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This commit is contained in:
rohskopf
2022-07-07 09:11:28 -06:00
parent 581503888f b8acd2e31d
commit 9975eecd2a
272 changed files with 42151 additions and 3135 deletions
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17
examples/PACKAGES/pace/plugin/CMakeLists.txt
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@ -31,6 +31,23 @@ elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CROSSCOMPILING)
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
find_program(MAKENSIS_PATH makensis)
if(MAKENSIS_PATH)
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/paceplugin.nsis ${CMAKE_BINARY_DIR})
if(BUILD_MPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI paceplugin.nsis
DEPENDS paceplugin
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}-MPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} paceplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
DEPENDS paceplugin lammps.ico lammps-text-logo-wide.bmp paceplugin.nsis
BYPRODUCTS LAMMPS-ML-PACE-plugin-${LAMMPS_VERSION}.exe)
endif()
endif()
else()
set_target_properties(paceplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

249
examples/mdi/README
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@ -2,10 +2,11 @@ These are examples that work the MDI package in LAMMPS which uses the
MolSSI MDI library for coupling codes together and communicating
between them with MDI messages.
In MDI lingo, one code is the driver and another code is the engine.
The 2 codes can be written in any language; C++ (LAMMPS) and Python
are illustrated here. The 2 codes can each be stand-alone codes, in
which case they can be run on different numbers of processors. The 2
Within the MDI context, one code is the driver and another code is
the engine. The 2 codes can be written in any language; C++ (LAMMPS)
and Python are illustrated here. The 2 codes can each be stand-alone
codes, in which case they can be run on different numbers of processors.
The 2
codes can communicate either via TCP (sockets) or via MPI. For the
TCP case, the driver and engine need to be launched separately,
e.g. in 2 windows on your desktop machine. For the MPI case, a single
@ -19,87 +20,99 @@ LAMMPS supports operating in all these MDI modes. It can be an engine
operating either as a stand-alone code or as a plugin. It can also be
a driver and couple to an engine that is either a stand-alone code or
a plugin. Examples for all these use cases are in this directory.
The example commands below illustrate how to run all the variants.
The Run.sh file shows how run in all the modes. Type "sh Run.sh"
to try them all out.
To use LAMMPS as a plugin engine, you must build it as a shared library.
Something like this, which also builds the normal LAMMPS executable
lmp_mpi:
To use LAMMPS as a plugin engine, you must build it as a shared
library. Something like this with make, which also builds the normal
LAMMPS executable lmp_mpi:
cd src
make yes-mdi
make mode=shlib mpi
To use the serial_driver.py example you will need Python 3 with Numpy
and mpi4py available in your Python. Make sure LAMMPS and Python are
using same the same version of MPI.
-------------------------------------------------
Examples 4 and 5 use Python scripts as MDI drivers. For this you will
need Python 3 with Numpy and mpi4py installed. Make sure LAMMPS and
Python/mpi4py are using same the same version of MPI.
You will also need MDI installed in your Python. You cannot use the
LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a
static library, not shared, which Python requires.
You can install MDI in your Python via conda:
% conda install -c conda-forge pymdi=1.4.1
or via pip:
% pip install pymdi==1.4.1
It is likely fine to leave off the version number, to get the latest
MDI version. But to be safe, 1.4.1 is the version LAMMPS is currently
using.
-------------------------------------------------
5 example use-cases are explained below.
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 initio MD (AIMD)
Two instances of LAMMPS operate as a driver and engine. As an engine,
LAMMPS is a surrogate for a quantum code.
You can compare the thermo output in log.aimd.alone.1 to the thermo output in
any of the log.aimd.driver* files. It should be identical.
Note that the "alone" and "driver" input scripts have options for
running in NVE vs NPT Comment in/out the appropriate line to make
change. Nothing needs to be changed in the "engine" scripts.
-------------------------------------------------
-------------------------------------------------
* Example #1 = run ab inito MD (AIMD)
Two instances of LAMMPS operate as a driver and engine
As an engine, LAMMPS is a surrogate for a quantum code
* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
have an option for running in NVE vs NPT mode. Comment in/out
the appropriate line to change modes. Nothing needs to be
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
Two instances of LAMMPS operate as a driver and engine. As an engine,
LAMMPS is a surrogate for a quantum code
---
You can compare the thermo output in log.snapshot.alone.1 to the
thermo output in any of the log.snapshot.driver* files. It should be
identical.
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
% lmp_mpi < in.aimd.alone
With MDI, the thermo output of the driver should match the thermo
output of the in.aimd.alone script.
---
Run with TCP: 1 proc each
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
---
Run with TCP: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
---
Run with MPI: 1 proc each
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
---
Run with MPI: 3 procs + 4 procs
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
---
Run in plugin mode: 1 proc
% lmp_mpi -mdi "-name aimd -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 aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
You can compare the dumped forces in dump.snapshot.alone.1 to the
forces in any of the dump.snapshot.* files. They should be identical,
although at step 0 the forces are "zero" and may be epsilon different.
-------------------------------------------------
-------------------------------------------------
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
Each calculation can be a single-point evaluation, MD run, or minimization
* 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
You can compare the thermo output in log.series.alone.1 to the thermo
output in any of the log.series.driver* files. It should be
identical.
You can compare the dumped forces in dump.series.alone.1 to the forces
in any of the dump.series.* files. They should be identical,
-------------------------------------------------
-------------------------------------------------
* Example #4 = 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
to -mdi (required) and the -plugin and -plugin_args switches which are
@ -128,101 +141,31 @@ copied here:
# -seed 12345
# random number seed > 0, default = 12345
---
Run with TCP: 1 proc each
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
---
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 LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
---
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
---
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 LAMMPS -method MPI" -log log.sequence -in in.sequence
---
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"
---
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"
You can compare the thermo output in any of the log.sequence.engine.*
files. It should be identical.
-------------------------------------------------
-------------------------------------------------
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
First LAMMPS instance performs the MD timestepping
Second LAMMPS instance is surrogate QM = computes forces
* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
First LAMMPS instance performs the MD timestepping. Second LAMMPS
instance is surrogate QM to compute forces.
The aimd_driver.py code allows for an optional switch in addition to
-mdi (required) and the -plugin and -plugin_args swiches which are
used to link to the 2 engines as a plugin libraries. The example run
commands below use the default values of the optional switch. The
switch is also explained the top of the file; the info is copied
here:
switch is also explained the top of the file; the info is copied here:
# -nsteps 5
# number of timesteps in dynamics runs, default = 5
# -nsteps 10
# number of timesteps in dynamics runs, default = 10
---
This calculation is the same as Example #1 with a LAMMPS driver and a
LAMMPS engine. Now there is a Python driver and two LAMMPS engines.
Run the entire calculation with a single instance of LAMMPS by itself
results should be identical to running this example with MDI
You can compare the thermo output in log.aimd.alone.1 output to the
thermo output is any of the log.sequence.engine.* files. It should be
identical for the Total Energy printed out by the Python driver script.
% lmp_mpi < 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
E.g. Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166

