add harmonic/cut to python example folder. small tweaks to docs and examples
This commit is contained in:
Axel Kohlmeyer
288
examples/python/log.18Mar22.pair_python_harmonic.opencl.1
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288
examples/python/log.18Mar22.pair_python_harmonic.opencl.1
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@ -0,0 +1,288 @@
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LAMMPS (17 Feb 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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package gpu 0
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# 3d soft repulsive particles
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units real
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atom_style atomic
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lattice fcc 5.0 origin 0.1 0.1 0.1
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Lattice spacing in x,y,z = 5 5 5
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region box block -5 5 -5 5 -5 5
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create_box 2 box
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Created orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
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create_atoms CPU = 0.000 seconds
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set type 1 type/ratio 2 0.5 424662346
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Setting atom values ...
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2000 settings made for type/ratio
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mass * 1.0
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velocity all create 3.0 87287
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pair_style python 9.0
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pair_coeff * * py_pot.Harmonic A B
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- GPU package (short-range, long-range and three-body potentials):
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@Article{Brown11,
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author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
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title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
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journal = {Comp.~Phys.~Comm.},
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year = 2011,
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volume = 182,
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pages = {898--911}
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}
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@Article{Brown12,
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author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
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title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
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journal = {Comp.~Phys.~Comm.},
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year = 2012,
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volume = 183,
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pages = {449--459}
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}
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@Article{Brown13,
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author = {W. M. Brown, Y. Masako},
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title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
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journal = {Comp.~Phys.~Comm.},
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year = 2013,
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volume = 184,
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pages = {2785--2793}
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}
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@Article{Trung15,
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author = {T. D. Nguyen, S. J. Plimpton},
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title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
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journal = {Comput.~Mater.~Sci.},
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year = 2015,
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volume = 100,
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pages = {173--180}
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}
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@Article{Trung17,
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author = {T. D. Nguyen},
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title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
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journal = {Comp.~Phys.~Comm.},
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year = 2017,
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volume = 212,
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pages = {113--122}
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}
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@Article{Nikolskiy19,
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author = {V. Nikolskiy, V. Stegailov},
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title = {GPU acceleration of four-site water models in LAMMPS},
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journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
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year = 2019
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 423789.56 0 423825.32 249259.3
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50 75.889551 422919.46 0 423824.08 248893.24
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100 105.20972 422570.47 0 423824.6 250756.6
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150 132.08764 422249.71 0 423824.23 251894.29
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200 118.14116 422416.43 0 423824.7 252088.96
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250 128.40086 422293.71 0 423824.28 252057.16
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Loop time of 21.1837 on 1 procs for 250 steps with 4000 atoms
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write_restart repulsive.restart
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System init for write_restart ...
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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package gpu 0
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.000 seconds
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pair_style python 10.0
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pair_coeff * * py_pot.Harmonic A B
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shell rm -f python.dat
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pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
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Creating table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 9 9 9
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/3d
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bin: standard
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pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
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Appending to table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
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Appending to table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 128.40086 422293.71 0 423824.28 252057.16
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300 119.72871 422397.4 0 423824.6 251985.11
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350 124.88375 422335.77 0 423824.42 252051.28
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400 121.76143 422373.11 0 423824.53 252006.39
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450 125.29847 422330.9 0 423824.49 251997.23
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500 126.87408 422312.08 0 423824.45 252053.51
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Loop time of 28.5184 on 1 procs for 250 steps with 4000 atoms
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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package gpu 0
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.000 seconds
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pair_style harmonic/cut
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pair_coeff 1 1 0.2 9.0
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pair_coeff 2 2 0.4 9.0
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shell rm -f harmonic.dat
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pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
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Creating table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair harmonic/cut, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/3d
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bin: standard
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pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
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Appending to table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
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Appending to table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 128.40086 422293.71 0 423824.28 252057.16
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300 119.72871 422397.4 0 423824.6 251985.11
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350 124.88375 422335.77 0 423824.42 252051.28
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400 121.76143 422373.11 0 423824.53 252006.39
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450 125.29847 422330.9 0 423824.49 251997.23
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500 126.87408 422312.08 0 423824.45 252053.51
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Loop time of 1.1146 on 1 procs for 250 steps with 4000 atoms
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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package gpu 0
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.000 seconds
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pair_style table spline 1000
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pair_coeff 1 1 python.dat PYTH_A_A
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Reading pair table potential file python.dat with DATE: 2022-03-18
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pair_coeff 1 2 python.dat PYTH_A_B
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Reading pair table potential file python.dat with DATE: 2022-03-18
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pair_coeff 2 2 python.dat PYTH_B_B
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Reading pair table potential file python.dat with DATE: 2022-03-18
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 128.40086 422293.71 0 423824.28 252057.14
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300 119.72876 422397.4 0 423824.6 251985.09
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350 124.88381 422335.77 0 423824.42 252051.26
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400 121.76148 422373.11 0 423824.53 252006.37
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450 125.29841 422330.9 0 423824.49 251997.2
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500 126.87418 422312.08 0 423824.45 252053.48
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Loop time of 0.389958 on 1 procs for 250 steps with 4000 atoms
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# remove temporary files
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shell rm repulsive.restart harmonic.dat python.dat
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Total wall time: 0:00:54
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