Merge pull request #2921 from lammps/mdi-expand
Enhance MDI support in LAMMPS in its MDI package
This commit is contained in:
Axel Kohlmeyer
@ -83,6 +83,7 @@ indent: spherical indenter into a 2d solid
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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latte: use of LATTE density-functional tight-binding quantum code
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mc: MC package models: GCMC, Widom, fix mol/swap
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mdi: use of the MDI package and MolSSI MDI code coupling library
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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message: client/server coupling of 2 codes
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228
examples/mdi/README
Normal file
228
examples/mdi/README
Normal file
@ -0,0 +1,228 @@
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These are examples that work the MDI package in LAMMPS which uses the
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MolSSI MDI library for coupling codes together and communicating
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between them with MDI messages.
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In MDI lingo, one code is the driver and another code is the engine.
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The 2 codes can be written in any language; C++ (LAMMPS) and Python
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are illustrated here. The 2 codes can each be stand-alone codes, in
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which case they can be run on different numbers of processors. The 2
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codes can communicate either via TCP (sockets) or via MPI. For the
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TCP case, the driver and engine need to be launched separately,
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e.g. in 2 windows on your desktop machine. For the MPI case, a single
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mpirun command launches both codes.
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Alternatively the engine code can be a plugin library which the driver
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code loads, in which case the driver and engine run on the same
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processors.
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LAMMPS supports operating in all these MDI modes. It can be an engine
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operating either as a stand-alone code or as a plugin. It can also be
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a driver and couple to an engine that is either a stand-alone code or
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a plugin. Examples for all these use cases are in this directory.
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The example commands below illustrate how to run all the variants.
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To use LAMMPS as a plugin engine, you must build it as a shared library.
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Something like this, which also builds the normal LAMMPS executable
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lmp_mpi:
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cd src
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make yes-mdi
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make mode=shlib mpi
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To use the serial_driver.py example you will need Python 3 with Numpy
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and mpi4py available in your Python. Make sure LAMMPS and Python are
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using same the same version of MPI.
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-------------------------------------------------
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-------------------------------------------------
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* Example #1 = run ab inito MD (AIMD)
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Two instances of LAMMPS operate as a driver and engine
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As an engine, LAMMPS is a surrogate for a quantum code
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Note that the 2 input scripts in.aimd.alone and in.aimd.driver
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have an option for running in NVE vs NPT mode. Comment in/out
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the appropriate line to change modes. Nothing needs to be
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changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
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---
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi < in.aimd.alone
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With MDI, the thermo output of the driver should match the thermo
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output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
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% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
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---
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Run with TCP: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
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% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
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---
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Run with MPI: 1 proc each
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% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
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---
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Run with MPI: 3 procs + 4 procs
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% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
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---
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Run in plugin mode: 1 proc
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% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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---
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Run in plugin mode: 3 procs
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% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
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-------------------------------------------------
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-------------------------------------------------
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* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
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Each calculation can be a single-point evaluation, MD run, or minimization
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The sequence_driver.py code allows for optional switches in addition
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to -mdi (required) and the -plugin and -plugin_args switches which are
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used to link to an engine as a plugin library. The example run
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commands below just use the default values of the optional switches.
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The switches are also explained at the top of the file; the info is
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copied here:
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# -n 3
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# number of calculations to perform, default = 3
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# -mode eval/run/min
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# style of calculations: single snapshot evals, dynamics, minimization
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# default = run
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# -size Nx Ny Nz
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# cubic lattice, default = 2 2 2
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# -rho 0.75 0.1
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# reduced density and random variation thereof, default = 0.75 0.1
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# -delta 0.1
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# randomly perturb atoms initially by this distance, default 0.1
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# -nsteps 100
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# number of timesteps in dynamics runs, default = 100
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# -temp 1.0
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# initial temperature in dynamics runs, default = 1.0
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# -tol 0.001
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# tolerance for minimizations, default = 0.001
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# -seed 12345
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# random number seed > 0, default = 12345
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---
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Run with TCP: 1 proc each
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% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
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---
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Run with TCP: 2 proc + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
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---
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Run with MPI: 1 proc each
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% 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
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---
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Run with MPI: 2 procs + 4 procs
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% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
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---
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Run in plugin mode: 1 proc
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% 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"
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---
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Run in plugin mode: 3 procs
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% 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"
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-------------------------------------------------
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-------------------------------------------------
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* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
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First LAMMPS instance performs the MD timestepping
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Second LAMMPS instance is surrogate QM = computes forces
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The aimd_driver.py code allows for an optional switch in addition to
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-mdi (required) and the -plugin and -plugin_args swiches which are
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used to link to the 2 engines as a plugin libraries. The example run
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commands below use the default values of the optional switch. The
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switch is also explained the top of the file; the info is copied
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here:
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# -nsteps 5
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# number of timesteps in dynamics runs, default = 5
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---
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Run the entire calculation with a single instance of LAMMPS by itself
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results should be identical to running this example with MDI
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% lmp_mpi < in.aimd.alone
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With MDI, the driver prints the QM and Total energies. These should
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match the PotEng and TotEng output of the in.aimd.alone script.