256
examples/mdi/Run.sh Normal file
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@ -0,0 +1,256 @@
# Run all the examples
# -------------------------------------------------
# -------------------------------------------------
# Example 1 = run ab initio MD (AIMD)
# ---
# 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 LAMMPS, compute QM forces on snapshots from a long run
# ---
# 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.4
# ---
# 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.4
# ---
# 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 LAMMPS, compute QM forces on series of independent systems
# ---
# 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.4
# ---
# 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.4
# ---
# 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 = Python driver runs a sequence of unrelated LAMMPS calculations
# ---
# 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 AIMD with Python driver code and 2 LAMMPS instances as engines
# ---
# Run with TCP: 1 proc each
python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.1 &
lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimdpy.mm &
lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimdpy.qm
# ---
# Run with TCP: 2 procs + 2 procs + 3 procs
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.2 &
mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.2 -in in.aimdpy.mm &
mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.3 -in in.aimdpy.qm
# ---
# Run with MPI: 1 proc each
mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.1 -in in.aimdpy.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.1 -in in.aimdpy.qm > log.aimdpy.driver.mpi.1
# ---
# Run with MPI: 2 procs + 2 procs + 3 procs
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.2 -in in.aimdpy.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.3 -in in.aimdpy.qm > log.aimdpy.driver.mpi.2

6
examples/mdi/aimd_driver.py
View File

@ -23,8 +23,8 @@
# -plugin_args arglist
# args to add when launching plugin library, only when using plugin mode
# enclose arglist in quotes if multiple words
# -nsteps 5
# number of timesteps, default = 5
# -nsteps 10
# number of timesteps, default = 10
import sys
import mdi
@ -182,7 +182,7 @@ mdiarg = ""
plugin = ""
plugin_args = ""
nsteps = 5
nsteps = 10
# parse command-line args

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2
examples/mdi/in.aimd.alone
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@ -29,4 +29,4 @@ fix 1 all nve
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
run 10

5
examples/mdi/in.aimd.driver
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@ -23,10 +23,9 @@ 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
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 5
run 10

7
examples/mdi/in.aimd.driver.plugin
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@ -23,12 +23,11 @@ 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
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
command "run 5"
command "run 10"

12
examples/mdi/in.aimd.engine
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@ -1,16 +1,11 @@
# 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
region box block 0 $x 0 $y 0 $z
lattice fcc 1.0
region box block 0 1 0 1 0 1
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
@ -19,4 +14,7 @@ pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine

0
examples/mdi/in.aimd.mm → examples/mdi/in.aimdpy.mm
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0
examples/mdi/in.aimd.qm → examples/mdi/in.aimdpy.qm
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1
examples/mdi/in.sequence → examples/mdi/in.sequence.python
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@ -19,3 +19,4 @@ fix 1 all nve
thermo 10
mdi engine

37
examples/mdi/in.series.alone Normal file
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@ -0,0 +1,37 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
displace_atoms all random 0.1 0.1 0.1 48294
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
run 0
write_dump all custom dump.series.alone &
id type x y z fx fy fz modify sort id append yes
clear
next rho
jump SELF LOOP

39
examples/mdi/in.series.driver Normal file
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@ -0,0 +1,39 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
mdi connect
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
displace_atoms all random 0.1 0.1 0.1 48294
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
write_dump all custom dump.series.driver &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
mdi exit

38
examples/mdi/in.series.driver.plugin Normal file
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@ -0,0 +1,38 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
displace_atoms all random 0.1 0.1 0.1 48294
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.series.engine &
extra "-log log.series.engine.plugin" &
command "run 0"
write_dump all custom dump.series.driver.plugin &
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP

