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LAMMPS (15 Feb 2016)
# 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
Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
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:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
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 0.848486 on 1 procs for 4 steps with 1400 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77228 | 0.77228 | 0.77228 | 0.0 | 91.02
Bond | 0.00031042 | 0.00031042 | 0.00031042 | 0.0 | 0.04
Kspace | 0.074903 | 0.074903 | 0.074903 | 0.0 | 8.83
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00057626 | 0.00057626 | 0.00057626 | 0.0 | 0.07
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004158 | | | 0.05
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:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
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 17.467 on 1 procs for 100 steps with 1400 atoms
Performance: 0.495 ns/day, 48.519 hours/ns, 5.725 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 | 16.477 | 16.477 | 16.477 | 0.0 | 94.33
Bond | 0.0069525 | 0.0069525 | 0.0069525 | 0.0 | 0.04
Kspace | 0.84704 | 0.84704 | 0.84704 | 0.0 | 4.85
Neigh | 0.10518 | 0.10518 | 0.10518 | 0.0 | 0.60
Comm | 0.015078 | 0.015078 | 0.015078 | 0.0 | 0.09
Output | 0.00010085 | 0.00010085 | 0.00010085 | 0.0 | 0.00
Modify | 0.0071354 | 0.0071354 | 0.0071354 | 0.0 | 0.04
Other | | 0.008824 | | | 0.05
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
Total wall time: 0:00:18

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LAMMPS (15 Feb 2016)
# 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
Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
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:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
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 0.254354 on 4 procs for 4 steps with 1400 atoms
99.0% CPU use with 4 MPI tasks x no OpenMP threads
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.07247 | 0.17424 | 0.22771 | 14.9 | 68.50
Bond | 8.5115e-05 | 9.495e-05 | 0.0001049 | 0.1 | 0.04
Kspace | 0.024093 | 0.07615 | 0.17696 | 22.2 | 29.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019753 | 0.0034024 | 0.0047915 | 2.0 | 1.34
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004643 | | | 0.18
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:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
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 4.80696 on 4 procs for 100 steps with 1400 atoms
Performance: 1.797 ns/day, 13.353 hours/ns, 20.803 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4587 | 3.5531 | 4.4418 | 64.9 | 73.91
Bond | 0.0018251 | 0.0019184 | 0.0019794 | 0.1 | 0.04
Kspace | 0.21553 | 0.22335 | 0.231 | 1.4 | 4.65
Neigh | 0.026918 | 0.02694 | 0.026957 | 0.0 | 0.56
Comm | 0.096146 | 0.98534 | 3.08 | 123.3 | 20.50
Output | 0.00012541 | 0.00017965 | 0.00030398 | 0.5 | 0.00
Modify | 0.0023086 | 0.0030754 | 0.0038064 | 1.2 | 0.06
Other | | 0.0131 | | | 0.27
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
Total wall time: 0:00:05