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---
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Run with TCP: 1 proc each
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% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with TCP: 2 procs + 2 procs + 3 procs
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% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
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% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
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% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
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---
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Run with MPI: 1 proc each
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% 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
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---
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Run with MPI: 2 procs + 2 procs + 3 procs
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% 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
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255
examples/mdi/aimd_driver.py
Normal file
255
examples/mdi/aimd_driver.py
Normal file
@ -0,0 +1,255 @@
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# MDI driver to perform an AIMD simulation
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# using one instance of LAMMPS as the MD timestepper
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# using second instance of LAMMPS as a QM surrogate to compute forces
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# NOTE: this script is derived from the MDI_AIMD_Driver.cpp code
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# included in the MDI distribution
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# it alters the timestepping to match a velocity Verlet algorithm
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# forces are computed once before timestepping beings
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# both the @COORDS and @FORCES nodes are triggered in the MM code
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# as the appropriate places to extract COORDS and provide FORCES
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# Syntax: python3 aimd_driver.py switch arg switch arg ...
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# possible switches:
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# -mdi "-role DRIVER ..."
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# required switch
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# example for stand-alone mode:
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# -mdi "-role DRIVER -name sequence -method TCP -port 8021"
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# example for plugin mode:
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# -mdi "-role DRIVER -name sequemce -method LINK
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# -plugin_path /home/sjplimp/lammps/src/"
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# -plugin name
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# name of plugin library, only when using plugin mode
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# -plugin_args arglist
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# args to add when launching plugin library, only when using plugin mode
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# enclose arglist in quotes if multiple words
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# -nsteps 5
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# number of timesteps, default = 5
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import sys,math,random
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import mdi
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import numpy as np
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from mpi4py import MPI
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# error message
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def error(txt=None):
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if txt: raise Exception(txt)
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raise Exception("Syntax: python3 aimd_driver.py switch arg switch arg ...")
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# run an AIMD simulation
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def perform_aimd(world,mm_comm,qm_comm):
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me = world.Get_rank()
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nprocs = world.Get_size()
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# receive number of atoms from the MM engine
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mdi.MDI_Send_command("<NATOMS",mm_comm)
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natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mm_comm)
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natoms = world.bcast(natoms,root=0)
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# allocate arrays for coordinates and forces
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coords = np.zeros(3*natoms,dtype=np.float64)
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forces = np.zeros(3*natoms,dtype=np.float64)
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# MM engine initializes a new MD simulation
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mdi.MDI_Send_command("@INIT_MD",mm_comm)
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# -----------------
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# compute initial forces for Verlet timestepping
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# and initial energy for output on step 0
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# -----------------
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# MM engine proceeds to @FORCES node in setup()
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mdi.MDI_Send_command("@FORCES",mm_comm)
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# get coords from MM engine
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mdi.MDI_Send_command("<COORDS",mm_comm)