17
examples/mdi/in.series.engine Normal file
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@ -0,0 +1,17 @@
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
region box block 0 1 0 1 0 1
create_box 1 box
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

28
examples/mdi/in.snapshot.alone Normal file
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@ -0,0 +1,28 @@
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.alone &
id type x y z fx fy fz
dump_modify 1 sort id
run 300

33
examples/mdi/in.snapshot.driver Normal file
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@ -0,0 +1,33 @@
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver &
id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 300 pre no post no every 100 &
"print 'QM eng = $(f_2/atoms)'" &
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"

42
examples/mdi/in.snapshot.driver.plugin Normal file
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@ -0,0 +1,42 @@
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
read_data data.snapshot
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver.plugin &
id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
infile in.snapshot.engine &
extra "-log log.snapshot.engine.plugin" &
command """
run 300 pre no post no every 100
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
"""

17
examples/mdi/in.snapshot.engine Normal file
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@ -0,0 +1,17 @@
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
region box block 0 1 0 1 0 1
create_box 1 box
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

51
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 → examples/mdi/log.17Jun22.aimd.alone.1
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@ -1,4 +1,4 @@
LAMMPS (17 Feb 2022)
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
@ -39,8 +39,8 @@ fix 1 all nve
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
run 10
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
@ -54,37 +54,42 @@ Neighbor list info ...
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
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 0.00919691 on 1 procs for 10 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
Performance: 469723.136 tau/day, 1087.322 timesteps/s
98.9% 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
Pair | 0.0066536 | 0.0066536 | 0.0066536 | 0.0 | 72.35
Neigh | 0.0017906 | 0.0017906 | 0.0017906 | 0.0 | 19.47
Comm | 0.0002554 | 0.0002554 | 0.0002554 | 0.0 | 2.78
Output | 0.00029976 | 0.00029976 | 0.00029976 | 0.0 | 3.26
Modify | 9.8718e-05 | 9.8718e-05 | 9.8718e-05 | 0.0 | 1.07
Other | | 9.887e-05 | | | 1.08
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
Neighs: 19396 ave 19396 max 19396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19500
Ave neighs/atom = 39
Neighbor list builds = 0
Total # of neighbors = 19396
Ave neighs/atom = 38.792
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

83
examples/mdi/log.17Jun22.aimd.driver.mpi.1 Normal file
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@ -0,0 +1,83 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 0.0078442 on 1 procs for 10 steps with 500 atoms
Performance: 550725.026 tau/day, 1274.826 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 1.592e-06 | 1.592e-06 | 1.592e-06 | 0.0 | 0.02
Comm | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.34
Output | 0.00021168 | 0.00021168 | 0.00021168 | 0.0 | 2.70
Modify | 0.0075488 | 0.0075488 | 0.0075488 | 0.0 | 96.23
Other | | 5.544e-05 | | | 0.71
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

83
examples/mdi/log.17Jun22.aimd.driver.mpi.3 Normal file
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@ -0,0 +1,83 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 0.00523112 on 3 procs for 10 steps with 500 atoms
Performance: 825827.658 tau/day, 1911.638 timesteps/s
98.8% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 5.95e-07 | 1.7073e-06 | 3.907e-06 | 0.0 | 0.03
Comm | 3.8259e-05 | 6.2707e-05 | 7.5974e-05 | 0.0 | 1.20
Output | 0.00017543 | 0.00021238 | 0.00028075 | 0.0 | 4.06
Modify | 0.004815 | 0.0048289 | 0.0048521 | 0.0 | 92.31
Other | | 0.0001254 | | | 2.40
Nlocal: 166.667 ave 176 max 150 min
Histogram: 1 0 0 0 0 0 0 0 0 2
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

84
examples/mdi/log.17Jun22.aimd.driver.plugin.1 Normal file
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@ -0,0 +1,84 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 0.00940117 on 1 procs for 10 steps with 500 atoms
Performance: 459517.175 tau/day, 1063.697 timesteps/s
96.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 1.9e-06 | 1.9e-06 | 1.9e-06 | 0.0 | 0.02
Comm | 3.0131e-05 | 3.0131e-05 | 3.0131e-05 | 0.0 | 0.32
Output | 0.00030359 | 0.00030359 | 0.00030359 | 0.0 | 3.23
Modify | 0.0090041 | 0.0090041 | 0.0090041 | 0.0 | 95.78
Other | | 6.144e-05 | | | 0.65
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

84
examples/mdi/log.17Jun22.aimd.driver.plugin.3 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 0.00613177 on 3 procs for 10 steps with 500 atoms
Performance: 704527.327 tau/day, 1630.850 timesteps/s
99.2% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 7.93e-07 | 1.8723e-06 | 3.996e-06 | 0.0 | 0.03
Comm | 4.4254e-05 | 7.4628e-05 | 9.321e-05 | 0.0 | 1.22
Output | 0.00019476 | 0.00024309 | 0.00032745 | 0.0 | 3.96
Modify | 0.005637 | 0.0056559 | 0.0056903 | 0.0 | 92.24
Other | | 0.0001563 | | | 2.55
Nlocal: 166.667 ave 176 max 150 min
Histogram: 1 0 0 0 0 0 0 0 0 2
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

