Update pair_kim to work with new neig. list Hints
This commit is contained in:
Ryan S. Elliott
@ -16,6 +16,7 @@ variable zz equal 20*$z
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units metal
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atom_style atomic
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newton off
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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@ -24,9 +25,8 @@ create_atoms 1 box
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#pair_style lj/cut 8.1500
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#pair_coeff 1 1 0.0104 3.4000
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#pair_modify shift no
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pair_style kim LAMMPSvirial LennardJones_Ar
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pair_style kim KIMvirial LennardJones_Ar
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pair_coeff * * Ar
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mass 1 39.95
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@ -10,6 +10,7 @@ variable zz equal 20*$z
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units metal
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atom_style atomic
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newton off
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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@ -18,7 +19,6 @@ create_atoms 1 box
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pair_style lj/cut 8.1500
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pair_coeff 1 1 0.0104 3.4000
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pair_modify shift no
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#pair_style kim KIMvirial LennardJones_Ar
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#pair_coeff * * Ar
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35
examples/kim/in.kim.lj.lmp.newton-on
Normal file
35
examples/kim/in.kim.lj.lmp.newton-on
Normal file
@ -0,0 +1,35 @@
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# 3d Lennard-Jones melt
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units metal
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atom_style atomic
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newton on
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lattice fcc 4.4300
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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pair_style lj/cut 8.1500
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pair_coeff 1 1 0.0104 3.4000
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#pair_style kim KIMvirial LennardJones_Ar
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#pair_coeff * * Ar
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
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run 100
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@ -1,5 +1,5 @@
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--------------------------------------------------------------------------
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[[30970,1],0]: A high-performance Open MPI point-to-point messaging module
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[[19053,1],0]: A high-performance Open MPI point-to-point messaging module
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was unable to find any relevant network interfaces:
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Module: OpenFabrics (openib)
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@ -16,13 +16,13 @@ Lattice spacing in x,y,z = 4.43 4.43 4.43
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Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
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1 by 1 by 1 MPI processor grid
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Created 32000 atoms
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Time spent = 0.0031676 secs
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Time spent = 0.00270113 secs
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7.85482
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ghost atom cutoff = 7.85482
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binsize = 3.92741, bins = 23 23 23
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master list distance cutoff = 8.45
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ghost atom cutoff = 8.45
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binsize = 4.225, bins = 21 21 21
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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@ -33,34 +33,34 @@ Setting up Verlet run ...
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Unit style : metal
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Current step : 0
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Time step : 0.001
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Per MPI rank memory allocation (min/avg/max) = 16.58 | 16.58 | 16.58 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -495.29247 0 331.94661 -978.84224
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100 212.66365 -547.67175 0 331.94665 -1054.2086
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Loop time of 1.40245 on 1 procs for 100 steps with 32000 atoms
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0 200 6290.8194 0 7118.0584 129712.25
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100 95.179725 6718.814 0 7112.496 133346.59
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Loop time of 2.18554 on 1 procs for 100 steps with 32000 atoms
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Performance: 6.161 ns/day, 3.896 hours/ns, 71.304 timesteps/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 3.953 ns/day, 6.071 hours/ns, 45.755 timesteps/s
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99.6% CPU use with 1 MPI tasks x no 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 | 1.2556 | 1.2556 | 1.2556 | 0.0 | 89.53
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Neigh | 0.098976 | 0.098976 | 0.098976 | 0.0 | 7.06
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Comm | 0.011525 | 0.011525 | 0.011525 | 0.0 | 0.82
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Output | 0.00021903 | 0.00021903 | 0.00021903 | 0.0 | 0.02
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Modify | 0.023739 | 0.023739 | 0.023739 | 0.0 | 1.69
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Other | | 0.01244 | | | 0.89
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Pair | 2.0006 | 2.0006 | 2.0006 | 0.0 | 91.54
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Neigh | 0.13933 | 0.13933 | 0.13933 | 0.0 | 6.38
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Comm | 0.011122 | 0.011122 | 0.011122 | 0.0 | 0.51
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Output | 0.00020978 | 0.00020978 | 0.00020978 | 0.0 | 0.01
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Modify | 0.022358 | 0.022358 | 0.022358 | 0.0 | 1.02
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Other | | 0.01188 | | | 0.54
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19911 ave 19911 max 19911 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.36493e+06 ave 1.36493e+06 max 1.36493e+06 min
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Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1364931
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Ave neighs/atom = 42.6541
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Total # of neighbors = 2126875
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Ave neighs/atom = 66.4648
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:01
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Total wall time: 0:00:02
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@ -1,5 +1,5 @@
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--------------------------------------------------------------------------
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[[30962,1],0]: A high-performance Open MPI point-to-point messaging module
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[[19045,1],0]: A high-performance Open MPI point-to-point messaging module
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was unable to find any relevant network interfaces:
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Module: OpenFabrics (openib)
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@ -16,13 +16,13 @@ Lattice spacing in x,y,z = 4.43 4.43 4.43
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Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
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1 by 2 by 2 MPI processor grid
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Created 32000 atoms
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Time spent = 0.00143054 secs
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Time spent = 0.00117056 secs
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7.85482
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ghost atom cutoff = 7.85482
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binsize = 3.92741, bins = 23 23 23
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master list distance cutoff = 8.45
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ghost atom cutoff = 8.45
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binsize = 4.225, bins = 21 21 21
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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@ -33,34 +33,34 @@ Setting up Verlet run ...
