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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11901 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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examples/nb3b/MOH.nb3b.harmonic Normal file
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# nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements
#
# multiple entries can be added to this file, LAMMPS reads the ones it needs
#
# these entries are in LAMMPS "real" units:
# k [kcal/mol/rad^2], theta_0 [degrees], cutoff [Angstroms]
#
# format of a single entry (one or more lines):
# element 1 (central atom), element 2, element 3,
# k_theta, theta_0, cutoff
#
# (ijj)-->determines cutoff for i-j distance
# (jik)-->determines k, theta_0 for i-j-k angle term
#
# ielem jelem kelem k theta_0 cutoff
O M M 0.00 0.00 2.80
O H H 0.00 0.00 1.20
O M H 6.35 120.00 0.00
O H M 6.35 120.00 0.00

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examples/nb3b/data.nb3b Normal file
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examples/nb3b/in.nb3b Normal file
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# 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
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
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
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
### 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

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examples/nb3b/log.nb3b.1Feb14.linux.1 Normal file
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LAMMPS (3 May 2014)
# 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:173)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 21.4036 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
3 -61506.574 0 0 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 2196.3697 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.969872 on 1 procs for 3 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5583555 -61506.5743242
Force two-norm initial, final = 17.893 9.98801
Force max component initial, final = 0.757547 0.314107
Final line search alpha, max atom move = 0.000178805 5.61639e-05
Iterations, force evaluations = 3 25
Pair time (%) = 0.747406 (77.0623)
Bond time (%) = 0.000653505 (0.0673806)
Kspce time (%) = 0.218625 (22.5416)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00222945 (0.229871)
Outpt time (%) = 0 (0)
Other time (%) = 0.000958443 (0.0988216)
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:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
Memory usage per processor = 20.9138 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
3 -60263.869 1242.7057 298 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 6988.0868 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58834.736 1260.2404 302.20481 -60094.977 213.89563 0 0 0 6132.6243 -20255.127 -46186.37 21262.808 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58828.252 1242.7057 298 -60070.958 437.82815 0 0 0 6455.2967 -20778.873 -46185.21 20113.98 22.5907 22.359 23.4708 0 0 0 11855.229
103 -58827.642 1235.2387 296.20942 -60062.881 453.5865 0 0 0 6411.1525 -20743.952 -46183.668 18788.656 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 5.86221 on 1 procs for 100 steps with 1400 atoms
Pair time (%) = 4.88784 (83.3788)
Bond time (%) = 0.00446033 (0.0760863)
Kspce time (%) = 0.840367 (14.3353)
Neigh time (%) = 0.0973861 (1.66125)
Comm time (%) = 0.01776 (0.302958)
Outpt time (%) = 0.000123978 (0.00211486)
Other time (%) = 0.0142703 (0.243429)
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: 595351 ave 595351 max 595351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.1907e+06 ave 1.1907e+06 max 1.1907e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1190702
Ave neighs/atom = 850.501
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0

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examples/nb3b/log.nb3b.1Feb14.linux.4 Normal file
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LAMMPS (3 May 2014)
# 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:173)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 10.9549 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
3 -61506.574 0 0 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 2196.3697 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.288323 on 4 procs for 3 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5583555 -61506.5743242
Force two-norm initial, final = 17.893 9.98801
Force max component initial, final = 0.757547 0.314107
Final line search alpha, max atom move = 0.000178805 5.61639e-05
Iterations, force evaluations = 3 25
Pair time (%) = 0.19587 (67.9344)
Bond time (%) = 0.000175655 (0.060923)
Kspce time (%) = 0.0835239 (28.9689)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00802237 (2.78243)
Outpt time (%) = 0 (0)
Other time (%) = 0.000730693 (0.253429)
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:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
Memory usage per processor = 10.7173 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
3 -60263.869 1242.7057 298 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 6988.0868 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58834.736 1260.2404 302.20481 -60094.977 213.89563 0 0 0 6132.6243 -20255.127 -46186.37 21262.808 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58828.252 1242.7057 298 -60070.958 437.82815 0 0 0 6455.2967 -20778.873 -46185.21 20113.98 22.5907 22.359 23.4708 0 0 0 11855.229
103 -58827.642 1235.2387 296.20942 -60062.881 453.5865 0 0 0 6411.1525 -20743.952 -46183.668 18788.656 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 1.67162 on 4 procs for 100 steps with 1400 atoms
Pair time (%) = 1.28323 (76.7654)
Bond time (%) = 0.00121307 (0.0725687)
Kspce time (%) = 0.22219 (13.2919)
Neigh time (%) = 0.0252143 (1.50837)
Comm time (%) = 0.123892 (7.4115)
Outpt time (%) = 0.000187218 (0.0111998)
Other time (%) = 0.0156981 (0.939097)
Nlocal: 350 ave 356 max 341 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 6638.5 ave 6656 max 6627 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 148838 ave 151622 max 145706 min
Histogram: 1 0 0 0 1 0 1 0 0 1
FullNghs: 297676 ave 302447 max 289666 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 1190702
Ave neighs/atom = 850.501
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0