83
examples/mdi/log.17Jun22.aimd.driver.tcp.1 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 2.41182 on 1 procs for 10 steps with 500 atoms
Performance: 1791.180 tau/day, 4.146 timesteps/s
0.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 2.596e-06 | 2.596e-06 | 2.596e-06 | 0.0 | 0.00
Comm | 4.9627e-05 | 4.9627e-05 | 4.9627e-05 | 0.0 | 0.00
Output | 0.00063707 | 0.00063707 | 0.00063707 | 0.0 | 0.03
Modify | 2.411 | 2.411 | 2.411 | 0.0 | 99.97
Other | | 0.0001146 | | | 0.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02

83
examples/mdi/log.17Jun22.aimd.driver.tcp.3 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
# NVE
fix 1 all nve
# NPT
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
fix 2 all mdi/qm virial yes
thermo_style custom step temp pe etotal press vol
thermo 1
run 10
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp PotEng TotEng Press Volume
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
Loop time of 2.39983 on 3 procs for 10 steps with 500 atoms
Performance: 1800.127 tau/day, 4.167 timesteps/s
66.7% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 3.75e-07 | 1.3583e-06 | 2.574e-06 | 0.0 | 0.00
Comm | 5.4167e-05 | 0.00010938 | 0.00015338 | 0.0 | 0.00
Output | 0.00030885 | 0.00042099 | 0.00064497 | 0.0 | 0.02
Modify | 2.3988 | 2.3989 | 2.3989 | 0.0 | 99.96
Other | | 0.0004276 | | | 0.02
Nlocal: 166.667 ave 176 max 150 min
Histogram: 1 0 0 0 0 0 0 0 0 2
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:03

55
examples/mdi/log.17Jun22.aimd.engine.mpi.1 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:00

55
examples/mdi/log.17Jun22.aimd.engine.mpi.4 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:00

55
examples/mdi/log.17Jun22.aimd.engine.plugin.1 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:00

55
examples/mdi/log.17Jun22.aimd.engine.plugin.3 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 3 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 3 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:00

55
examples/mdi/log.17Jun22.aimd.engine.tcp.1 Normal file
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@ -0,0 +1,55 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:02

55
examples/mdi/log.17Jun22.aimd.engine.tcp.4 Normal file
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@ -0,0 +1,55 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
thermo_style custom step temp pe etotal press vol
thermo 1
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp PotEng TotEng Press Volume
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
8 0 -6.502724 -6.502724 -4.5844158 592.27671
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
Total wall time: 0:00:02

77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1 Normal file
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@ -0,0 +1,77 @@
LAMMPS (2 Jun 2022)
LAMMPS (2 Jun 2022)
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.000 seconds
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 0 -6.7699814 0 -6.7699814 -6.2120481
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
1 1.4377309 0 0 2.1522832 1.211305
2 0 -6.7596844 0 -6.7596844 -6.1418368
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
2 1.430825 0 0 2.141945 1.2054866
3 0 -6.7420029 0 -6.7420029 -6.0231905
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
3 1.4189655 0 0 2.1241913 1.1954949
4 0 -6.7161132 0 -6.7161132 -5.8534999
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
4 1.4016029 0 0 2.0981995 1.1808667
5 0 -6.6808361 0 -6.6808361 -5.6291449
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
5 1.3779738 0 0 2.0628267 1.1609589
6 0 -6.6344152 0 -6.6344152 -5.3453369
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
6 1.3471497 0 0 2.016683 1.1349892
7 0 -6.5752633 0 -6.5752633 -4.9977496
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
7 1.3081237 0 0 1.9582612 1.1021094
8 0 -6.502724 0 -6.502724 -4.5844158
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
8 1.2599751 0 0 1.8861828 1.0615437
9 0 -6.4153971 0 -6.4153971 -4.103842
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
9 1.2021373 0 0 1.7995995 1.0128146
10 0 -6.3153532 0 -6.3153532 -3.5633405
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:00
Total wall time: 0:00:00

77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2 Normal file
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@ -0,0 +1,77 @@
LAMMPS (2 Jun 2022)
LAMMPS (2 Jun 2022)
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 2 MPI processor grid
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.000 seconds
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 0 -6.7699814 0 -6.7699814 -6.2120481
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
1 1.4377309 0 0 2.1522832 1.211305
2 0 -6.7596844 0 -6.7596844 -6.1418368
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
2 1.430825 0 0 2.141945 1.2054866
3 0 -6.7420029 0 -6.7420029 -6.0231905
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
3 1.4189655 0 0 2.1241913 1.1954949
4 0 -6.7161132 0 -6.7161132 -5.8534999
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
4 1.4016029 0 0 2.0981995 1.1808667
5 0 -6.6808361 0 -6.6808361 -5.6291449
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
5 1.3779738 0 0 2.0628267 1.1609589
6 0 -6.6344152 0 -6.6344152 -5.3453369
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
6 1.3471497 0 0 2.016683 1.1349892
7 0 -6.5752633 0 -6.5752633 -4.9977496
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
7 1.3081237 0 0 1.9582612 1.1021094
8 0 -6.502724 0 -6.502724 -4.5844158
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
8 1.2599751 0 0 1.8861828 1.0615437
9 0 -6.4153971 0 -6.4153971 -4.103842
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
9 1.2021373 0 0 1.7995995 1.0128146
10 0 -6.3153532 0 -6.3153532 -3.5633405
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:00
Total wall time: 0:00:00