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Unit style : metal
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Current step : 0
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Time step : 0.001
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Per MPI rank memory allocation (min/avg/max) = 6.875 | 6.875 | 6.875 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -495.29247 0 331.94661 -978.84224
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100 212.66365 -547.67175 0 331.94665 -1054.2086
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Loop time of 1.55473 on 4 procs for 100 steps with 32000 atoms
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0 200 6290.8194 0 7118.0584 129712.25
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100 95.179725 6718.814 0 7112.496 133346.59
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Loop time of 2.34104 on 4 procs for 100 steps with 32000 atoms
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Performance: 5.557 ns/day, 4.319 hours/ns, 64.320 timesteps/s
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23.8% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 3.691 ns/day, 6.503 hours/ns, 42.716 timesteps/s
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24.0% CPU use with 4 MPI tasks x no 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 | 0.47168 | 0.51922 | 0.58923 | 6.2 | 33.40
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Neigh | 0.061309 | 0.077009 | 0.10276 | 5.7 | 4.95
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Comm | 0.87185 | 0.92596 | 0.95327 | 3.4 | 59.56
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Output | 0.00035269 | 0.00047555 | 0.00055331 | 0.0 | 0.03
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Modify | 0.0060711 | 0.00616 | 0.0062612 | 0.1 | 0.40
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Other | | 0.0259 | | | 1.67
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Pair | 0.91499 | 0.96396 | 1.0567 | 5.6 | 41.18
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Neigh | 0.092245 | 0.11781 | 0.14572 | 6.0 | 5.03
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Comm | 1.1264 | 1.2287 | 1.2906 | 5.6 | 52.49
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Output | 0.00045199 | 0.00051154 | 0.00060273 | 0.0 | 0.02
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Modify | 0.0058738 | 0.0059629 | 0.0061675 | 0.2 | 0.25
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Other | | 0.02406 | | | 1.03
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Nlocal: 8000 ave 8014 max 7988 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 9131 ave 9143 max 9117 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 341233 ave 341715 max 340679 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nlocal: 8000 ave 8018 max 7967 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 9131 ave 9164 max 9113 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 531719 ave 533273 max 529395 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 1364931
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Ave neighs/atom = 42.6541
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Total # of neighbors = 2126875
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Ave neighs/atom = 66.4648
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:01
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Total wall time: 0:00:02
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@ -1,5 +1,5 @@
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--------------------------------------------------------------------------
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[[30495,1],0]: A high-performance Open MPI point-to-point messaging module
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[[19074,1],0]: A high-performance Open MPI point-to-point messaging module
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was unable to find any relevant network interfaces:
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Module: OpenFabrics (openib)
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@ -16,53 +16,51 @@ Lattice spacing in x,y,z = 4.43 4.43 4.43
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Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
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1 by 1 by 1 MPI processor grid
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Created 32000 atoms
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Time spent = 0.00259765 secs
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Time spent = 0.00251478 secs
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7.85482
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ghost atom cutoff = 7.85482
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binsize = 3.92741, bins = 23 23 23
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master list distance cutoff = 8.45
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ghost atom cutoff = 8.45
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binsize = 4.225, bins = 21 21 21
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair kim, perpetual
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attributes: full, newton on, ghost, cut 7.55482
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pair build: full/bin/ghost
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stencil: full/ghost/bin/3d
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(1) pair lj/cut, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: half/bin/3d/newtoff
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bin: standard
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Setting up Verlet run ...
