add harmonic/cut to python example folder. small tweaks to docs and examples
This commit is contained in:
Axel Kohlmeyer
268
examples/python/log.18Mar22.pair_python_harmonic.openmp.1
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268
examples/python/log.18Mar22.pair_python_harmonic.openmp.1
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LAMMPS (17 Feb 2022)
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using 4 OpenMP thread(s) per MPI task
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package omp 0
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using multi-threaded neighbor list subroutines
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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 = 0.001 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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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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No /omp style for force computation currently active
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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 on, omp
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pair build: half/bin/atomonly/newton/omp
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.024 | 6.024 | 6.024 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 18.9294 on 4 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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No /omp style for force computation currently active
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clear
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using 4 OpenMP thread(s) per MPI task
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package omp 0
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using multi-threaded neighbor list subroutines
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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 = 0.001 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 on
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pair build: half/bin/atomonly/newton
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stencil: half/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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No /omp style for force computation currently active
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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 on, omp
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pair build: half/bin/atomonly/newton/omp
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.626 | 7.626 | 7.626 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 24.3294 on 4 procs for 250 steps with 4000 atoms
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clear
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using 4 OpenMP thread(s) per MPI task
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package omp 0
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using multi-threaded neighbor list subroutines
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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/omp, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/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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Last active /omp style is pair_style harmonic/cut/omp
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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 harmonic/cut/omp, perpetual
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attributes: half, newton on, omp
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pair build: half/bin/atomonly/newton/omp
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.023 | 6.023 | 6.023 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 0.219199 on 4 procs for 250 steps with 4000 atoms
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clear
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using 4 OpenMP thread(s) per MPI task
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package omp 0
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using multi-threaded neighbor list subroutines
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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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Last active /omp style is pair_style table/omp
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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 = 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 table/omp, perpetual
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attributes: half, newton on, omp
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pair build: half/bin/atomonly/newton/omp
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.056 | 6.056 | 6.056 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 251985.1
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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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450 125.29842 422330.9 0 423824.49 251997.21
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500 126.87418 422312.08 0 423824.46 252053.48
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Loop time of 0.374806 on 4 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: 0:00:44
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