mirror of https://github.com/lammps/lammps.git
188 lines
8.1 KiB
Groff
188 lines
8.1 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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: 2016-07-29
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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: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/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 (src/pair.cpp:218)
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G vector = 0.269426 accuracy = 0.0332064
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
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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 = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 4 4 4
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4 neighbor lists, perpetual/occasional/extra = 4 0 0
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(1) pair nb3b/harmonic, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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(2) pair lj/cut/coul/long, perpetual, half/full from (1)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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(3) pair nb3b/harmonic, perpetual, copy from (1)
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attributes: full, newton on
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pair build: copy
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stencil: none
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bin: none
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(4) pair lj/cut/coul/long, perpetual, copy from (2)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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vectors: nbox = 6, nkvec = 478
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Per MPI rank memory allocation (min/avg/max) = 20.64 | 21.18 | 22.02 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 -46194.919 979.72822 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 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229
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Loop time of 0.164255 on 4 procs for 4 steps with 1400 atoms
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99.1% CPU use with 4 MPI tasks x 1 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 -61506.5882615 -61506.60415
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Force two-norm initial, final = 17.893 3.40909
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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 | 0.11101 | 0.12473 | 0.13747 | 3.3 | 75.93
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Bond | 5.8889e-05 | 6.2823e-05 | 6.6757e-05 | 0.0 | 0.04
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Kspace | 0.025273 | 0.036047 | 0.047969 | 5.3 | 21.95
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.001081 | 0.0030527 | 0.0048478 | 2.8 | 1.86
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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 | | 0.000367 | | | 0.22
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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 (src/pair.cpp:218)
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G vector = 0.269426 accuracy = 0.0332064
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WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
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Per MPI rank memory allocation (min/avg/max) = 20.26 | 20.8 | 21.65 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 6449.1472 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 3.0299 on 4 procs for 100 steps with 1400 atoms
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Performance: 2.852 ns/day, 8.416 hours/ns, 33.004 timesteps/s
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99.0% CPU use with 4 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 | 2.424 | 2.5288 | 2.6552 | 6.3 | 83.46
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Bond | 0.0011241 | 0.0011699 | 0.0011907 | 0.1 | 0.04
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Kspace | 0.24584 | 0.25484 | 0.26259 | 1.5 | 8.41
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Neigh | 0.031059 | 0.031067 | 0.031075 | 0.0 | 1.03
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Comm | 0.070014 | 0.19745 | 0.30262 | 22.7 | 6.52
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Output | 0.00011683 | 0.0002265 | 0.00050616 | 0.0 | 0.01
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Modify | 0.0022085 | 0.0030763 | 0.0039916 | 1.3 | 0.10
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Other | | 0.01331 | | | 0.44
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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: 0:00:03
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