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Unit style : metal
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Current step : 0
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Time step : 0.001
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Per MPI rank memory allocation (min/avg/max) = 27.14 | 27.14 | 27.14 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -495.29247 0 331.94661 -978.84224
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100 212.65961 -547.66877 0 331.93294 -1053.7732
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Loop time of 2.12331 on 1 procs for 100 steps with 32000 atoms
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0 200 6290.8194 0 7118.0584 129712.25
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100 95.179725 6718.814 0 7112.496 133346.59
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Loop time of 2.6218 on 1 procs for 100 steps with 32000 atoms
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Performance: 4.069 ns/day, 5.898 hours/ns, 47.096 timesteps/s
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Performance: 3.295 ns/day, 7.283 hours/ns, 38.142 timesteps/s
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99.9% CPU use with 1 MPI tasks x no 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 | 1.7197 | 1.7197 | 1.7197 | 0.0 | 80.99
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Neigh | 0.35501 | 0.35501 | 0.35501 | 0.0 | 16.72
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Comm | 0.012289 | 0.012289 | 0.012289 | 0.0 | 0.58
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Output | 0.00021102 | 0.00021102 | 0.00021102 | 0.0 | 0.01
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Modify | 0.023484 | 0.023484 | 0.023484 | 0.0 | 1.11
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Other | | 0.01266 | | | 0.60
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Pair | 2.2623 | 2.2623 | 2.2623 | 0.0 | 86.29
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Neigh | 0.31859 | 0.31859 | 0.31859 | 0.0 | 12.15
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Comm | 0.005914 | 0.005914 | 0.005914 | 0.0 | 0.23
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Output | 0.00033105 | 0.00033105 | 0.00033105 | 0.0 | 0.01
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Modify | 0.023461 | 0.023461 | 0.023461 | 0.0 | 0.89
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Other | | 0.01123 | | | 0.43
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19911 ave 19911 max 19911 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 2.569e+06 ave 2.569e+06 max 2.569e+06 min
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Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2568996
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Ave neighs/atom = 80.2811
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Total # of neighbors = 2370499
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Ave neighs/atom = 74.0781
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:02
|
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66
examples/kim/log.04Jul2018.kim.lj.lmp.ubuntu.4
Normal file
66
examples/kim/log.04Jul2018.kim.lj.lmp.ubuntu.4
Normal file
@ -0,0 +1,66 @@
|
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--------------------------------------------------------------------------
|
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[[19098,1],0]: A high-performance Open MPI point-to-point messaging module
|
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was unable to find any relevant network interfaces:
|
||||
|
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Module: OpenFabrics (openib)
|
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Host: ubuntu-artful
|
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|
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Another transport will be used instead, although this may result in
|
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lower performance.
|
||||
|
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NOTE: You can disable this warning by setting the MCA parameter
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btl_base_warn_component_unused to 0.
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--------------------------------------------------------------------------
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LAMMPS (22 Jun 2018)
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Lattice spacing in x,y,z = 4.43 4.43 4.43
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Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
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1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00123697 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
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attributes: half, newton off
|
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pair build: half/bin/newtoff
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stencil: half/bin/3d/newtoff
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bin: standard
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Setting up Verlet run ...
|
||||
Unit style : metal
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Current step : 0
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Time step : 0.001
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||||
Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
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||||
Step Temp E_pair E_mol TotEng Press
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0 200 6290.8194 0 7118.0584 129712.25
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100 95.179725 6718.814 0 7112.496 133346.59
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Loop time of 2.88232 on 4 procs for 100 steps with 32000 atoms
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Performance: 2.998 ns/day, 8.006 hours/ns, 34.694 timesteps/s
|
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24.6% CPU use with 4 MPI tasks x no 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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Pair | 1.3577 | 1.415 | 1.467 | 3.7 | 49.09
|
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Neigh | 0.25761 | 0.28189 | 0.29894 | 3.2 | 9.78
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Comm | 0.58287 | 0.73218 | 0.85561 | 11.5 | 25.40
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Output | 0.00082721 | 0.0029034 | 0.0051877 | 3.1 | 0.10
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Modify | 0.0058569 | 0.015767 | 0.033242 | 8.6 | 0.55
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Other | | 0.4346 | | | 15.08
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Nlocal: 8000 ave 8018 max 7967 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 9131 ave 9164 max 9113 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 630904 ave 632094 max 628209 min
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Histogram: 1 0 0 0 0 0 0 1 0 2
|
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|
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Total # of neighbors = 2523614
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Ave neighs/atom = 78.8629
|
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Neighbor list builds = 3
|
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Dangerous builds = 0
|
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Total wall time: 0:00:03
|
||||
69
examples/kim/log.04Jul2018.kim.lj.ubuntu.1
Normal file
69
examples/kim/log.04Jul2018.kim.lj.ubuntu.1
Normal file
@ -0,0 +1,69 @@
|
||||
--------------------------------------------------------------------------
|
||||
[[19111,1],0]: A high-performance Open MPI point-to-point messaging module
|
||||
was unable to find any relevant network interfaces:
|
||||
|
||||
Module: OpenFabrics (openib)
|
||||
Host: ubuntu-artful
|
||||
|
||||
Another transport will be used instead, although this may result in
|
||||
lower performance.
