diff --git a/examples/mdi/README b/examples/mdi/README index 9298e9c59c..9380e2e79a 100644 --- a/examples/mdi/README +++ b/examples/mdi/README @@ -21,9 +21,9 @@ a driver and couple to an engine that is either a stand-alone code or a plugin. Examples for all these use cases are in this directory. The example commands below illustrate how to run all the variants. -To use LAMMPS as a plugin engine, you must build it as a shared library. -Something like this, which also builds the normal LAMMPS executable -lmp_mpi: +To use LAMMPS as a plugin engine, you must build it as a shared +library. Something like this with make, which also builds the normal +LAMMPS executable lmp_mpi: cd src make yes-mdi @@ -33,189 +33,59 @@ To use the serial_driver.py example you will need Python 3 with Numpy and mpi4py available in your Python. Make sure LAMMPS and Python are using same the same version of MPI. +5 use-case examples are explained below. + +See the Run.sh file for commands to run each of the examples +in all the different modes. + +In the first 3 examples, results running with MDI should be identical +to running without MDI (alone log files). Example #4 has no non-MDI +run. Example #5 results should match the non-MDI run of example #1. + ------------------------------------------------- ------------------------------------------------- -* Example #1 = run ab inito MD (AIMD) - Two instances of LAMMPS operate as a driver and engine - As an engine, LAMMPS is a surrogate for a quantum code +* Example #1 = run ab initio MD (AIMD) + +See the log aimd files. + +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code. Note that the 2 input scripts in.aimd.alone and in.aimd.driver have an option for running in NVE vs NPT mode. Comment in/out the appropriate line to change modes. Nothing needs to be changed in the in.aimd.engine or in.aimd.engine.plugin scripts. ---- +------------------------------------------------- +------------------------------------------------- -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI +* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run -% lmp_mpi -log log.aimd.alone < in.aimd.alone +See the log snapshot and dump snapshot files. -With MDI, the thermo output of the driver should match the thermo -output of the in.aimd.alone script. - ---- - -Run with TCP: 1 proc each - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver - -% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine - ---- - -Run with TCP: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp -in in.aimd.driver - -% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp -in in.aimd.engine - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine - ---- - -Run with MPI: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi -in in.aimd.engine - ---- - -Run in plugin mode: 1 proc - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code ------------------------------------------------- ------------------------------------------------- -* Example #1b = run LAMMPS, compute QM forces on snapshots from a long run - Two instances of LAMMPS operate as a driver and engine - As an engine, LAMMPS is a surrogate for a quantum code +* Example #3 = run LAMMPS, compute QM forces on series of independent systems ---- +files See the log series and dump series files. -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI - -% lmp_mpi -log log.snapshot.alone < in.snapshot.alone - -With MDI, the thermo output of the driver should match the thermo -output of the in.snapshot.alone script. Likewise the dump file written -by the driver should match dump.snapshot.alone. - ---- - -Run with TCP: 1 proc each - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver - -% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine - ---- - -Run with TCP: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp -in in.snapshot.driver - -% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp -in in.snapshot.engine - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine - ---- - -Run with MPI: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi -in in.snapshot.engine - ---- - -Run in plugin mode: 1 proc - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin -in in.snapshot.driver.plugin +Two instances of LAMMPS operate as a driver and engine. As an engine, +LAMMPS is a surrogate for a quantum code ------------------------------------------------- ------------------------------------------------- -* Example #1c = run LAMMPS, compute QM forces on series of independent systems - Two instances of LAMMPS operate as a driver and engine - As an engine, LAMMPS is a surrogate for a quantum code +* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations ---- +See the log sequence files. -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI - -% lmp_mpi -log log.series.alone < in.series.alone - -With MDI, the thermo output of the driver should match the thermo -output of the in.series.alone script. Likewise the dump files written -by the driver should match dump.series.alone files. - ---- - -Run with TCP: 1 proc each - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver - -% lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine - ---- - -Run with TCP: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp -in in.series.driver - -% mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp -in in.series.engine - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine - ---- - -Run with MPI: 3 procs + 4 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi -in in.series.engine - ---- - -Run in plugin mode: 1 proc - -% lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin -in in.series.driver.plugin - -------------------------------------------------- -------------------------------------------------- - -* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations - Each calculation can be a single-point evaluation, MD run, or minimization +Each calculation can be a single-point evaluation, MD run, or +minimization The sequence_driver.py code allows for optional switches in addition to -mdi (required) and the -plugin and -plugin_args switches which are @@ -244,101 +114,21 @@ copied here: # -seed 12345 # random number seed > 0, default = 12345 ---- - -Run with TCP: 1 proc each - -% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" - -% lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python - ---- - -Run with TCP: 2 proc + 4 procs - -% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" - -% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence.python - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence.python - ---- - -Run with MPI: 2 procs + 4 procs - -% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence -in in.sequence.python - ---- - -Run in plugin mode: 1 proc - -% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python - ---- - -Run in plugin mode: 3 procs - -% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence".python - ------------------------------------------------- ------------------------------------------------- -* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines - First LAMMPS instance performs the MD timestepping - Second LAMMPS instance is surrogate QM = computes forces +* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines + +See the log aimdpy files. + +First LAMMPS instance performs the MD timestepping. Second LAMMPS +instance is surrogate QM to compute forces. The aimd_driver.py code allows for an optional switch in addition to -mdi (required) and the -plugin and -plugin_args swiches which are used to link to the 2 engines as a plugin libraries. The example run commands below use the default values of the optional switch. The -switch is also explained the top of the file; the info is copied -here: +switch is also explained the top of the file; the info is copied here: # -nsteps 5 # number of timesteps in dynamics runs, default = 5 - ---- - -Run the entire calculation with a single instance of LAMMPS by itself - results should be identical to running this example with MDI - -% lmp_mpi -log log.aimd.alone < in.aimd.alone - -With MDI, the driver prints the QM and Total energies. These should -match the PotEng and TotEng output of the in.aimd.alone script. - ---- - -Run with TCP: 1 proc each - -% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" - -% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm - -% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with TCP: 2 procs + 2 procs + 3 procs - -% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" - -% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm - -% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with MPI: 1 proc each - -% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm - ---- - -Run with MPI: 2 procs + 2 procs + 3 procs - -% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm diff --git a/examples/mdi/Run.sh b/examples/mdi/Run.sh new file mode 100644 index 0000000000..55c5638841 --- /dev/null +++ b/examples/mdi/Run.sh @@ -0,0 +1,256 @@ +# Run all the examples + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 1 + +# --- + +# Run without MDI + +lmp_mpi -log log.aimd.alone.1 < in.aimd.alone + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin +mv log.aimd.engine.plugin log.aimd.engine.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin +mv log.aimd.engine.plugin log.aimd.engine.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 2 + +# --- + +# Run without MDI + +lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone +mv dump.snapshot.alone dump.snapshot.alone.1 + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.tcp.1 + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.tcp.3 + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.mpi.1 + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine +mv dump.snapshot.driver dump.snapshot.driver.mpi.3 + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin +mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1 +mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin +mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3 +mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 3 + +# --- + +# Run without MDI + +lmp_mpi -log log.series.alone.1 < in.series.alone +mv dump.series.alone dump.series.alone.1 + +# --- + +# Run with TCP: 1 proc each + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver & + +lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine +mv dump.series.driver dump.series.driver.tcp.1 + +# --- + +# Run with TCP: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver & + +mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine +mv dump.series.driver dump.series.driver.tcp.3 + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine +mv dump.series.driver dump.series.driver.mpi.1 + +# --- + +# Run with MPI: 3 procs + 4 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine +mv dump.series.driver dump.series.driver.mpi.3 + +# --- + +# Run in plugin mode: 1 proc + +lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin +mv log.series.engine.plugin log.series.engine.plugin.1 +mv dump.series.driver.plugin dump.series.driver.plugin.1 + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin +mv log.series.engine.plugin log.series.engine.plugin.3 +mv dump.series.driver.plugin dump.series.driver.plugin.3 + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 4 + +# --- + +# Run with TCP: 1 proc each + +python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" & + +lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python + +# --- + +# Run with TCP: 2 proc + 4 procs + +mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" & + +mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python + +# --- + +# Run with MPI: 2 procs + 4 procs + +mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python + +# --- + +# Run in plugin mode: 1 proc + +python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python + +# --- + +# Run in plugin mode: 3 procs + +mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python + +# ------------------------------------------------- +# ------------------------------------------------- + +# Example 5 + +# --- + +# Run with TCP: 1 proc each + +python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" & + +lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimd.mm & + +lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimd.qm + +# --- + +# Run with TCP: 2 procs + 2 procs + 3 procs + +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021" & + +mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm.tcp.2 -in in.aimd.mm & + +mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm.tcp.3 -in in.aimd.qm + +# --- + +# Run with MPI: 1 proc each + +mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.1 -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.qm.1 -in in.aimd.qm + +# --- + +# Run with MPI: 2 procs + 2 procs + 3 procs + +mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm.mpi.2 -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm.mpi.3 -in in.aimd.qm diff --git a/examples/mdi/in.sequence.python b/examples/mdi/in.sequence.python index c094326ae7..6f28922a66 100644 --- a/examples/mdi/in.sequence.python +++ b/examples/mdi/in.sequence.python @@ -19,3 +19,4 @@ fix 1 all nve thermo 10 mdi engine + diff --git a/examples/mdi/in.series.alone b/examples/mdi/in.series.alone index d08b72d386..f359581c50 100644 --- a/examples/mdi/in.series.alone +++ b/examples/mdi/in.series.alone @@ -4,7 +4,6 @@ variable x index 5 variable y index 5 variable z index 5 -variable ifile loop 3 variable rho index 0.7 0.8 0.9 label LOOP @@ -32,12 +31,11 @@ label LOOP run 0 - write_dump all custom dump.series.alone.${ifile} & - id type x y z fx fy fz modify sort id + write_dump all custom dump.series.alone & + id type x y z fx fy fz modify sort id append yes clear -next ifile next rho jump SELF LOOP diff --git a/examples/mdi/in.series.driver b/examples/mdi/in.series.driver index d8b4df1f8c..4089dd66ec 100644 --- a/examples/mdi/in.series.driver +++ b/examples/mdi/in.series.driver @@ -4,10 +4,9 @@ variable x index 5 variable y index 5 variable z index 5 -variable ifile loop 3 variable rho index 0.7 0.8 0.9 -mdi start +mdi connect label LOOP @@ -25,24 +24,20 @@ label LOOP neighbor 0.3 bin neigh_modify delay 0 every 1 check yes - fix 1 all mdi/qm add no virial yes external yes + fix 1 all mdi/qm add no virial yes connect no variable epress equal (f_1[1]+f_1[2]+f_1[3])/3 thermo_style custom step temp f_1 v_epress f_1[1] f_1[2] f_1[3] run 0 - write_dump all custom dump.series.driver.${ifile} & - id type x y z f_1[1] f_1[2] f_1[3] modify sort id + write_dump all custom dump.series.driver & + id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes - # cannot do "clear" b/c will shutdown MDI engine - # have to - clear -next ifile next rho jump SELF LOOP -mdi stop +mdi exit diff --git a/examples/mdi/in.series.driver.plugin b/examples/mdi/in.series.driver.plugin index 4a4364c447..8096b56886 100644 --- a/examples/mdi/in.series.driver.plugin +++ b/examples/mdi/in.series.driver.plugin @@ -4,7 +4,6 @@ variable x index 5 variable y index 5 variable z index 5 -variable ifile loop 3 variable rho index 0.7 0.8 0.9 label LOOP @@ -33,12 +32,11 @@ label LOOP extra "-log log.series.engine.plugin" & command "run 0" - write_dump all custom dump.series.driver.${ifile} & - id type x y z f_1[1] f_1[2] f_1[3] modify sort id + write_dump all custom dump.series.driver.plugin & + id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes clear -next ifile next rho jump SELF LOOP diff --git a/examples/mdi/in.snapshot.driver.plugin b/examples/mdi/in.snapshot.driver.plugin index 7592c5fb59..2fdca3f6cd 100644 --- a/examples/mdi/in.snapshot.driver.plugin +++ b/examples/mdi/in.snapshot.driver.plugin @@ -32,7 +32,7 @@ thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3] thermo 100 -dump 1 all custom 500 dump.snapshot.driver & +dump 1 all custom 500 dump.snapshot.driver.plugin & id type x y z f_2[1] f_2[2] f_2[3] dump_modify 1 sort id diff --git a/examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 deleted file mode 100644 index 5fa3743530..