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mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
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world.Bcast(coords,root=0)
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# send coords to QM engine
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mdi.MDI_Send_command(">COORDS",qm_comm)
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mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
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# get QM potential energy
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mdi.MDI_Send_command("<PE",qm_comm)
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qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
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qm_pe = world.bcast(qm_pe,root=0)
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# get forces from QM engine
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mdi.MDI_Send_command("<FORCES",qm_comm)
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mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
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world.Bcast(forces,root=0)
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# send forces to MM engine
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mdi.MDI_Send_command(">FORCES",mm_comm)
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mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
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# get MM kinetic energy
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mdi.MDI_Send_command("<KE",mm_comm)
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mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
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mm_ke = world.bcast(mm_ke,root=0)
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# output by driver
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# normalize energies by atom count
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if me == 0:
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print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
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(0,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
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# -----------------
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# timestepping loop
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# -----------------
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for istep in range(nsteps):
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# MM engine proceeds to @FORCES node
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mdi.MDI_Send_command("@FORCES",mm_comm)
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# get coords from MM engine
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mdi.MDI_Send_command("<COORDS",mm_comm)
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mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mm_comm,buf=coords)
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world.Bcast(coords,root=0)
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# send coords to QM engine
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mdi.MDI_Send_command(">COORDS",qm_comm)
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mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,qm_comm)
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# get QM potential energy
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mdi.MDI_Send_command("<PE",qm_comm)
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qm_pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,qm_comm)
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qm_pe = world.bcast(qm_pe,root=0)
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# get forces from QM engine
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mdi.MDI_Send_command("<FORCES",qm_comm)
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mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,qm_comm,buf=forces)
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world.Bcast(forces,root=0)
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# send forces to MM engine
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mdi.MDI_Send_command(">FORCES",mm_comm)
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mdi.MDI_Send(forces,3*natoms,mdi.MDI_DOUBLE,mm_comm)
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# MM engine proceeds to @ENDSTEP node
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# so that KE will be for fully updated velocity
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mdi.MDI_Send_command("@ENDSTEP",mm_comm)
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# get MM kinetic energy
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mdi.MDI_Send_command("<KE",mm_comm)
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mm_ke = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mm_comm)
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mm_ke = world.bcast(mm_ke,root=0)
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# output by driver
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# normalize energies by atom count
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if me == 0:
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print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
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(istep+1,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
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# send EXIT to each engine
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mdi.MDI_Send_command("EXIT",mm_comm)
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mdi.MDI_Send_command("EXIT",qm_comm)
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# ------------------------
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# main program
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# ------------------------
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args = sys.argv[1:]
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narg = len(args)
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# defaults for command-line args