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 → examples/mdi/log.17Jun22.aimdpy.driver.tcp.1
View File

@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166

5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 → examples/mdi/log.17Jun22.aimdpy.driver.tcp.2
View File

@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166

49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1 Normal file
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@ -0,0 +1,49 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
6 1.3471497 0 0 2.016683 1.1349892
7 1.3081237 0 0 1.9582612 1.1021094
8 1.2599751 0 0 1.8861828 1.0615437
9 1.2021373 0 0 1.7995995 1.0128146
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:00

49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2 Normal file
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@ -0,0 +1,49 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.000 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
6 1.3471497 0 0 2.016683 1.1349892
7 1.3081237 0 0 1.9582612 1.1021094
8 1.2599751 0 0 1.8861828 1.0615437
9 1.2021373 0 0 1.7995995 1.0128146
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:00

49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1 Normal file
View File

@ -0,0 +1,49 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
6 1.3471497 0 0 2.016683 1.1349892
7 1.3081237 0 0 1.9582612 1.1021094
8 1.2599751 0 0 1.8861828 1.0615437
9 1.2021373 0 0 1.7995995 1.0128146
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:02

49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2 Normal file
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@ -0,0 +1,49 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z
region box block 0 5 0 5 0 $z
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
mdi engine
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 0 0 2.15568 1.2132167
1 1.4377309 0 0 2.1522832 1.211305
2 1.430825 0 0 2.141945 1.2054866
3 1.4189655 0 0 2.1241913 1.1954949
4 1.4016029 0 0 2.0981995 1.1808667
5 1.3779738 0 0 2.0628267 1.1609589
6 1.3471497 0 0 2.016683 1.1349892
7 1.3081237 0 0 1.9582612 1.1021094
8 1.2599751 0 0 1.8861828 1.0615437
9 1.2021373 0 0 1.7995995 1.0128146
10 1.1347688 0 0 1.6987489 0.95605588
Total wall time: 0:00:02

25
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 → examples/mdi/log.17Jun22.aimdpy.qm.mpi.1
View File

@ -1,4 +1,4 @@
LAMMPS (17 Feb 2022)
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
@ -20,7 +20,7 @@ Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
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
create_atoms CPU = 0.000 seconds
mass 1 1.0
pair_style lj/cut 2.5
@ -31,7 +31,7 @@ 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
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
@ -45,11 +45,16 @@ Neighbor list info ...
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
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
6 0 -6.6344152 0 -6.6344152 -5.3453369
7 0 -6.5752633 0 -6.5752633 -4.9977496
8 0 -6.502724 0 -6.502724 -4.5844158
9 0 -6.4153971 0 -6.4153971 -4.103842
10 0 -6.3153532 0 -6.3153532 -3.5633405
Total wall time: 0:00:00

23
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 → examples/mdi/log.17Jun22.aimdpy.qm.mpi.3
View File

@ -1,4 +1,4 @@
LAMMPS (17 Feb 2022)
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
@ -31,7 +31,7 @@ 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
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
@ -45,11 +45,16 @@ Neighbor list info ...
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
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
6 0 -6.6344152 0 -6.6344152 -5.3453369
7 0 -6.5752633 0 -6.5752633 -4.9977496
8 0 -6.502724 0 -6.502724 -4.5844158
9 0 -6.4153971 0 -6.4153971 -4.103842
10 0 -6.3153532 0 -6.3153532 -3.5633405
Total wall time: 0:00:00

25
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 → examples/mdi/log.17Jun22.aimdpy.qm.tcp.1
View File

@ -1,4 +1,4 @@
LAMMPS (17 Feb 2022)
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
@ -31,7 +31,7 @@ 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
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
@ -45,11 +45,16 @@ Neighbor list info ...
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
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
6 0 -6.6344152 0 -6.6344152 -5.3453369
7 0 -6.5752633 0 -6.5752633 -4.9977496
8 0 -6.502724 0 -6.502724 -4.5844158
9 0 -6.4153971 0 -6.4153971 -4.103842
10 0 -6.3153532 0 -6.3153532 -3.5633405
Total wall time: 0:00:02

25
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 → examples/mdi/log.17Jun22.aimdpy.qm.tcp.3
View File

@ -1,4 +1,4 @@
LAMMPS (17 Feb 2022)
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
variable x index 5
@ -31,7 +31,7 @@ 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
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
@ -45,11 +45,16 @@ Neighbor list info ...
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
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -6.7699814 0 -6.7699814 -6.2120481
2 0 -6.7596844 0 -6.7596844 -6.1418368
3 0 -6.7420029 0 -6.7420029 -6.0231905
4 0 -6.7161132 0 -6.7161132 -5.8534999
5 0 -6.6808361 0 -6.6808361 -5.6291449
6 0 -6.6344152 0 -6.6344152 -5.3453369
7 0 -6.5752633 0 -6.5752633 -4.9977496
8 0 -6.502724 0 -6.502724 -4.5844158
9 0 -6.4153971 0 -6.4153971 -4.103842
10 0 -6.3153532 0 -6.3153532 -3.5633405
Total wall time: 0:00:02