|
||||
|
||||
NOTE: You can disable this warning by setting the MCA parameter
|
||||
btl_base_warn_component_unused to 0.
|
||||
--------------------------------------------------------------------------
|
||||
LAMMPS (22 Jun 2018)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00257231 secs
|
||||
WARNING: KIM Model does not provide `partialVirial'. pair_kim will always use `LAMMPSvirial' option. (../pair_kim.cpp:987)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:992)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:996)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: half, newton off, cut 8.45
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.26 | 21.26 | 21.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 1270.4248
|
||||
100 95.179725 6718.814 0 7112.496 604.59343
|
||||
Loop time of 3.22934 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.675 ns/day, 8.970 hours/ns, 30.966 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.821 | 2.821 | 2.821 | 0.0 | 87.36
|
||||
Neigh | 0.35198 | 0.35198 | 0.35198 | 0.0 | 10.90
|
||||
Comm | 0.0081757 | 0.0081757 | 0.0081757 | 0.0 | 0.25
|
||||
Output | 0.00030922 | 0.00030922 | 0.00030922 | 0.0 | 0.01
|
||||
Modify | 0.032856 | 0.032856 | 0.032856 | 0.0 | 1.02
|
||||
Other | | 0.01501 | | | 0.46
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2370499
|
||||
Ave neighs/atom = 74.0781
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
78
examples/kim/log.04Jul2018.kim.lj.ubuntu.4
Normal file
78
examples/kim/log.04Jul2018.kim.lj.ubuntu.4
Normal file
@ -0,0 +1,78 @@
|
||||
--------------------------------------------------------------------------
|
||||
[[19135,1],1]: A high-performance Open MPI point-to-point messaging module
|
||||
was unable to find any relevant network interfaces:
|
||||
|
||||
Module: OpenFabrics (openib)
|
||||
Host: ubuntu-artful
|
||||
|
||||
Another transport will be used instead, although this may result in
|
||||
lower performance.
|
||||
|
||||
NOTE: You can disable this warning by setting the MCA parameter
|
||||
btl_base_warn_component_unused to 0.
|
||||
--------------------------------------------------------------------------
|
||||
LAMMPS (22 Jun 2018)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00154417 secs
|
||||
WARNING: KIM Model does not provide `partialVirial'. pair_kim will always use `LAMMPSvirial' option. (../pair_kim.cpp:987)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:992)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:996)
|
||||
WARNING: KIM Model does not provide `partialVirial'. pair_kim will always use `LAMMPSvirial' option. (../pair_kim.cpp:987)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:992)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:996)
|
||||
WARNING: KIM Model does not provide `partialVirial'. pair_kim will always use `LAMMPSvirial' option. (../pair_kim.cpp:987)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:992)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:996)
|
||||
WARNING: KIM Model does not provide `partialVirial'. pair_kim will always use `LAMMPSvirial' option. (../pair_kim.cpp:987)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:992)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:996)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: half, newton off, cut 8.45
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.528 | 8.528 | 8.528 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 1270.4248
|
||||
100 95.179725 6718.814 0 7112.496 604.59343
|
||||
Loop time of 3.17877 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.718 ns/day, 8.830 hours/ns, 31.459 timesteps/s
|
||||
24.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.0514 | 2.1009 | 2.1859 | 3.6 | 66.09
|
||||
Neigh | 0.29304 | 0.31706 | 0.33568 | 2.7 | 9.97
|
||||
Comm | 0.61926 | 0.72709 | 0.77083 | 7.3 | 22.87
|
||||
Output | 0.00035457 | 0.00043741 | 0.000547 | 0.0 | 0.01
|
||||
Modify | 0.0066107 | 0.0067653 | 0.0069097 | 0.1 | 0.21
|
||||
Other | | 0.02653 | | | 0.83
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 630904 ave 632094 max 628209 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 2523614
|
||||
Ave neighs/atom = 78.8629
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,68 +0,0 @@
|
||||
--------------------------------------------------------------------------
|
||||
[[30487,1],0]: A high-performance Open MPI point-to-point messaging module
|
||||
was unable to find any relevant network interfaces:
|
||||
|
||||
Module: OpenFabrics (openib)
|
||||
Host: ubuntu-artful
|
||||
|
||||
Another transport will be used instead, although this may result in
|
||||
lower performance.