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1 +++ /dev/null @@ -1,90 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms - -Performance: 505739.085 tau/day, 1170.692 timesteps/s -73.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04 -Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49 -Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53 -Other | | 6.054e-05 | | | 1.42 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1956 ave 1956 max 1956 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 19500 ave 19500 max 19500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 19500 -Ave neighs/atom = 39 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 deleted file mode 100644 index d817aed5a3..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms - -Performance: 731582.413 tau/day, 1693.478 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43 -Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58 -Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98 -Other | | 3e-05 | | | 1.02 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 deleted file mode 100644 index eaf806cfc9..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms - -Performance: 684416.574 tau/day, 1584.298 timesteps/s -99.5% CPU use with 3 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17 -Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92 -Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88 -Other | | 0.0001272 | | | 4.03 - -Nlocal: 166.667 ave 200 max 150 min -Histogram: 2 0 0 0 0 0 0 0 0 1 -Nghost: 55.3333 ave 92 max 32 min -Histogram: 1 1 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -3 -Ave neighs/atom = -0.006 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 deleted file mode 100644 index dea662c157..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1 +++ /dev/null @@ -1,80 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd plugin -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5" -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms - -Performance: 544685.246 tau/day, 1260.845 timesteps/s -98.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40 -Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91 -Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89 -Other | | 3.184e-05 | | | 0.80 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 deleted file mode 100644 index ff9e2dd8f5..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3 +++ /dev/null @@ -1,80 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd plugin -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5" -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms - -Performance: 752045.581 tau/day, 1740.846 timesteps/s -99.1% CPU use with 3 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36 -Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21 -Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42 -Other | | 8.637e-05 | | | 3.01 - -Nlocal: 166.667 ave 200 max 150 min -Histogram: 2 0 0 0 0 0 0 0 0 1 -Nghost: 55.3333 ave 92 max 32 min -Histogram: 1 1 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -3 -Ave neighs/atom = -0.006 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 deleted file mode 100644 index 1ff358e269..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1 +++ /dev/null @@ -1,79 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI driver script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -# NVE -fix 1 all nve -# NPT -#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0 - -fix 2 all mdi/aimd -fix_modify 2 energy yes virial yes - -thermo_style custom step temp pe etotal press vol -thermo 1 - -run 5 -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp PotEng TotEng Press Volume - 0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671 - 1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671 - 2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671 - 3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671 - 4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671 - 5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671 -Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms - -Performance: 1792.736 tau/day, 4.150 timesteps/s -0.1% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00 -Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02 -Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97 -Other | | 6.184e-05 | | | 0.01 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 166 ave 166 max 166 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = -1 -Ave neighs/atom = -0.002 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:08 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 deleted file mode 100644 index 6abf6b3928..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3 +++ /dev/null @@ -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 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 deleted file mode 100644 index 615dae0578..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 b/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 deleted file mode 100644 index 88d5c66892..