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mdiarg = ""
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plugin = ""
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plugin_args = ""
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nsteps = 5
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# parse command-line args
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iarg = 0
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while iarg < narg:
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if args[iarg] == "-mdi":
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if iarg+2 > narg: error()
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mdiarg = args[iarg+1]
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iarg += 2
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elif args[iarg] == "-plugin":
|
||||
if iarg+2 > narg: error()
|
||||
plugin = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin_args":
|
||||
if iarg+2 > narg: error()
|
||||
plugin_args = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nsteps":
|
||||
if iarg+2 > narg: error()
|
||||
nsteps = int(args[iarg+1])
|
||||
if nsteps < 0: error()
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
if not mdiarg: error()
|
||||
|
||||
# LAMMPS engines are stand-alone codes
|
||||
# world = MPI communicator for just this driver
|
||||
# invoke perform_tasks() directly
|
||||
|
||||
if not plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
|
||||
# connect to 2 engines, determine which is MM vs QM
|
||||
|
||||
mdicomm1 = mdi.MDI_Accept_Communicator()
|
||||
mdicomm2 = mdi.MDI_Accept_Communicator()
|
||||
|
||||
mdi.MDI_Send_command("<NAME",mdicomm1)
|
||||
name1 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm1)
|
||||
name1 = world.bcast(name1,root=0)
|
||||
mdi.MDI_Send_command("<NAME",mdicomm2)
|
||||
name2 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH,mdi.MDI_CHAR,mdicomm2)
|
||||
name2 = world.bcast(name2,root=0)
|
||||
|
||||
if name1 == "MM" and name2 == "QM":
|
||||
mm_comm = mdicomm1
|
||||
qm_comm = mdicomm2
|
||||
elif name1 == "QM" and name2 == "MM":
|
||||
mm_comm = mdicomm2
|
||||
qm_comm = mdicomm1
|
||||
else: error("Two engines have invalid names")
|
||||
|
||||
perform_aimd(world,mm_comm,qm_comm)
|
||||
|
||||
# LAMMPS engines are plugin libraries
|
||||
# launch plugins
|
||||
# NOTE: need to run driver on 2 or more procs
|
||||
# partition driver into 2 MPI comms
|
||||
# launch one plugin on each partition
|
||||
# each with their own callback function
|
||||
|
||||
if plugin:
|
||||
error("Cannot yet run in plugin mode")
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = MPI.COMM_WORLD
|
||||
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
|
||||
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)
|
||||
32
examples/mdi/in.aimd.alone
Normal file
32
examples/mdi/in.aimd.alone
Normal file
@ -0,0 +1,32 @@
|
||||
# 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
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
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
|
||||
32
examples/mdi/in.aimd.driver
Normal file
32
examples/mdi/in.aimd.driver
Normal file
@ -0,0 +1,32 @@
|
||||
# 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
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
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
|
||||
34
examples/mdi/in.aimd.driver.plugin
Normal file
34
examples/mdi/in.aimd.driver.plugin
Normal file
@ -0,0 +1,34 @@
|
||||
# 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
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
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"
|
||||
22
examples/mdi/in.aimd.engine
Normal file
22
examples/mdi/in.aimd.engine
Normal file
@ -0,0 +1,22 @@
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
23
examples/mdi/in.aimd.mm
Normal file
23
examples/mdi/in.aimd.mm
Normal file
@ -0,0 +1,23 @@
|
||||
# 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
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
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
|
||||
22
examples/mdi/in.aimd.qm
Normal file
22
examples/mdi/in.aimd.qm
Normal file
@ -0,0 +1,22 @@
|
||||
# 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
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
21
examples/mdi/in.sequence
Normal file
21
examples/mdi/in.sequence
Normal file
@ -0,0 +1,21 @@
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
Normal file
90
examples/mdi/log.7Apr22.mdi.aimd.alone.g++.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 505739.085 tau/day, 1170.692 timesteps/s
|
||||
73.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
|
||||
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
|
||||
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
|
||||
Other | | 6.054e-05 | | | 1.42
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.0029525 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 731582.413 tau/day, 1693.478 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.2632e-05 | 1.2632e-05 | 1.2632e-05 | 0.0 | 0.43
|
||||
Output | 0.00010561 | 0.00010561 | 0.00010561 | 0.0 | 3.58
|
||||
Modify | 0.0028043 | 0.0028043 | 0.0028043 | 0.0 | 94.98
|
||||
Other | | 3e-05 | | | 1.02
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.mpi.g++.3
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00315597 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 684416.574 tau/day, 1584.298 timesteps/s
|
||||
99.5% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.769e-05 | 3.7059e-05 | 4.7808e-05 | 0.0 | 1.17
|
||||
Output | 0.00011556 | 0.00015516 | 0.00021954 | 0.0 | 4.92
|
||||
Modify | 0.002819 | 0.0028366 | 0.0028599 | 0.0 | 89.88
|
||||
Other | | 0.0001272 | | | 4.03
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1
Normal file
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.1
Normal file
@ -0,0 +1,80 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00396559 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 544685.246 tau/day, 1260.845 timesteps/s
|
||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.5936e-05 | 1.5936e-05 | 1.5936e-05 | 0.0 | 0.40
|
||||
Output | 0.00011527 | 0.00011527 | 0.00011527 | 0.0 | 2.91
|
||||
Modify | 0.0038025 | 0.0038025 | 0.0038025 | 0.0 | 95.89