90
examples/mdi/log.17Jun22.sequence.engine.mpi.1 Normal file
View File

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

90
examples/mdi/log.17Jun22.sequence.engine.mpi.4 Normal file
View File

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

90
examples/mdi/log.17Jun22.sequence.engine.plugin.1 Normal file
View File

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

90
examples/mdi/log.17Jun22.sequence.engine.plugin.3 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (2 Jun 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 3 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 3 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 3 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
3 by 1 by 1 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

90
examples/mdi/log.17Jun22.sequence.engine.tcp.1 Normal file
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LAMMPS (2 Jun 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 1 by 1 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

90
examples/mdi/log.17Jun22.sequence.engine.tcp.4 Normal file
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LAMMPS (2 Jun 2022)
# MDI engine script to process a series of evaulate, run, minimize commands
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
thermo 10
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.9713146 0 -2.4947521 3.1253597
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -4.1934138 0 -2.7168513 0.72358299
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
90 1.219283 -4.5483185 0 -2.747971 0.17898549
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
delete_atoms group all
Deleted 64 atoms, new total = 0
1 by 2 by 2 MPI processor grid
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -3.8524214 0 -2.3758589 4.6814052
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
20 1.1791601 -4.117932 0 -2.3768284 3.8565
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
100 1.43934 -4.5009545 0 -2.375679 3.0923444
Total wall time: 0:00:00

248
examples/mdi/log.17Jun22.series.alone.1 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 2.729e-06 on 1 procs for 0 steps with 500 atoms
109.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.729e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15687 ave 15687 max 15687 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15687
Ave neighs/atom = 31.374
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.135 | 3.135 | 3.135 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 1.434e-06 on 1 procs for 0 steps with 500 atoms
139.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.434e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18734 ave 18734 max 18734 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18734
Ave neighs/atom = 37.468
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 1.483e-06 on 1 procs for 0 steps with 500 atoms
134.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.483e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1956 ave 1956 max 1956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 20023 ave 20023 max 20023 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 20023
Ave neighs/atom = 40.046
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
clear
next rho
jump SELF LOOP
Total wall time: 0:00:00

213
examples/mdi/log.17Jun22.series.driver.mpi.1 Normal file
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@ -0,0 +1,213 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
mdi connect
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 1.919e-06 on 1 procs for 0 steps with 500 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.919e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 1.141e-06 on 1 procs for 0 steps with 500 atoms
87.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.141e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.002 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 1.019e-06 on 1 procs for 0 steps with 500 atoms
98.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.019e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
mdi exit
Total wall time: 0:00:00

213
examples/mdi/log.17Jun22.series.driver.mpi.3 Normal file
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@ -0,0 +1,213 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
mdi connect
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 4.00933e-06 on 3 procs for 0 steps with 500 atoms
91.5% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 4.009e-06 | | |100.00
Nlocal: 166.667 ave 177 max 150 min
Histogram: 1 0 0 0 0 0 0 0 1 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 3.11833e-06 on 3 procs for 0 steps with 500 atoms
117.6% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.118e-06 | | |100.00
Nlocal: 166.667 ave 178 max 150 min
Histogram: 1 0 0 0 0 0 0 1 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
3 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 2.85467e-06 on 3 procs for 0 steps with 500 atoms
140.1% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.855e-06 | | |100.00
Nlocal: 166.667 ave 181 max 150 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
mdi exit
Total wall time: 0:00:00

212
examples/mdi/log.17Jun22.series.driver.plugin.1 Normal file
View File

@ -0,0 +1,212 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 2.359e-06 on 1 procs for 0 steps with 500 atoms
127.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.359e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 1.468e-06 on 1 procs for 0 steps with 500 atoms
204.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.468e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 1.378e-06 on 1 procs for 0 steps with 500 atoms
145.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.378e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
Total wall time: 0:00:00

212
examples/mdi/log.17Jun22.series.driver.plugin.3 Normal file
View File

@ -0,0 +1,212 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 3.50867e-06 on 3 procs for 0 steps with 500 atoms
114.0% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.509e-06 | | |100.00
Nlocal: 166.667 ave 177 max 150 min
Histogram: 1 0 0 0 0 0 0 0 1 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 3.225e-06 on 3 procs for 0 steps with 500 atoms
82.7% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.225e-06 | | |100.00
Nlocal: 166.667 ave 178 max 150 min
Histogram: 1 0 0 0 0 0 0 1 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
3 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 2.713e-06 on 3 procs for 0 steps with 500 atoms
98.3% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.713e-06 | | |100.00
Nlocal: 166.667 ave 181 max 150 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
Total wall time: 0:00:00

213
examples/mdi/log.17Jun22.series.driver.tcp.1 Normal file
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@ -0,0 +1,213 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
mdi connect
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 3.017e-06 on 1 procs for 0 steps with 500 atoms
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.017e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 1.977e-06 on 1 procs for 0 steps with 500 atoms
101.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.977e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 2.042e-06 on 1 procs for 0 steps with 500 atoms
97.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.042e-06 | | |100.00
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
mdi exit
Total wall time: 0:00:00