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 deleted file mode 100644 index 615dae0578..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 deleted file mode 100644 index fb8034972f..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 deleted file mode 100644 index 72becb2bba..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 b/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 deleted file mode 100644 index 3154bd0b27..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - MDI engine script - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 deleted file mode 100644 index 741e8a1dfe..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1 +++ /dev/null @@ -1,5 +0,0 @@ -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 deleted file mode 100644 index 741e8a1dfe..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2 +++ /dev/null @@ -1,5 +0,0 @@ -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 deleted file mode 100644 index 2205a0f051..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1 +++ /dev/null @@ -1,6 +0,0 @@ -Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769 -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 deleted file mode 100644 index 2205a0f051..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2 +++ /dev/null @@ -1,6 +0,0 @@ -Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769 -Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177 -Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774 -Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781 -Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791 -Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 deleted file mode 100644 index 55825ab30a..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 deleted file mode 100644 index 4c636b8486..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 deleted file mode 100644 index 7eb94ac4c6..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:11 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 b/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 deleted file mode 100644 index 6d253ee790..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2 +++ /dev/null @@ -1,44 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 2 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -velocity all create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -mdi engine -WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141) -WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209) -Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 0 0 2.15568 1.2132167 - 1 1.4377309 0 0 2.1522832 1.211305 - 2 1.430825 0 0 2.141945 1.2054866 - 3 1.4189655 0 0 2.1241913 1.1954949 - 4 1.4016029 0 0 2.0981995 1.1808667 - 5 1.3779738 0 0 2.0628267 1.1609589 -Total wall time: 0:00:11 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 deleted file mode 100644 index e75a12c948..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 b/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 deleted file mode 100644 index 5d6702100c..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 deleted file mode 100644 index 8750392def..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 b/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 deleted file mode 100644 index cd5d443e65..0000000000 --- a/examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3 +++ /dev/null @@ -1,55 +0,0 @@ -LAMMPS (17 Feb 2022) -# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py - -variable x index 5 -variable y index 5 -variable z index 5 - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 $x 0 $y 0 $z -region box block 0 5 0 $y 0 $z -region box block 0 5 0 5 0 $z -region box block 0 5 0 5 0 5 -create_box 1 box -Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - 1 by 1 by 3 MPI processor grid -create_atoms 1 box -Created 500 atoms - using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) - create_atoms CPU = 0.001 seconds -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -mdi engine -WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60) - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -6.7733681 0 -6.7733681 -6.2353173 - 1 0 -6.7699814 0 -6.7699814 -6.2120481 - 2 0 -6.7596844 0 -6.7596844 -6.1418368 - 3 0 -6.7420029 0 -6.7420029 -6.0231905 - 4 0 -6.7161132 0 -6.7161132 -5.8534999 - 5 0 -6.6808361 0 -6.6808361 -5.6291449 -Total wall time: 0:00:01 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 b/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 deleted file mode 100644 index 17e040d0d7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 deleted file mode 100644 index e634b156b8..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 deleted file mode 100644 index 86d23d382b..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 b/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 deleted file mode 100644 index 17e040d0d7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2 +++ /dev/null @@ -1,3 +0,0 @@ -Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16 -Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16 -Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 b/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 deleted file mode 100644 index ada69c6ca7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 2 by 2 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 b/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 deleted file mode 100644 index df8d258715..