|
||||
Other | | 3.184e-05 | | | 0.80
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3
Normal file
80
examples/mdi/log.7Apr22.mdi.aimd.driver.plugin.g++.3
Normal file
@ -0,0 +1,80 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd plugin
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 5"
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 0.00287217 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 752045.581 tau/day, 1740.846 timesteps/s
|
||||
99.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.6368e-05 | 3.9139e-05 | 5.1029e-05 | 0.0 | 1.36
|
||||
Output | 9.6932e-05 | 0.00012081 | 0.00016442 | 0.0 | 4.21
|
||||
Modify | 0.0026109 | 0.0026258 | 0.0026494 | 0.0 | 91.42
|
||||
Other | | 8.637e-05 | | | 3.01
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.1
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.20486 on 1 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1792.736 tau/day, 4.150 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.4487e-05 | 2.4487e-05 | 2.4487e-05 | 0.0 | 0.00
|
||||
Output | 0.00026499 | 0.00026499 | 0.00026499 | 0.0 | 0.02
|
||||
Modify | 1.2045 | 1.2045 | 1.2045 | 0.0 | 99.97
|
||||
Other | | 6.184e-05 | | | 0.01
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 166 ave 166 max 166 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -1
|
||||
Ave neighs/atom = -0.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3
Normal file
79
examples/mdi/log.7Apr22.mdi.aimd.driver.tcp.g++.3
Normal file
@ -0,0 +1,79 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI driver script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# NVE
|
||||
fix 1 all nve
|
||||
# NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||
|
||||
fix 2 all mdi/aimd
|
||||
fix_modify 2 energy yes virial yes
|
||||
|
||||
thermo_style custom step temp pe etotal press vol
|
||||
thermo 1
|
||||
|
||||
run 5
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume
|
||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||
Loop time of 1.19983 on 3 procs for 5 steps with 500 atoms
|
||||
|
||||
Performance: 1800.259 tau/day, 4.167 timesteps/s
|
||||
66.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.604e-06 | 4.8462e-05 | 7.527e-05 | 0.0 | 0.00
|
||||
Output | 0.00015266 | 0.00020593 | 0.00031177 | 0.0 | 0.02
|
||||
Modify | 1.1993 | 1.1994 | 1.1994 | 0.0 | 99.96
|
||||
Other | | 0.0002123 | | | 0.02
|
||||
|
||||
Nlocal: 166.667 ave 200 max 150 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 55.3333 ave 92 max 32 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = -3
|
||||
Ave neighs/atom = -0.006
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.mpi.g++.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.plugin.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4
Normal file
55
examples/mdi/log.7Apr22.mdi.aimd.engine.tcp.g++.4
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - MDI engine script
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1
Normal file
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.1
Normal file
@ -0,0 +1,5 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2
Normal file
5
examples/mdi/log.7Apr22.mdi.aimdpy.driver.mpi.g++.2
Normal file
@ -0,0 +1,5 @@
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1
Normal file
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.1
Normal file
@ -0,0 +1,6 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2
Normal file
6
examples/mdi/log.7Apr22.mdi.aimdpy.driver.tcp.g++.2
Normal file
@ -0,0 +1,6 @@
|
||||
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.mpi.g++.2
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:00
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.1
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2
Normal file
44
examples/mdi/log.7Apr22.mdi.aimdpy.mm.tcp.g++.2
Normal file
@ -0,0 +1,44 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
mdi engine
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2141)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:209)
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 2.15568 1.2132167
|
||||
1 1.4377309 0 0 2.1522832 1.211305
|
||||
2 1.430825 0 0 2.141945 1.2054866
|
||||
3 1.4189655 0 0 2.1241913 1.1954949
|
||||
4 1.4016029 0 0 2.0981995 1.1808667
|
||||
5 1.3779738 0 0 2.0628267 1.1609589
|
||||
Total wall time: 0:00:11
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.mpi.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:00
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.1
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3
Normal file
55
examples/mdi/log.7Apr22.mdi.aimdpy.qm.tcp.g++.3
Normal file
@ -0,0 +1,55 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
mdi engine
|
||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||
Total wall time: 0:00:01
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.mpi.g++.2
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.plugin.g++.3
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -1.1102e-16 8.3267e-16 1.9429e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 9.0206e-17 4.996e-16 1.5959e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -1.4849e-15 -8.1879e-16 -1.7347e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.1
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce 4.4409e-16 -1.1102e-16 6.6613e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce 7.0083e-16 1.1796e-16 5.4384e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce 0 2.0817e-16 -4.3021e-16
|
||||
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2
Normal file
3
examples/mdi/log.7Apr22.mdi.sequence.driver.tcp.g++.2
Normal file
@ -0,0 +1,3 @@
|
||||
Calc 1: eng -4.5209 pressure 0.98188 aveForce -2.2204e-16 0 2.2204e-16
|
||||
Calc 2: eng -4.5432 pressure -0.53137 aveForce -2.498e-16 -1.8735e-16 -3.4001e-16
|
||||
Calc 3: eng -4.501 pressure 2.0049 aveForce -7.9103e-16 3.4694e-16 4.0246e-16
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.mpi.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 2 by 2 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.plugin.g++.3
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 3 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 3 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