213
examples/mdi/log.17Jun22.series.driver.tcp.3 Normal file
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@ -0,0 +1,213 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
variable rho index 0.7 0.8 0.9
mdi connect
label LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.7
Reading data file ...
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
Loop time of 9.08933e-06 on 3 procs for 0 steps with 500 atoms
95.3% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 9.089e-06 | | |100.00
Nlocal: 166.667 ave 177 max 150 min
Histogram: 1 0 0 0 0 0 0 0 1 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.8
Reading data file ...
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
Loop time of 3.63567e-06 on 3 procs for 0 steps with 500 atoms
100.9% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.636e-06 | | |100.00
Nlocal: 166.667 ave 178 max 150 min
Histogram: 1 0 0 0 0 0 0 1 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
units lj
atom_style atomic
read_data data.series.${rho}
read_data data.series.0.9
Reading data file ...
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
3 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
displace_atoms all random 0.1 0.1 0.1 48294
Displacing atoms ...
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all mdi/qm add no virial yes connect no
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
run 0
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
Loop time of 3.806e-06 on 3 procs for 0 steps with 500 atoms
105.1% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.806e-06 | | |100.00
Nlocal: 166.667 ave 181 max 150 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
clear
next rho
jump SELF LOOP
mdi exit
Total wall time: 0:00:00

58
examples/mdi/log.17Jun22.series.engine.mpi.1 Normal file
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@ -0,0 +1,58 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -5.200819 0 -5.200819 -4.5647906
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.0419499 0 -6.0419499 -4.2737827
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

58
examples/mdi/log.17Jun22.series.engine.mpi.4 Normal file
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@ -0,0 +1,58 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -5.200819 0 -5.200819 -4.5647906
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.0419499 0 -6.0419499 -4.2737827
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

42
examples/mdi/log.17Jun22.series.engine.plugin.1 Normal file
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@ -0,0 +1,42 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

42
examples/mdi/log.17Jun22.series.engine.plugin.3 Normal file
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@ -0,0 +1,42 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 3 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
3 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.105 | 3.107 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

58
examples/mdi/log.17Jun22.series.engine.tcp.1 Normal file
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@ -0,0 +1,58 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -5.200819 0 -5.200819 -4.5647906
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.0419499 0 -6.0419499 -4.2737827
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

58
examples/mdi/log.17Jun22.series.engine.tcp.4 Normal file
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@ -0,0 +1,58 @@
LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -5.200819 0 -5.200819 -4.5647906
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.0419499 0 -6.0419499 -4.2737827
delete_atoms group all
Deleted 500 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.4477578 0 -6.4477578 -1.5268553
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
compute 1 all pressure NULL virial
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.alone id type x y z fx fy fz
dump_modify 1 sort id
run 300
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.159268 on 1 procs for 300 steps with 500 atoms
Performance: 813725.152 tau/day, 1883.623 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.10659 | 0.10659 | 0.10659 | 0.0 | 66.93
Neigh | 0.038637 | 0.038637 | 0.038637 | 0.0 | 24.26
Comm | 0.0053144 | 0.0053144 | 0.0053144 | 0.0 | 3.34
Output | 0.0048583 | 0.0048583 | 0.0048583 | 0.0 | 3.05
Modify | 0.002043 | 0.002043 | 0.002043 | 0.0 | 1.28
Other | | 0.001821 | | | 1.14
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18744 ave 18744 max 18744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.003 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.052449 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734575789
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.0497171 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7528640103266583949
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.0506296 on 1 procs for 100 steps with 500 atoms
Performance: 853255.432 tau/day, 1975.128 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032111 | 0.032111 | 0.032111 | 0.0 | 63.42
Neigh | 0.012403 | 0.012403 | 0.012403 | 0.0 | 24.50
Comm | 0.0016352 | 0.0016352 | 0.0016352 | 0.0 | 3.23
Output | 0.001556 | 0.001556 | 0.001556 | 0.0 | 3.07
Modify | 0.0023767 | 0.0023767 | 0.0023767 | 0.0 | 4.69
Other | | 0.0005478 | | | 1.08
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18744 ave 18744 max 18744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7527974697327088904
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.0242313 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734558025
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.0269411 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.752864010326673494
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.022648 on 3 procs for 100 steps with 500 atoms
Performance: 1907449.463 tau/day, 4415.392 timesteps/s
100.0% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0091419 | 0.010422 | 0.011089 | 0.9 | 46.02
Neigh | 0.0036491 | 0.0040749 | 0.0043554 | 0.5 | 17.99
Comm | 0.004713 | 0.0056035 | 0.0073471 | 1.6 | 24.74
Output | 0.00062782 | 0.00063348 | 0.00064461 | 0.0 | 2.80
Modify | 0.0013385 | 0.0013655 | 0.0013943 | 0.1 | 6.03
Other | | 0.0005485 | | | 2.42
Nlocal: 166.667 ave 175 max 157 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 1254.33 ave 1264 max 1246 min
Histogram: 1 0 0 1 0 0 0 0 0 1
Neighs: 6248 ave 6632 max 5774 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.752797469732716884
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
run 300 pre no post no every 100
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
"""
run 300 pre no post no every 100
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.0623265 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734575789
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.0498825 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7528640103266583949
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.050109 on 1 procs for 100 steps with 500 atoms
Performance: 862120.560 tau/day, 1995.649 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031747 | 0.031747 | 0.031747 | 0.0 | 63.36
Neigh | 0.012304 | 0.012304 | 0.012304 | 0.0 | 24.55
Comm | 0.0016113 | 0.0016113 | 0.0016113 | 0.0 | 3.22
Output | 0.0015529 | 0.0015529 | 0.0015529 | 0.0 | 3.10
Modify | 0.0023537 | 0.0023537 | 0.0023537 | 0.0 | 4.70
Other | | 0.0005398 | | | 1.08
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18744 ave 18744 max 18744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7527974697327088904
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
variable x index 5
variable y index 5
variable z index 5
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
run 300 pre no post no every 100
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
"""
run 300 pre no post no every 100
"print 'QM eng = $(f_2/atoms)'"
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.0245664 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734442562
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566498001 -0.48020228608205661747 -0.33571704057970125357 -0.43928725961523629184
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.0221302 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7528640103266690531
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957305301251 -0.51524577748319111414 -0.27940441114042025017 -0.42108499009554783976
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.0224519 on 3 procs for 100 steps with 500 atoms
Performance: 1924114.069 tau/day, 4453.968 timesteps/s
100.0% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0096043 | 0.010493 | 0.011044 | 0.6 | 46.74
Neigh | 0.0037658 | 0.0041299 | 0.004422 | 0.4 | 18.39
Comm | 0.0048946 | 0.0055617 | 0.0068824 | 1.3 | 24.77
Output | 0.00063471 | 0.00063884 | 0.00064691 | 0.0 | 2.85
Modify | 0.0010632 | 0.0010754 | 0.0010895 | 0.0 | 4.79
Other | | 0.0005531 | | | 2.46
Nlocal: 166.667 ave 175 max 157 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 1254.33 ave 1264 max 1246 min
Histogram: 1 0 0 1 0 0 0 0 0 1
Neighs: 6248 ave 6632 max 5774 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7527974697327239895
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315521697958 -0.24280603320323956851 -0.42189158691169470483 -0.59061971935071611028
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 1 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.004 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.276735 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734575789
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.276667 on 1 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7528640103266583949
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.278602 on 1 procs for 100 steps with 500 atoms
Performance: 155060.058 tau/day, 358.935 timesteps/s
26.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.049067 | 0.049067 | 0.049067 | 0.0 | 17.61
Neigh | 0.01894 | 0.01894 | 0.01894 | 0.0 | 6.80
Comm | 0.0026936 | 0.0026936 | 0.0026936 | 0.0 | 0.97
Output | 0.002919 | 0.002919 | 0.002919 | 0.0 | 1.05
Modify | 0.20406 | 0.20406 | 0.20406 | 0.0 | 73.24
Other | | 0.0009253 | | | 0.33
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18744 ave 18744 max 18744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7527974697327088904
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
Total wall time: 0:00:01