|
||||
|
||||
NOTE: You can disable this warning by setting the MCA parameter
|
||||
btl_base_warn_component_unused to 0.
|
||||
--------------------------------------------------------------------------
|
||||
LAMMPS (22 Jun 2018)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.00128874 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 7.85482
|
||||
ghost atom cutoff = 7.85482
|
||||
binsize = 3.92741, bins = 23 23 23
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton on, ghost, cut 7.55482
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.82 | 10.82 | 10.82 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -495.29247 0 331.94661 -978.84224
|
||||
100 212.65961 -547.66877 0 331.93294 -1053.7732
|
||||
Loop time of 2.58934 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.337 ns/day, 7.193 hours/ns, 38.620 timesteps/s
|
||||
24.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.85344 | 0.94031 | 1.0212 | 7.2 | 36.31
|
||||
Neigh | 0.40159 | 0.42603 | 0.43728 | 2.2 | 16.45
|
||||
Comm | 1.1013 | 1.1823 | 1.2796 | 6.9 | 45.66
|
||||
Output | 0.00041301 | 0.00056702 | 0.00081648 | 0.0 | 0.02
|
||||
Modify | 0.0062882 | 0.0063459 | 0.0064657 | 0.1 | 0.25
|
||||
Other | | 0.03375 | | | 1.30
|
||||
|
||||
Nlocal: 8000 ave 8014 max 7988 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 9131 ave 9143 max 9117 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 642249 ave 643365 max 641215 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2568996
|
||||
Ave neighs/atom = 80.2811
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -12,13 +12,11 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Ryan S. Elliott,
|
||||
Valeriu Smirichinski,
|
||||
Ellad Tadmor
|
||||
Contributing authors: Ryan S. Elliott (UMinn)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Designed for use with the kim-api-v1.6.0 (and newer) package
|
||||
Designed for use with the kim-api-v2.0.0-beta.1 (and newer) package
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cstring>
|
||||
@ -45,9 +43,9 @@ PairKIM::PairKIM(LAMMPS *lmp) :
|
||||
Pair(lmp),
|
||||
settings_call_count(0),
|
||||
init_style_call_count(0),
|
||||
kim_modelname(0),
|
||||
lmps_map_species_to_unique(0),
|
||||
lmps_unique_elements(0),
|
||||
kim_modelname(NULL),
|
||||
lmps_map_species_to_unique(NULL),
|
||||
lmps_unique_elements(NULL),
|
||||
lmps_num_unique_elements(0),
|
||||
lmps_units(METAL),
|
||||
lengthUnit(KIM::LENGTH_UNIT::unused),
|
||||
@ -55,8 +53,8 @@ PairKIM::PairKIM(LAMMPS *lmp) :
|
||||
chargeUnit(KIM::CHARGE_UNIT::unused),
|
||||
temperatureUnit(KIM::TEMPERATURE_UNIT::unused),
|
||||
timeUnit(KIM::TIME_UNIT::unused),
|
||||
pkim(0),
|
||||
pargs(0),
|
||||
pkim(NULL),
|
||||
pargs(NULL),
|
||||
kim_model_support_for_energy(KIM::SUPPORT_STATUS::notSupported),
|
||||
kim_model_support_for_forces(KIM::SUPPORT_STATUS::notSupported),
|
||||
kim_model_support_for_virial(KIM::SUPPORT_STATUS::notSupported),
|
||||
@ -64,15 +62,17 @@ PairKIM::PairKIM(LAMMPS *lmp) :
|
||||
kim_model_support_for_particleVirial(KIM::SUPPORT_STATUS::notSupported),
|
||||
lmps_local_tot_num_atoms(0),
|
||||
kim_global_influence_distance(0.0),
|
||||
kim_number_of_cutoffs(0),
|
||||
kim_cutoff_values(0),
|
||||
neighborLists(0),
|
||||
kim_particle_codes(0),
|
||||
kim_number_of_neighbor_lists(0),
|
||||
kim_cutoff_values(NULL),
|
||||
padding_neighbor_hints(NULL),
|
||||
half_list_hints(NULL),
|
||||
neighborLists(NULL),
|
||||
kim_particle_codes(NULL),
|
||||
lmps_maxalloc(0),