3 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.1
Normal file
@ -0,0 +1,89 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi engine
|
||||
delete_atoms group all
|
||||
Deleted 0 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||
delete_atoms group all
|
||||
Deleted 64 atoms, new total = 0
|
||||
1 by 1 by 1 MPI processor grid
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||
Total wall time: 0:00:00
|
||||
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4
Normal file
89
examples/mdi/log.7Apr22.mdi.sequence.engine.tcp.g++.4
Normal file
@ -0,0 +1,89 @@
|
||||
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
|
||||
311
examples/mdi/sequence_driver.py
Normal file
311
examples/mdi/sequence_driver.py
Normal file
@ -0,0 +1,311 @@
|
||||
# MDI driver to perform a series of independent calculations
|
||||
# using LAMMPS (or a QM code with MDI support) as an MDI engine,
|
||||
# the engine can be either a standalone code or a plugin library
|
||||
|
||||
# Syntax: python3 series_driver.py switch arg switch arg ...
|
||||
# possible switches:
|
||||
# -mdi "-role DRIVER ..."
|
||||
# required switch
|
||||
# example for stand-alone mode:
|
||||
# -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
||||
# example for plugin mode:
|
||||
# -mdi "-role DRIVER -name sequemce -method LINK
|
||||
# -plugin_path /home/sjplimp/lammps/src/"
|
||||
# -plugin name
|
||||
# name of plugin library, only when using plugin mode
|
||||
# -plugin_args arglist
|
||||
# args to add when launching plugin library, only when using plugin mode
|
||||
# enclose arglist in quotes if multiple words
|
||||
# -n 3
|
||||
# number of calculations to perform, default = 3
|
||||
# -mode eval/run/min
|
||||
# style of calculations: single snapshot evals, dynamics, minimization
|
||||
# default = run
|
||||
# -size Nx Ny Nz
|
||||
# cubic lattice, default = 4 4 4
|
||||
# -rho 0.75 0.1
|
||||
# reduced density and random variation thereof, default = 0.75 0.1
|
||||
# -delta 0.1
|
||||
# randomly perturb atoms initially by this distance, default 0.1
|
||||
# -nsteps 100
|
||||
# number of timesteps in dynamics runs, default = 100
|
||||
# -temp 1.0
|
||||
# initial temperature in dynamics runs, default = 1.0
|
||||
# -tol 0.001
|
||||
# tolerance for minimizations, default = 0.001
|
||||
# -seed 12345
|
||||
# random number seed > 0, default = 12345
|
||||
|
||||
import sys,math,random
|
||||
import mdi
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
|
||||
# error message
|
||||
|
||||
def error(txt=None):
|
||||
if txt: raise Exception(txt)
|
||||
raise Exception("Syntax: python3 series_driver.py switch arg switch arg ...")
|
||||
|
||||
# loop over all the tasks to exchange MDI Sends/Receives with the engine
|
||||
# for standalone mode, this is called by main program below
|
||||
# for plugin mode, this is a callback function invoked by MDI
|
||||
|
||||
def perform_tasks(world,mdicomm,dummy):
|
||||
|
||||
me = world.Get_rank()
|
||||
nprocs = world.Get_size()
|
||||
|
||||
# allocate vectors for per-atom types, coords, vels, forces
|
||||
|
||||
natoms = nx * ny * nz
|
||||
atypes = np.zeros(natoms,dtype=np.int)
|
||||
coords = np.zeros(3*natoms,dtype=np.float64)
|
||||
vels = np.zeros(3*natoms,dtype=np.float64)
|
||||
forces = np.zeros(3*natoms,dtype=np.float64)
|
||||
|
||||
atypes[:] = 1
|
||||
|
||||
# initialize RN generator
|
||||
|
||||
random.seed(seed)
