 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
--- files See the log series and dump series files.
Run the entire calculation with a single instance of LAMMPS by itself Two instances of LAMMPS operate as a driver and engine. As an engine,
results should be identical to running this example with MDI LAMMPS is a surrogate for a quantum code
% 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
------------------------------------------------- -------------------------------------------------
------------------------------------------------- -------------------------------------------------
* Example #1c = run LAMMPS, compute QM forces on series of independent systems * Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
--- See the log sequence files.
Run the entire calculation with a single instance of LAMMPS by itself Each calculation can be a single-point evaluation, MD run, or
results should be identical to running this example with MDI minimization
% 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
The sequence_driver.py code allows for optional switches in addition The sequence_driver.py code allows for optional switches in addition
to -mdi (required) and the -plugin and -plugin_args switches which are to -mdi (required) and the -plugin and -plugin_args switches which are
@ -244,101 +114,21 @@ copied here:
# -seed 12345 # -seed 12345
# random number seed > 0, default = 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 * Example #5 = 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 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 The aimd_driver.py code allows for an optional switch in addition to
-mdi (required) and the -plugin and -plugin_args swiches which are -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 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 commands below use the default values of the optional switch. The
switch is also explained the top of the file; the info is copied switch is also explained the top of the file; the info is copied here:
here:
# -nsteps 5 # -nsteps 5
# number of timesteps in dynamics runs, default = 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 thermo 10
mdi engine mdi engine

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

15
examples/mdi/in.series.driver
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@ -4,10 +4,9 @@ variable x index 5
variable y index 5 variable y index 5
variable z index 5 variable z index 5
variable ifile loop 3
variable rho index 0.7 0.8 0.9 variable rho index 0.7 0.8 0.9
mdi start mdi connect
label LOOP label LOOP
@ -25,24 +24,20 @@ label LOOP
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes 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 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] thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3]
run 0 run 0
write_dump all custom dump.series.driver.${ifile} & write_dump all custom dump.series.driver &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id 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 clear
next ifile
next rho next rho
jump SELF LOOP jump SELF LOOP
mdi stop mdi exit

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

2
examples/mdi/in.snapshot.driver.plugin
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@ -32,7 +32,7 @@ thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100 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] id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id dump_modify 1 sort id

90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
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@ -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
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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 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
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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 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
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@ -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
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@ -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
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.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: 0:00:00

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
View File

@ -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
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.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
View File

@ -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
View File

@ -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.tcp.g++.4
View File

@ -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

49
src/MDI/fix_mdi_qm.cpp
View File

@ -48,7 +48,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
virialflag = 0; virialflag = 0;
addflag = 1; addflag = 1;
every = 1; every = 1;
extflag = 0; connectflag = 1;
int iarg = 3; int iarg = 3;
while (iarg < narg) { while (iarg < narg) {
@ -69,10 +69,10 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
every = utils::inumeric(FLERR,arg[iarg+1],false,lmp); every = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command"); if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"external") == 0) { } else if (strcmp(arg[iarg],"connect") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
if (strcmp(arg[iarg+1],"yes") == 0) extflag = 1; if (strcmp(arg[iarg+1],"yes") == 0) connectflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) extflag = 0; else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0;
else error->all(FLERR,"Illegal fix mdi/qm command"); else error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else error->all(FLERR,"Illegal fix mdi/qm command"); } else error->all(FLERR,"Illegal fix mdi/qm command");
@ -100,8 +100,8 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
thermo_energy = thermo_virial = 1; thermo_energy = thermo_virial = 1;
} }
// mdicomm will be one-time initialized in init() // mdicomm will be initialized in init()
// cannot be done here for a plugin library, b/c mdi plugin command is later // cannot do here for a plugin library, b/c mdi plugin command comes later
mdicomm = MDI_COMM_NULL; mdicomm = MDI_COMM_NULL;
@ -143,10 +143,11 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
FixMDIQM::~FixMDIQM() FixMDIQM::~FixMDIQM()
{ {
// send exit command to engine if it is a stand-alone code // send exit command to stand-alone engine code
// for plugin, this happens in MDIPlugin::plugin_wrapper() // for connnectflag = 0, this is done via "mdi exit" command
// for plugin, this is done in MDIPlugin::plugin_wrapper()
if (!plugin && !extflag) { if (mdicomm != MDI_COMM_NULL && connectflag && !plugin) {
int ierr = MDI_Send_command("EXIT", mdicomm); int ierr = MDI_Send_command("EXIT", mdicomm);
if (ierr) error->all(FLERR, "MDI: EXIT command"); if (ierr) error->all(FLERR, "MDI: EXIT command");
} }
@ -176,19 +177,26 @@ int FixMDIQM::setmask()
void FixMDIQM::init() void FixMDIQM::init()
{ {
// one-time auto-detect whether engine is stand-alone code or plugin library // set local mdicomm one-time only
// also initializes mdicomm // also set plugin = 0/1 for engine = stand-alone code vs plugin library
// set plugin = 0/1 for engine = stand-alone code vs plugin library
if (!extflag) {
if (mdicomm == MDI_COMM_NULL) { if (mdicomm == MDI_COMM_NULL) {
// this fix makes one-time connection to engine
if (connectflag) {
// if MDI's mdicomm not set, need to Accept_comm() with stand-alone engine
// othewise are already connected to plugin engine
MDI_Get_communicator(&mdicomm, 0); MDI_Get_communicator(&mdicomm, 0);
if (mdicomm == MDI_COMM_NULL) { if (mdicomm == MDI_COMM_NULL) {
plugin = 0; plugin = 0;
MDI_Accept_communicator(&mdicomm); MDI_Accept_communicator(&mdicomm);
if (mdicomm == MDI_COMM_NULL) if (mdicomm == MDI_COMM_NULL)
error->all(FLERR, "MDI unable to connect to stand-alone engine"); error->all(FLERR, "MDI unable to connect to stand-alone engine");
} else { } else {
plugin = 1; plugin = 1;
int method; int method;
@ -196,11 +204,20 @@ void FixMDIQM::init()
if (method != MDI_PLUGIN) if (method != MDI_PLUGIN)
error->all(FLERR, "MDI internal error for plugin engine"); error->all(FLERR, "MDI internal error for plugin engine");
} }
}
// connection should have been already made by "mdi connect" command
// only works for stand-alone engines
} else { } else {
plugin = 0; plugin = 0;
mdicomm = lmp->mdicomm;
if (lmp->mdicomm == nullptr)
error->all(FLERR,"Fix mdi/qm is not connected to engine via mdi connect");
int nbytes = sizeof(MDI_Comm);
char *ptrcomm = (char *) lmp->mdicomm;
memcpy(&mdicomm,ptrcomm,nbytes);
}
} }
// send natoms, atom types, and simulation box to engine // send natoms, atom types, and simulation box to engine