|
||||
kim_particleSpecies(0),
|
||||
kim_particleContributing(0),
|
||||
lmps_stripped_neigh_list(0),
|
||||
lmps_stripped_neigh_ptr(0)
|
||||
kim_particleSpecies(NULL),
|
||||
kim_particleContributing(NULL),
|
||||
lmps_stripped_neigh_list(NULL),
|
||||
lmps_stripped_neigh_ptr(NULL)
|
||||
{
|
||||
// Initialize Pair data members to appropriate values
|
||||
single_enable = 0; // We do not provide the Single() function
|
||||
@ -101,6 +101,13 @@ PairKIM::~PairKIM()
|
||||
delete [] lmps_unique_elements[i];
|
||||
delete [] lmps_unique_elements;
|
||||
|
||||
if (kim_particle_codes_ok)
|
||||
{
|
||||
delete [] kim_particle_codes;
|
||||
kim_particle_codes = NULL;
|
||||
kim_particle_codes_ok = false;
|
||||
}
|
||||
|
||||
// clean up local memory used to support KIM interface
|
||||
memory->destroy(kim_particleSpecies);
|
||||
memory->destroy(kim_particleContributing);
|
||||
@ -281,20 +288,6 @@ void PairKIM::settings(int narg, char **arg)
|
||||
// set lmps_* bool flags
|
||||
set_lmps_flags();
|
||||
|
||||
// set virial handling
|
||||
if (strcmp(arg[0],"LAMMPSvirial") == 0)
|
||||
{
|
||||
no_virial_fdotr_compute = 0;
|
||||
}
|
||||
else if (strcmp(arg[0],"KIMvirial") == 0)
|
||||
{
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"Unrecognized virial argument in pair_style command");
|
||||
}
|
||||
|
||||
// set KIM Model name
|
||||
int nmlen = strlen(arg[1]);
|
||||
if (kim_modelname != 0)
|
||||
@ -305,6 +298,26 @@ void PairKIM::settings(int narg, char **arg)
|
||||
kim_modelname = new char[nmlen+1];
|
||||
strcpy(kim_modelname, arg[1]);
|
||||
|
||||
// initialize KIM Model
|
||||
kim_init();
|
||||
|
||||
// set virial handling
|
||||
if (strcmp(arg[0],"KIMvirial") == 0)
|
||||
{
|
||||
if (kim_model_support_for_virial == KIM::SUPPORT_STATUS::notSupported)
|
||||
no_virial_fdotr_compute = 0;
|
||||
else
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
else if (strcmp(arg[0],"LAMMPSvirial") == 0)
|
||||
{
|
||||
no_virial_fdotr_compute = 0;
|
||||
}
|
||||
else
|
||||
{
|
||||
error->all(FLERR,"Unrecognized virial argument in pair_style command");
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
@ -351,7 +364,7 @@ void PairKIM::coeff(int narg, char **arg)
|
||||
|
||||
|
||||
// Assume all species arguments are valid
|
||||
// errors will be detected by kim_api_init() matching
|
||||
// errors will be detected by below
|
||||
lmps_num_unique_elements = 0;
|
||||
for (i = 2; i < narg; i++) {
|
||||
for (j = 0; j < lmps_num_unique_elements; j++)
|
||||
@ -378,6 +391,29 @@ void PairKIM::coeff(int narg, char **arg)
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// setup mapping between LAMMPS unique elements and KIM species codes
|
||||
if (kim_particle_codes_ok)
|
||||
{
|
||||
delete [] kim_particle_codes;
|
||||
kim_particle_codes = NULL;
|
||||
kim_particle_codes_ok = false;
|
||||
}
|
||||
kim_particle_codes = new int[lmps_num_unique_elements];
|
||||
kim_particle_codes_ok = true;
|
||||
for(int i = 0; i < lmps_num_unique_elements; i++){
|
||||
int kimerror;
|
||||
int supported;
|
||||
int code;
|
||||
kimerror = pkim->GetSpeciesSupportAndCode(
|
||||
KIM::SpeciesName(lmps_unique_elements[i]),
|
||||
&supported,
|
||||
&code);
|
||||
if (supported)
|
||||
kim_particle_codes[i] = code;
|
||||
else
|
||||
error->all(FLERR,"create_kim_particle_codes: symbol not found ");
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
@ -394,22 +430,16 @@ void PairKIM::init_style()
|
||||
error->all(FLERR,"PairKIM only works with 3D problems");
