67962b15fc
- make all python potential classes derived from LAMMPSPairPotential which contains shared functionality. We currently don't check for supported atom types. may want to add that again later. - keep track of skipped atom types in the C++ code. - add test against units setting. must set self.units='...' in constructor - make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force. - rename potentials.py to py_pot.py - update test runs. some small tweaks.
215 lines
7.2 KiB
Groff
215 lines
7.2 KiB
Groff
LAMMPS (4 May 2017)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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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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mass * 1.0
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velocity all create 3.0 87287
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6758903 -4.7955425 0 -2.2823355 5.670064
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100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
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150 1.6324555 -4.7286791 0 -2.280608 5.9589514
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200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
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250 1.6275257 -4.7224992 0 -2.281821 5.9567365
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Loop time of 21.6481 on 1 procs for 250 steps with 4000 atoms
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Performance: 4988.899 tau/day, 11.548 timesteps/s
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98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 21.529 | 21.529 | 21.529 | 0.0 | 99.45
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Neigh | 0.08819 | 0.08819 | 0.08819 | 0.0 | 0.41
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Comm | 0.013276 | 0.013276 | 0.013276 | 0.0 | 0.06
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Output | 0.00025654 | 0.00025654 | 0.00025654 | 0.0 | 0.00
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Modify | 0.014466 | 0.014466 | 0.014466 | 0.0 | 0.07
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Other | | 0.003143 | | | 0.01
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5499 ave 5499 max 5499 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 151513 ave 151513 max 151513 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 151513
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Ave neighs/atom = 37.8783
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Neighbor list builds = 12
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Dangerous builds not checked
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write_data melt.data
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write_restart melt.restart
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart melt.restart
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orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 1 by 1 MPI processor grid
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4000 atoms
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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fix 1 all nve
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thermo 50
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run 250
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 1.6275257 -4.7224992 0 -2.281821 5.9567365
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300 1.645592 -4.7496711 0 -2.2819002 5.8734193
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350 1.6514972 -4.7580756 0 -2.2814491 5.810167
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400 1.6540555 -4.7622999 0 -2.281837 5.8200413
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450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
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500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
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Loop time of 21.9592 on 1 procs for 250 steps with 4000 atoms
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Performance: 4918.203 tau/day, 11.385 timesteps/s
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98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 21.74 | 21.74 | 21.74 | 0.0 | 99.00
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Neigh | 0.18588 | 0.18588 | 0.18588 | 0.0 | 0.85
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Comm | 0.01476 | 0.01476 | 0.01476 | 0.0 | 0.07
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Output | 0.00022244 | 0.00022244 | 0.00022244 | 0.0 | 0.00
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Modify | 0.01356 | 0.01356 | 0.01356 | 0.0 | 0.06
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Other | | 0.004382 | | | 0.02
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5472 ave 5472 max 5472 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 151513 ave 151513 max 151513 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 151513
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Ave neighs/atom = 37.8783
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Neighbor list builds = 25
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Dangerous builds = 25
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clear
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using 1 OpenMP thread(s) per MPI task
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units lj
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atom_style atomic
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read_data melt.data
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orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4000 atoms
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reading velocities ...
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4000 velocities
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.6275257 -4.7224992 0 -2.281821 5.9567365
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50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
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100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
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150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
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200 1.6258731 -4.7205017 0 -2.2823017 5.952511
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250 1.6370862 -4.7373176 0 -2.2823022 5.925807
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Loop time of 21.8255 on 1 procs for 250 steps with 4000 atoms
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Performance: 4948.331 tau/day, 11.454 timesteps/s
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98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 21.707 | 21.707 | 21.707 | 0.0 | 99.46
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Neigh | 0.088455 | 0.088455 | 0.088455 | 0.0 | 0.41
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Comm | 0.01311 | 0.01311 | 0.01311 | 0.0 | 0.06
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Output | 0.00025082 | 0.00025082 | 0.00025082 | 0.0 | 0.00
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Modify | 0.013836 | 0.013836 | 0.013836 | 0.0 | 0.06
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Other | | 0.003096 | | | 0.01
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5487 ave 5487 max 5487 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 151490 ave 151490 max 151490 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 151490
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Ave neighs/atom = 37.8725
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Neighbor list builds = 12
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Dangerous builds not checked
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shell rm melt.data melt.restart
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Total wall time: 0:01:07
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