2
src/MDI/fix_mdi_qm.h
View File

@ -40,7 +40,7 @@ class FixMDIQM : public Fix {
private: private:
int nprocs; int nprocs;
int virialflag,addflag,extflag,every; int every,virialflag,addflag,connectflag;
int plugin; int plugin;
int maxlocal; int maxlocal;
int sumflag; int sumflag;

39
src/MDI/mdi_command.cpp
View File

@ -16,13 +16,19 @@
#include "error.h" #include "error.h"
#include "mdi_engine.h" #include "mdi_engine.h"
#include "mdi_plugin.h" #include "mdi_plugin.h"
#include "memory.h"
#include <cstring> #include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
mdi command: engine or plugin mdi command: engine or plugin or connect or exit
engine is used when LAMMPS is an MDI engine, to start listening for requests
plugin is used when LAMMPS is an MDI driver to load a plugin library
connect and exit are used when LAMMPS is an MDI driver to
(a) connect = setup comm with a stand-alone MDI engine
(b) exit = terminate comm with a stand-alone MDI engine
---------------------------------------------------------------------- */ ---------------------------------------------------------------------- */
void MDICommand::command(int narg, char **arg) void MDICommand::command(int narg, char **arg)
@ -35,22 +41,41 @@ void MDICommand::command(int narg, char **arg)
} else if (strcmp(arg[0], "plugin") == 0) { } else if (strcmp(arg[0], "plugin") == 0) {
MDIPlugin(lmp, narg - 1, &arg[1]); MDIPlugin(lmp, narg - 1, &arg[1]);
} else if (strcmp(arg[0], "start") == 0) { } else if (strcmp(arg[0], "connect") == 0) {
if (lmp->mdicomm != nullptr)
error->all(FLERR,"MDI cannot connect to already connected engine");
MDI_Comm mdicomm; MDI_Comm mdicomm;
MDI_Get_communicator(&mdicomm, 0); MDI_Get_communicator(&mdicomm, 0);
if (mdicomm == MDI_COMM_NULL) { if (mdicomm == MDI_COMM_NULL) {
MDI_Accept_communicator(&mdicomm); MDI_Accept_communicator(&mdicomm);
if (mdicomm == MDI_COMM_NULL) if (mdicomm == MDI_COMM_NULL)
error->all(FLERR, "MDI unable to connect to stand-alone engine"); error->all(FLERR, "MDI unable to connect to stand-alone engine");
} else error->all(FLERR, "Cannot use mdi start in plugin mode"); } else error->all(FLERR, "Cannot use mdi connect with plugin engine");
lmp->mdicomm = mdicomm;
} else if (strcmp(arg[0], "stop") == 0) { int nbytes = sizeof(MDI_Comm);
char *ptrcomm = (char *) memory->smalloc(nbytes,"mdi:mdicomm");
memcpy(ptrcomm,&mdicomm,nbytes);
lmp->mdicomm = (void *) ptrcomm;
} else if (strcmp(arg[0], "exit") == 0) {
if (lmp->mdicomm == nullptr)
error->all(FLERR,"MDI cannot send exit to unconnected engine");
MDI_Comm mdicomm;
int nbytes = sizeof(MDI_Comm);
char *ptrcomm = (char *) lmp->mdicomm;
memcpy(&mdicomm,ptrcomm,nbytes);
MDI_Comm mdicomm = lmp->mdicomm;
int ierr = MDI_Send_command("EXIT", mdicomm); int ierr = MDI_Send_command("EXIT", mdicomm);
if (ierr) error->all(FLERR, "MDI: EXIT command"); if (ierr) error->all(FLERR, "MDI: EXIT command");
lmp->mdicomm = MDI_COMM_NULL;
memory->sfree(ptrcomm);
lmp->mdicomm = nullptr;
} else error->all(FLERR, "Illegal mdi command"); } else error->all(FLERR, "Illegal mdi command");
} }

2
src/lammps.cpp
View File

@ -130,7 +130,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
num_ver = utils::date2num(version); num_ver = utils::date2num(version);
external_comm = 0; external_comm = 0;
mdicomm = 0; mdicomm = nullptr;
skiprunflag = 0; skiprunflag = 0;

2
src/lammps.h
View File

@ -69,7 +69,7 @@ class LAMMPS {
// when multiple programs launched by mpirun // when multiple programs launched by mpirun
// set by -mpicolor command line arg // set by -mpicolor command line arg
int mdicomm; // for use with MDI code coupling library void *mdicomm; // for use with MDI code coupling library
const char *match_style(const char *style, const char *name); const char *match_style(const char *style, const char *name);
static const char *installed_packages[]; static const char *installed_packages[];