|
||||
|
||||
# loop over sequence of calculations
|
||||
|
||||
for icalc in range(ncalc):
|
||||
|
||||
# define simulation box
|
||||
|
||||
onerho = rho + (random.random()-0.5)*rhodelta;
|
||||
sigma = pow(1.0/onerho,1.0/3.0)
|
||||
|
||||
xlo = ylo = zlo = 0.0
|
||||
xhi = nx * sigma
|
||||
yhi = ny * sigma
|
||||
zhi = nz * sigma
|
||||
|
||||
# send simulation box to engine
|
||||
|
||||
vec = [xhi-xlo,0.0,0.0] + [0.0,yhi-ylo,0.0] + [0.0,0.0,zhi-zlo]
|
||||
mdi.MDI_Send_command(">CELL",mdicomm)
|
||||
mdi.MDI_Send(vec,9,mdi.MDI_DOUBLE,mdicomm)
|
||||
|
||||
# create atoms on perfect lattice
|
||||
|
||||
m = 0
|
||||
for k in range(nz):
|
||||
for j in range(ny):
|
||||
for i in range(nx):
|
||||
coords[m] = i * sigma
|
||||
coords[m+1] = j * sigma
|
||||
coords[m+2] = k * sigma
|
||||
m += 3
|
||||
|
||||
# perturb lattice
|
||||
|
||||
for m in range(3*natoms):
|
||||
coords[m] += 2.0*random.random()*delta - delta
|
||||
|
||||
# define initial velocities
|
||||
|
||||
for m in range(3*natoms):
|
||||
vels[m] = random.random() - 0.5
|
||||
|
||||
tcurrent = 0.0
|
||||
for m in range(3*natoms):
|
||||
tcurrent += vels[m]*vels[m]
|
||||
tcurrent /= 3*(natoms-1)
|
||||
|
||||
factor = math.sqrt(tinitial/tcurrent)
|
||||
|
||||
for m in range(3*natoms):
|
||||
vels[m] *= factor
|
||||
|
||||
# send atoms and their properties to engine
|
||||
|
||||
mdi.MDI_Send_command(">NATOMS",mdicomm)
|
||||
mdi.MDI_Send(natoms,1,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command(">TYPES",mdicomm)
|
||||
mdi.MDI_Send(atypes,natoms,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command(">COORDS",mdicomm)
|
||||
mdi.MDI_Send(coords,3*natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
mdi.MDI_Send_command(">VELOCITIES",mdicomm)
|
||||
mdi.MDI_Send(vels,3*natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
|
||||
# eval or run or minimize
|
||||
|
||||
if mode == "eval":
|
||||
pass
|
||||
elif mode == "run":
|
||||
mdi.MDI_Send_command(">NSTEPS",mdicomm)
|
||||
mdi.MDI_Send(nsteps,1,mdi.MDI_INT,mdicomm)
|
||||
mdi.MDI_Send_command("MD",mdicomm)
|
||||
elif mode == "min":
|
||||
mdi.MDI_Send_command(">TOLERANCE",mdicomm)
|
||||
params = [tol,tol,1000.0,1000.0]
|
||||
mdi.MDI_Send(params,4,mdi.MDI_DOUBLE,mdicomm)
|
||||
mdi.MDI_Send_command("OPTG",mdicomm)
|
||||
|
||||
# request potential energy
|
||||
|
||||
mdi.MDI_Send_command("<PE",mdicomm)
|
||||
pe = mdi.MDI_Recv(1,mdi.MDI_DOUBLE,mdicomm)
|
||||
pe = world.bcast(pe,root=0)
|
||||
|
||||
# request virial tensor
|
||||
|
||||
mdi.MDI_Send_command("<STRESS",mdicomm)
|
||||
virial = mdi.MDI_Recv(6,mdi.MDI_DOUBLE,mdicomm)
|
||||
virial = world.bcast(virial,root=0)
|
||||
|
||||
# request forces
|
||||
|
||||
mdi.MDI_Send_command("<FORCES",mdicomm)
|
||||
mdi.MDI_Recv(3*natoms,mdi.MDI_DOUBLE,mdicomm,buf=forces)
|
||||
world.Bcast(forces,root=0)
|
||||
|
||||
# final output from each calculation
|
||||
# pressure = just virial component, no kinetic component
|
||||
|
||||
aveeng = pe/natoms
|
||||
pressure = (virial[0] + virial[1] + virial[2]) / 3.0
|
||||
|
||||
m = 0
|
||||
fx = fy = fz = 0.0
|
||||
for i in range(natoms):
|
||||
fx += forces[m]
|
||||
fy += forces[m+1]
|
||||
fz += forces[m+2]
|
||||
m += 3
|
||||
|
||||
fx /= natoms
|
||||
fy /= natoms
|
||||
fz /= natoms
|
||||
|
||||
line = "Calc %d: eng %7.5g pressure %7.5g aveForce %7.5g %7.5g %7.5g" % \
|
||||
(icalc+1,aveeng,pressure,fx,fy,fz)