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI driver script
units lj
atom_style atomic
read_data data.snapshot
Reading data file ...
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
1 by 1 by 3 MPI processor grid
reading atoms ...
500 atoms
reading velocities ...
500 velocities
read_data CPU = 0.005 seconds
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all mdi/qm add no every 100 virial yes
compute 1 all pressure NULL virial
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
thermo 100
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
dump_modify 1 sort id
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
Loop time of 0.271725 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.7579933325734558025
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
Loop time of 0.275711 on 3 procs for 100 steps with 500 atoms
print 'QM eng = $(f_2/atoms)'
QM eng = -5.752864010326673494
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
Loop time of 0.27674 on 3 procs for 100 steps with 500 atoms
Performance: 156103.145 tau/day, 361.350 timesteps/s
71.1% CPU use with 3 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0086137 | 0.01236 | 0.019756 | 4.7 | 4.47
Neigh | 0.003253 | 0.0047355 | 0.0075676 | 2.9 | 1.71
Comm | 0.0065383 | 0.016521 | 0.021738 | 5.5 | 5.97
Output | 0.0011823 | 0.0011972 | 0.0012111 | 0.0 | 0.43
Modify | 0.24066 | 0.24076 | 0.24093 | 0.0 | 87.00
Other | | 0.001171 | | | 0.42
Nlocal: 166.667 ave 175 max 157 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Nghost: 1254.33 ave 1264 max 1246 min
Histogram: 1 0 0 1 0 0 0 0 0 1
Neighs: 6248 ave 6632 max 5774 min
Histogram: 1 0 0 0 0 0 1 0 0 1
Total # of neighbors = 18744
Ave neighs/atom = 37.488
Neighbor list builds = 31
Dangerous builds = 0
print 'QM eng = $(f_2/atoms)'
QM eng = -5.752797469732716884
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
Total wall time: 0:00:01

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:00

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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:00

45
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:00

45
examples/mdi/log.17Jun22.snapshot.engine.plugin.3 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 3 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 3 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:00

45
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 1 by 1 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 1 by 1 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:01

45
examples/mdi/log.17Jun22.snapshot.engine.tcp.4 Normal file
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LAMMPS (2 Jun 2022)
# 3d Lennard-Jones melt - MDI engine script
units lj
atom_style atomic
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region box block 0 1 0 1 0 1
create_box 1 box
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
1 by 2 by 2 MPI processor grid
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
mdi engine
delete_atoms group all
Deleted 0 atoms, new total = 0
1 by 2 by 2 MPI processor grid
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -6.7733681 0 -6.7733681 -6.2353173
1 0 -5.7579933 0 -5.7579933 -0.4184022
2 0 -5.752864 0 -5.752864 -0.40524506
3 0 -5.7527975 0 -5.7527975 -0.41843911
Total wall time: 0:00:01

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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
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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
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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
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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
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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

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