|
||||
|
||||
int kimerror;
|
||||
// KIM and Model initialization (only once)
|
||||
// also sets kim_ind_* and kim_* bool flags
|
||||
if (!kim_init_ok)
|
||||
{
|
||||
kim_init();
|
||||
}
|
||||
|
||||
// setup lmps_stripped_neigh_list for neighbors of one atom, if needed
|
||||
if (lmps_using_molecular) {
|
||||
memory->destroy(lmps_stripped_neigh_list);
|
||||
memory->create(lmps_stripped_neigh_list,
|
||||
kim_number_of_cutoffs*neighbor->oneatom,
|
||||
kim_number_of_neighbor_lists*neighbor->oneatom,
|
||||
"pair:lmps_stripped_neigh_list");
|
||||
delete [] lmps_stripped_neigh_ptr;
|
||||
lmps_stripped_neigh_ptr = new int*[kim_number_of_cutoffs];
|
||||
for (int i = 0; i < kim_number_of_cutoffs; ++i)
|
||||
lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists];
|
||||
for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
|
||||
{
|
||||
lmps_stripped_neigh_ptr[0]
|
||||
= &(lmps_stripped_neigh_list[(i-1)*(neighbor->oneatom)]);
|
||||
@ -420,14 +450,32 @@ void PairKIM::init_style()
|
||||
// make sure comm_reverse expects (at most) 9 values when newton is off
|
||||
if (!lmps_using_newton) comm_reverse_off = 9;
|
||||
|
||||
// request full neighbor lists
|
||||
for (int i = 0; i < kim_number_of_cutoffs; ++i)
|
||||
// request full neighbor lists (unless hints allow for better alternatives)
|
||||
for (int i = 0; i < kim_number_of_neighbor_lists; ++i)
|
||||
{
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->id = i;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->requests[irequest]->ghost = 1;
|
||||
if (half_list_hints[i])
|
||||
{
|
||||
neighbor->requests[irequest]->half = 1;
|
||||
if (! lmps_using_newton) neighbor->requests[irequest]->newton = 2;
|
||||
neighbor->requests[irequest]->full = 0;
|
||||
}
|
||||
else
|
||||
{
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
if (! lmps_using_newton) neighbor->requests[irequest]->newton = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
}
|
||||
if (padding_neighbor_hints[i])
|
||||
{
|
||||
neighbor->requests[irequest]->ghost = 0;
|
||||
}
|
||||
else
|
||||
{
|
||||
neighbor->requests[irequest]->ghost = 1;
|
||||
|
||||
}
|
||||
neighbor->requests[irequest]->cut = 1;
|
||||
neighbor->requests[irequest]->cutoff
|
||||
= kim_cutoff_values[i] + neighbor->skin;
|
||||
@ -604,7 +652,8 @@ double PairKIM::memory_usage()
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int PairKIM::get_neigh(void const * const dataObject,
|
||||
int const numberOfCutoffs, double const * const cutoffs,
|
||||
int const numberOfNeighborLists,
|
||||
double const * const cutoffs,
|
||||
int const neighborListIndex, int const particleNumber,
|
||||
int * const numberOfNeighbors,
|
||||
int const ** const neighborsOfParticle)
|
||||
@ -612,8 +661,9 @@ int PairKIM::get_neigh(void const * const dataObject,
|
||||
PairKIM const * const Model
|
||||
= reinterpret_cast<PairKIM const * const>(dataObject);
|
||||
|
||||
if (numberOfCutoffs != Model->kim_number_of_cutoffs) return true;
|
||||
for (int i = 0; i < numberOfCutoffs; ++i)
|
||||
if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists)
|
||||
return true;
|
||||
for (int i = 0; i < numberOfNeighborLists; ++i)
|
||||
{
|
||||
if (Model->kim_cutoff_values[i] < cutoffs[i]) return true;
|
||||
}
|
||||
@ -666,13 +716,6 @@ void PairKIM::kim_free()
|
||||
}
|
||||
kim_init_ok = false;
|
||||
|
||||
if (kim_particle_codes_ok)
|
||||
{
|
||||
delete [] kim_particle_codes;
|
||||
kim_particle_codes = 0;
|
||||