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 3 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 3 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 3 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 3 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 b/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 deleted file mode 100644 index 929cdce5cf..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 1 by 1 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 1 by 1 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 b/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 deleted file mode 100644 index ada69c6ca7..0000000000 --- a/examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4 +++ /dev/null @@ -1,89 +0,0 @@ -LAMMPS (17 Feb 2022) -# MDI engine script to process a series of evaulate, run, minimize commands - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 -region box block 0 1 0 1 0 1 -create_box 1 box -Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962) - 1 by 2 by 2 MPI processor grid -mass 1 1.0 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -thermo 10 - -mdi engine -delete_atoms group all -Deleted 0 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 4 4 4 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.9713146 0 -2.4947521 3.1253597 - 10 1.2380002 -4.3210346 0 -2.4930499 2.0015258 - 20 1.173596 -4.2234559 0 -2.4905682 2.3587731 - 30 1.2989994 -4.4124445 0 -2.4943907 1.903698 - 40 1.4510255 -4.6467459 0 -2.504216 1.2196259 - 50 1.4631454 -4.6641774 0 -2.5037518 1.2838406 - 60 1.2694188 -4.3794267 0 -2.5050505 2.4497113 - 70 1.3363814 -4.4759884 0 -2.5027378 2.2441463 - 80 1.402534 -4.5752515 0 -2.5043224 1.9011715 - 90 1.3870321 -4.5512479 0 -2.5032084 2.0040237 - 100 1.3635651 -4.5209384 0 -2.5075493 1.9773816 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -4.1934138 0 -2.7168513 0.72358299 - 10 1.0170498 -4.2225288 0 -2.7207912 0.7556766 - 20 0.92567967 -4.0920979 0 -2.725274 1.2463143 - 30 1.0851758 -4.3346599 0 -2.73233 0.53176652 - 40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153 - 50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153 - 60 1.1172288 -4.3979372 0 -2.7482791 0.52752067 - 70 1.2228415 -4.5540741 0 -2.7484722 0.11937533 - 80 1.1776333 -4.4870195 0 -2.7481704 0.33904864 - 90 1.219283 -4.5483185 0 -2.747971 0.17898549 - 100 1.2138939 -4.5432229 0 -2.7508327 0.3076354 -delete_atoms group all -Deleted 64 atoms, new total = 0 - 1 by 2 by 2 MPI processor grid - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -3.8524214 0 -2.3758589 4.6814052 - 10 1.3356745 -4.3481612 0 -2.3759544 3.061856 - 20 1.1791601 -4.117932 0 -2.3768284 3.8565 - 30 1.3435556 -4.3613609 0 -2.3775171 3.0728735 - 40 1.5628445 -4.6886004 0 -2.3809628 2.0989245 - 50 1.4735556 -4.5569123 0 -2.3811152 2.6364099 - 60 1.609387 -4.7581056 0 -2.3817452 1.8988642 - 70 1.5014902 -4.5938759 0 -2.3768318 2.458161 - 80 1.3763383 -4.4089865 0 -2.3767369 3.0379808 - 90 1.498202 -4.5909613 0 -2.3787724 2.5543714 - 100 1.43934 -4.5009545 0 -2.375679 3.0923444 -Total wall time: 0:00:00 diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index 9a6e415a8c..99f23f7e59 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -48,7 +48,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) virialflag = 0; addflag = 1; every = 1; - extflag = 0; + connectflag = 1; int iarg = 3; while (iarg < narg) { @@ -69,10 +69,10 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) every = utils::inumeric(FLERR,arg[iarg+1],false,lmp); if (every <= 0) error->all(FLERR,"Illegal fix mdi/qm command"); iarg += 2; - } else if (strcmp(arg[iarg],"external") == 0) { + } else if (strcmp(arg[iarg],"connect") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix mdi/qm command"); - if (strcmp(arg[iarg+1],"yes") == 0) extflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) extflag = 0; + if (strcmp(arg[iarg+1],"yes") == 0) connectflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0; else error->all(FLERR,"Illegal fix mdi/qm command"); iarg += 2; } else error->all(FLERR,"Illegal fix mdi/qm command"); @@ -100,8 +100,8 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) thermo_energy = thermo_virial = 1; } - // mdicomm will be one-time initialized in init() - // cannot be done here for a plugin library, b/c mdi plugin command is later + // mdicomm will be initialized in init() + // cannot do here for a plugin library, b/c mdi plugin command comes later mdicomm = MDI_COMM_NULL; @@ -143,10 +143,11 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) FixMDIQM::~FixMDIQM() { - // send exit command to engine if it is a stand-alone code - // for plugin, this happens in MDIPlugin::plugin_wrapper() + // send exit command to stand-alone engine code + // for connnectflag = 0, this is done via "mdi exit" command + // for plugin, this is done in MDIPlugin::plugin_wrapper() - if (!plugin && !extflag) { + if (mdicomm != MDI_COMM_NULL && connectflag && !plugin) { int ierr = MDI_Send_command("EXIT", mdicomm); if (ierr) error->all(FLERR, "MDI: EXIT command"); } @@ -176,31 +177,47 @@ int FixMDIQM::setmask() void FixMDIQM::init() { - // one-time auto-detect whether engine is stand-alone code or plugin library - // also initializes mdicomm - // set plugin = 0/1 for engine = stand-alone code vs plugin library - - if (!extflag) { + // set local mdicomm one-time only + // also set plugin = 0/1 for engine = stand-alone code vs plugin library if (mdicomm == MDI_COMM_NULL) { - MDI_Get_communicator(&mdicomm, 0); - if (mdicomm == MDI_COMM_NULL) { - plugin = 0; - MDI_Accept_communicator(&mdicomm); - if (mdicomm == MDI_COMM_NULL) - error->all(FLERR, "MDI unable to connect to stand-alone engine"); - } else { - plugin = 1; - int method; - MDI_Get_method(&method, mdicomm); - if (method != MDI_PLUGIN) - error->all(FLERR, "MDI internal error for plugin engine"); - } - } - } else { - plugin = 0; - mdicomm = lmp->mdicomm; + // this fix makes one-time connection to engine + + if (connectflag) { + + // if MDI's mdicomm not set, need to Accept_comm() with stand-alone engine + // othewise are already connected to plugin engine + + MDI_Get_communicator(&mdicomm, 0); + + if (mdicomm == MDI_COMM_NULL) { + plugin = 0; + MDI_Accept_communicator(&mdicomm); + if (mdicomm == MDI_COMM_NULL) + error->all(FLERR, "MDI unable to connect to stand-alone engine"); + + } else { + plugin = 1; + int method; + MDI_Get_method(&method, mdicomm); + if (method != MDI_PLUGIN) + error->all(FLERR, "MDI internal error for plugin engine"); + } + + // connection should have been already made by "mdi connect" command + // only works for stand-alone engines + + } else { + plugin = 0; + + if (lmp->mdicomm == nullptr) + error->all(FLERR,"Fix mdi/qm is not connected to engine via mdi connect"); + + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) lmp->mdicomm; + memcpy(&mdicomm,ptrcomm,nbytes); + } } // send natoms, atom types, and simulation box to engine diff --git a/src/MDI/fix_mdi_qm.h b/src/MDI/fix_mdi_qm.h index b805f7e3d2..2d6f4b0d23 100644 --- a/src/MDI/fix_mdi_qm.h +++ b/src/MDI/fix_mdi_qm.h @@ -40,7 +40,7 @@ class FixMDIQM : public Fix { private: int nprocs; - int virialflag,addflag,extflag,every; + int every,virialflag,addflag,connectflag; int plugin; int maxlocal; int sumflag; diff --git a/src/MDI/mdi_command.cpp b/src/MDI/mdi_command.cpp index 9fdc1f8a04..96ba839dfc 100644 --- a/src/MDI/mdi_command.cpp +++ b/src/MDI/mdi_command.cpp @@ -16,13 +16,19 @@ #include "error.h" #include "mdi_engine.h" #include "mdi_plugin.h" +#include "memory.h" #include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- - mdi command: engine or plugin + mdi command: engine or plugin or connect or exit + engine is used when LAMMPS is an MDI engine, to start listening for requests + plugin is used when LAMMPS is an MDI driver to load a plugin library + connect and exit are used when LAMMPS is an MDI driver to + (a) connect = setup comm with a stand-alone MDI engine + (b) exit = terminate comm with a stand-alone MDI engine ---------------------------------------------------------------------- */ void MDICommand::command(int narg, char **arg) @@ -35,22 +41,41 @@ void MDICommand::command(int narg, char **arg) } else if (strcmp(arg[0], "plugin") == 0) { MDIPlugin(lmp, narg - 1, &arg[1]); - } else if (strcmp(arg[0], "start") == 0) { + } else if (strcmp(arg[0], "connect") == 0) { + + if (lmp->mdicomm != nullptr) + error->all(FLERR,"MDI cannot connect to already connected engine"); + MDI_Comm mdicomm; MDI_Get_communicator(&mdicomm, 0); + if (mdicomm == MDI_COMM_NULL) { MDI_Accept_communicator(&mdicomm); if (mdicomm == MDI_COMM_NULL) error->all(FLERR, "MDI unable to connect to stand-alone engine"); - } else error->all(FLERR, "Cannot use mdi start in plugin mode"); - lmp->mdicomm = mdicomm; + } else error->all(FLERR, "Cannot use mdi connect with plugin engine"); - } else if (strcmp(arg[0], "stop") == 0) { + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) memory->smalloc(nbytes,"mdi:mdicomm"); + memcpy(ptrcomm,&mdicomm,nbytes); + + lmp->mdicomm = (void *) ptrcomm; + + } else if (strcmp(arg[0], "exit") == 0) { + + if (lmp->mdicomm == nullptr) + error->all(FLERR,"MDI cannot send exit to unconnected engine"); + + MDI_Comm mdicomm; + int nbytes = sizeof(MDI_Comm); + char *ptrcomm = (char *) lmp->mdicomm; + memcpy(&mdicomm,ptrcomm,nbytes); - MDI_Comm mdicomm = lmp->mdicomm; int ierr = MDI_Send_command("EXIT", mdicomm); if (ierr) error->all(FLERR, "MDI: EXIT command"); - lmp->mdicomm = MDI_COMM_NULL; + + memory->sfree(ptrcomm); + lmp->mdicomm = nullptr; } else error->all(FLERR, "Illegal mdi command"); } diff --git a/src/lammps.cpp b/src/lammps.cpp index d4c7288451..3ddfafeb5d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -130,7 +130,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : num_ver = utils::date2num(version); external_comm = 0; - mdicomm = 0; + mdicomm = nullptr; skiprunflag = 0; diff --git a/src/lammps.h b/src/lammps.h index 04ab9a9673..4cdb873db9 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -69,7 +69,7 @@ class LAMMPS { // when multiple programs launched by mpirun // set by -mpicolor command line arg - int mdicomm; // for use with MDI code coupling library + void *mdicomm; // for use with MDI code coupling library const char *match_style(const char *style, const char *name); static const char *installed_packages[];