|
||||
if me == 0: print(line)
|
||||
|
||||
# send EXIT command to engine
|
||||
# in plugin mode, removes the plugin library
|
||||
|
||||
mdi.MDI_Send_command("EXIT",mdicomm)
|
||||
|
||||
# return needed for plugin mode
|
||||
|
||||
return 0
|
||||
|
||||
# ------------------------
|
||||
# main program
|
||||
# ------------------------
|
||||
|
||||
args = sys.argv[1:]
|
||||
narg = len(args)
|
||||
|
||||
# defaults for command-line args
|
||||
|
||||
mdiarg = ""
|
||||
plugin = ""
|
||||
plugin_args = ""
|
||||
|
||||
ncalc = 3
|
||||
mode = "run"
|
||||
nx = ny = nz = 4
|
||||
rho = 0.75
|
||||
rhodelta = 0.1
|
||||
delta = 0.1
|
||||
nsteps = 100
|
||||
tinitial = 1.0
|
||||
tol = 0.001
|
||||
seed = 12345
|
||||
|
||||
# parse command-line args
|
||||
|
||||
iarg = 0
|
||||
while iarg < narg:
|
||||
if args[iarg] == "-mdi":
|
||||
if iarg+2 > narg: error()
|
||||
mdiarg = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin":
|
||||
if iarg+2 > narg: error()
|
||||
plugin = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-plugin_args":
|
||||
if iarg+2 > narg: error()
|
||||
plugin_args = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-n":
|
||||
if iarg+2 > narg: error()
|
||||
ncalc = int(args[iarg+1])
|
||||
iarg += 2
|
||||
elif args[iarg] == "-mode":
|
||||
if iarg+2 > narg: error()
|
||||
mode = args[iarg+1]
|
||||
if mode != "eval" and mode != "run" and mode != "min": error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-size":
|
||||
if iarg+4 > narg: error()
|
||||
nx = int(args[iarg+1])
|
||||
ny = int(args[iarg+2])
|
||||
nz = int(args[iarg+3])
|
||||
if nx <= 0 or ny <= 0 or nz <= 0: error()
|
||||
iarg += 4
|
||||
elif args[iarg] == "-rho":
|
||||
if iarg+3 > narg: error()
|
||||
rho = float(args[iarg+1])
|
||||
rhodelta = float(args[iarg+2])
|
||||
if rho-rhodelta <= 0.0: error()
|
||||
iarg += 3
|
||||
elif args[iarg] == "-delta":
|
||||
if iarg+2 > narg: error()
|
||||
delta = float(args[iarg+1])
|
||||
if delta < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nsteps":
|
||||
if iarg+2 > narg: error()
|
||||
nsteps = int(args[iarg+1])
|
||||
if nsteps < 0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-temp":
|
||||
if iarg+2 > narg: error()
|
||||
tinitial = float(args[iarg+1])
|
||||
if tinitial < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-tol":
|
||||
if iarg+2 > narg: error()
|
||||
tol = float(args[iarg+1])
|
||||
if tol < 0.0: error()
|
||||
iarg += 2
|
||||
elif args[iarg] == "-seed":
|
||||
if iarg+2 > narg: error()
|
||||
seed = int(args[iarg+1])
|
||||
if seed <= 0: error()
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
if not mdiarg: error()
|
||||
|
||||
# LAMMPS engine is a stand-alone code
|
||||
# world = MPI communicator for just this driver
|
||||
# invoke perform_tasks() directly
|
||||
|
||||
if not plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
|
||||
# connect to engine
|
||||
|
||||
mdicomm = mdi.MDI_Accept_Communicator()
|
||||
|
||||
perform_tasks(world,mdicomm,None)
|
||||
|
||||
# LAMMPS engine is a plugin library
|
||||
# launch plugin
|
||||
# MDI will call back to perform_tasks()
|
||||
|
||||
if plugin:
|
||||
mdi.MDI_Init(mdiarg)
|
||||
world = MPI.COMM_WORLD
|
||||
plugin_args += " -mdi \"-role ENGINE -name lammps -method LINK\""
|
||||
mdi.MDI_Launch_plugin(plugin,plugin_args,world,perform_tasks,None)
|
||||
Reference in New Issue
Block a user