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LAMMPS (30 Apr 2015)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
1 by 1 by 1 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 12
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 16.5817 Mbytes
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
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
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
Loop time of 0.825997 on 1 procs for 4 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5882212 -61506.6041431
Force two-norm initial, final = 17.893 3.40908
Force max component initial, final = 0.757547 0.131738
Final line search alpha, max atom move = 0.394559 0.0519786
Iterations, force evaluations = 4 8
Pair time (%) = 0.750684 (90.8822)
Bond time (%) = 0.000310898 (0.0376391)
Kspce time (%) = 0.0739563 (8.95357)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000602961 (0.0729979)
Outpt time (%) = 0 (0)
Other time (%) = 0.000442505 (0.0535722)
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10804 ave 10804 max 10804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 596960 ave 596960 max 596960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.19392e+06 ave 1.19392e+06 max 1.19392e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
Memory usage per processor = 16.2067 Mbytes
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
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
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
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
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
Loop time of 17.4198 on 1 procs for 100 steps with 1400 atoms
Pair time (%) = 16.4306 (94.3215)
Bond time (%) = 0.00661898 (0.037997)
Kspce time (%) = 0.846369 (4.85867)
Neigh time (%) = 0.105605 (0.606238)
Comm time (%) = 0.0149999 (0.0861084)
Outpt time (%) = 0.000102997 (0.000591265)
Other time (%) = 0.0154905 (0.0889251)
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10843 ave 10843 max 10843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 595307 ave 595307 max 595307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.19061e+06 ave 1.19061e+06 max 1.19061e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1190614
Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (30 Apr 2015)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
2 by 1 by 2 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 12
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 16.9507 Mbytes
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
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
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
Loop time of 0.247166 on 4 procs for 4 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5882212 -61506.6041431
Force two-norm initial, final = 17.893 3.40908
Force max component initial, final = 0.757547 0.131738
Final line search alpha, max atom move = 0.394559 0.0519786
Iterations, force evaluations = 4 8
Pair time (%) = 0.114075 (46.1533)
Bond time (%) = 8.34465e-05 (0.0337613)
Kspce time (%) = 0.12952 (52.4018)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00310308 (1.25546)
Outpt time (%) = 0 (0)
Other time (%) = 0.000384748 (0.155664)
Nlocal: 350 ave 399 max 305 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6602 ave 6647 max 6553 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 149240 ave 170954 max 129384 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 298480 ave 340157 max 260160 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:211)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
Memory usage per processor = 16.5757 Mbytes
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
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
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
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
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
Loop time of 4.71994 on 4 procs for 100 steps with 1400 atoms
Pair time (%) = 2.2751 (48.2019)
Bond time (%) = 0.00181025 (0.0383533)
Kspce time (%) = 0.222529 (4.71465)
Neigh time (%) = 0.026421 (0.559774)
Comm time (%) = 2.17822 (46.1493)
Outpt time (%) = 0.000155747 (0.00329977)
Other time (%) = 0.0157004 (0.33264)
Nlocal: 350 ave 357 max 340 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6639.25 ave 6657 max 6627 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 148827 ave 152055 max 145212 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 297654 ave 303283 max 288784 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 1190614
Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0