kim_particle_codes_ok = false;
|
||||
}
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
@ -713,32 +756,17 @@ void PairKIM::kim_init()
|
||||
// determine KIM Model capabilities (used in this function below)
|
||||
set_kim_model_has_flags();
|
||||
|
||||
// setup mapping between LAMMPS unique elements and KIM species codes
|
||||
kim_particle_codes = new int[lmps_num_unique_elements];
|
||||
kim_particle_codes_ok = true;
|
||||
for(int i = 0; i < lmps_num_unique_elements; i++){
|
||||
int kimerror;
|
||||
int supported;
|
||||
int code;
|
||||
kimerror = pkim->GetSpeciesSupportAndCode(
|
||||
KIM::SpeciesName(lmps_unique_elements[i]),
|
||||
&supported,
|
||||
&code);
|
||||
if (supported)
|
||||
kim_particle_codes[i] = code;
|
||||
else
|
||||
error->all(FLERR,"create_kim_particle_codes: symbol not found ");
|
||||
}
|
||||
|
||||
pkim->GetInfluenceDistance(&kim_global_influence_distance);
|
||||
pkim->GetNeighborListCutoffsPointer(&kim_number_of_cutoffs,
|
||||
&kim_cutoff_values);
|
||||
pkim->GetNeighborListPointers(&kim_number_of_neighbor_lists,
|
||||
&kim_cutoff_values,
|
||||
&padding_neighbor_hints,
|
||||
&half_list_hints);
|
||||
if (neighborLists)
|
||||
{
|
||||
delete [] neighborLists;
|
||||
neighborLists = 0;
|
||||
}
|
||||
neighborLists = new NeighList*[kim_number_of_cutoffs];
|
||||
neighborLists = new NeighList*[kim_number_of_neighbor_lists];
|
||||
|
||||
kimerror = pargs->SetArgumentPointer(
|
||||
KIM::COMPUTE_ARGUMENT_NAME::numberOfParticles,
|
||||
@ -932,7 +960,7 @@ void PairKIM::set_kim_model_has_flags()
|
||||
int kimerror = GetComputeArgumentName(i, &computeArgumentName);
|
||||
KIM::SupportStatus supportStatus;
|
||||
kimerror = pargs->GetArgumentSupportStatus(computeArgumentName,
|
||||
&supportStatus);
|
||||
&supportStatus);
|
||||
|
||||
if (computeArgumentName == partialEnergy)
|
||||
kim_model_support_for_energy = supportStatus;
|
||||
@ -958,12 +986,10 @@ void PairKIM::set_kim_model_has_flags()
|
||||
error->warning(FLERR,"KIM Model does not provide `partialForce'; "
|
||||
"Forces will be zero");
|
||||
|
||||
if ((no_virial_fdotr_compute == 1) &&
|
||||
(kim_model_support_for_virial == notSupported))
|
||||
if (kim_model_support_for_virial == notSupported)
|
||||
{
|
||||
error->warning(FLERR,"KIM Model does not provide `partialVirial'. "
|
||||
"pair_kim now using `LAMMPSvirial' option.");
|
||||
no_virial_fdotr_compute = 0;
|
||||
"pair_kim will always use `LAMMPSvirial' option.");
|
||||
}
|
||||
|
||||
if (kim_model_support_for_particleEnergy == notSupported)
|
||||
|
||||
@ -12,13 +12,11 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Ryan S. Elliott,
|
||||
Valeriu Smirichinski,
|
||||
Ellad Tadmor (U Minn)
|
||||
Contributing authors: Ryan S. Elliott (UMinn)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Designed for use with the kim-api-v1.6.0 (and newer) package
|
||||
Designed for use with the kim-api-v2.0.0-beta.1 (and newer) package
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
@ -100,8 +98,10 @@ namespace LAMMPS_NS {
|
||||
bool kim_init_ok;
|
||||
int lmps_local_tot_num_atoms;
|
||||
double kim_global_influence_distance; // KIM Model cutoff value
|
||||
int kim_number_of_cutoffs;
|
||||
int kim_number_of_neighbor_lists;
|
||||
double const * kim_cutoff_values;
|
||||
int const * padding_neighbor_hints;
|
||||
int const * half_list_hints;
|
||||
class NeighList ** neighborLists;
|
||||
|
||||
// values set in init_style()
|
||||
|
||||
Reference in New Issue
Block a user