forked from lijiext/lammps
174 lines
7.5 KiB
Groff
174 lines
7.5 KiB
Groff
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LAMMPS (15 Feb 2016)
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# test of NB3B pair style with pair hybrid and KSpace solver
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units real
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atom_style full
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bond_style morse
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angle_style none
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dihedral_style none
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improper_style none
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read_data data.nb3b
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orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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1400 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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560 bonds
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
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pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
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Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
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pair_modify mix arithmetic
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pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
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pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
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pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
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pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
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pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
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pair_coeff 3 3 lj/cut/coul/long 0 0
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kspace_style ewald/disp 0.0001
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neighbor 2.0 bin
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neigh_modify delay 5
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special_bonds lj/coul 0.0 0.0 1.0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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1 = max # of special neighbors
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thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
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timestep 1.0
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run_style respa 2 2 pair 1 kspace 2
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Respa levels:
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1 = bond angle dihedral improper pair
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2 = kspace
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thermo 50
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### Minimize forces in structure ###
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minimize 1.0e-06 1.0e-08 1000 10000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
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EwaldDisp initialization ...
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
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G vector = 0.269426
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
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Neighbor list info ...
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4 neighbor list requests
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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 = 12
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ghost atom cutoff = 12
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binsize = 6 -> bins = 4 4 4
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vectors: nbox = 6, nkvec = 478
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Memory usage per processor = 16.9507 Mbytes
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Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
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0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
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4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.4299 22.5907 22.359 23.4708 0 0 0 11855.229
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Loop time of 0.254354 on 4 procs for 4 steps with 1400 atoms
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99.0% CPU use with 4 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-61505.9829 -61506.5882212 -61506.6041431
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Force two-norm initial, final = 17.893 3.40908
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Force max component initial, final = 0.757547 0.131738
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Final line search alpha, max atom move = 0.394559 0.0519786
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Iterations, force evaluations = 4 8
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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 | 0.07247 | 0.17424 | 0.22771 | 14.9 | 68.50
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Bond | 8.5115e-05 | 9.495e-05 | 0.0001049 | 0.1 | 0.04
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Kspace | 0.024093 | 0.07615 | 0.17696 | 22.2 | 29.94
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0019753 | 0.0034024 | 0.0047915 | 2.0 | 1.34
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0004643 | | | 0.18
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Nlocal: 350 ave 399 max 305 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 6602 ave 6647 max 6553 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Neighs: 149240 ave 170954 max 129384 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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FullNghs: 298480 ave 340157 max 260160 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 1193920
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Ave neighs/atom = 852.8
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Ave special neighs/atom = 0.8
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Neighbor list builds = 0
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Dangerous builds = 0
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### Run NVE to equilibrate velocities ###
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velocity all create 298.0 4928459 mom yes rot yes dist gaussian
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fix 1 all nve
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fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
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run 100
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EwaldDisp initialization ...
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
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G vector = 0.269426
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
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Neighbor list info ...
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4 neighbor list requests
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update every 1 steps, delay 5 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 = 4 4 4
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Memory usage per processor = 16.5757 Mbytes
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Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
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4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.147 22.5907 22.359 23.4708 0 0 0 11855.229
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50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
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100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
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104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
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Loop time of 4.80696 on 4 procs for 100 steps with 1400 atoms
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Performance: 1.797 ns/day, 13.353 hours/ns, 20.803 timesteps/s
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99.4% 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 | 1.4587 | 3.5531 | 4.4418 | 64.9 | 73.91
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Bond | 0.0018251 | 0.0019184 | 0.0019794 | 0.1 | 0.04
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Kspace | 0.21553 | 0.22335 | 0.231 | 1.4 | 4.65
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Neigh | 0.026918 | 0.02694 | 0.026957 | 0.0 | 0.56
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Comm | 0.096146 | 0.98534 | 3.08 | 123.3 | 20.50
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Output | 0.00012541 | 0.00017965 | 0.00030398 | 0.5 | 0.00
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Modify | 0.0023086 | 0.0030754 | 0.0038064 | 1.2 | 0.06
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Other | | 0.0131 | | | 0.27
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Nlocal: 350 ave 357 max 340 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6639.25 ave 6657 max 6627 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 148827 ave 152055 max 145212 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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FullNghs: 297654 ave 303283 max 288784 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 1190614
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Ave neighs/atom = 850.439
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Ave special neighs/atom = 0.8
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:05
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