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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7497 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-01-10 01:54:14 +00:00
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LAMMPS (10 Jan 2012)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.96579 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
6000 2.1073992 0.0076702482 2.1127279 0.097655994 21544.211
7000 2.0845788 -0.0022301947 2.0800324 0.1101457 17791.284
8000 2.0651397 0.0033390713 2.0661842 0.12822835 15494.655
9000 2.0578744 0.0021876274 2.0577755 0.14877329 13860.573
10000 2.050871 0.0074002268 2.0559924 0.16711807 12582.351
11000 2.0393903 0.02180458 2.0589289 0.21757395 11491.106
12000 2.0417078 0.014064648 2.0535038 0.21091044 10565.52
13000 2.0453265 0.0142046 2.0572586 0.23958431 9773.8989
14000 2.0241495 0.030159631 2.05206 0.25409138 9178.076
15000 2.0352822 0.019352462 2.0523732 0.26816816 8601.8792
16000 2.0396728 0.013649097 2.0510556 0.2897209 8117.7222
17000 2.0021829 0.051638556 2.0515968 0.35978072 7694.4722
18000 2.0323755 0.021980006 2.0520973 0.33886022 7331.3619
19000 2.012523 0.039400171 2.049687 0.38829143 7030.9065
20000 2.0210256 0.032912605 2.0516927 0.4026689 6790.5438
21000 2.0346845 0.01996079 2.0523846 0.40076736 6532.5103
22000 2.024663 0.027946479 2.0503599 0.42145195 6305.942
23000 2.019905 0.039007463 2.0566681 0.48378424 6097.1834
24000 2.0128761 0.043306652 2.0539462 0.49890589 5931.4039
25000 2.0426669 0.01677892 2.0571762 0.43582414 5761.8463
26000 2.0048718 0.055983728 2.0586279 0.56571575 5567.6133
27000 2.0444253 0.020459712 2.0626134 0.48337889 5415.7979
28000 1.9933145 0.065049949 2.0561496 0.54116421 5309.9562
29000 2.0046319 0.055203466 2.057608 0.59270605 5195.3249
30000 2.008193 0.057534886 2.0634966 0.601137 5072.6056
31000 1.999698 0.06580978 2.0632859 0.67924433 4956.2611
32000 2.0122296 0.055833298 2.0658271 0.59245863 4874.1707
33000 2.0007781 0.069519235 2.0680742 0.6326113 4802.2499
34000 2.0066804 0.064593938 2.0690447 0.63378518 4717.4744
35000 2.0326851 0.042701702 2.0731283 0.62301292 4626.0976
36000 2.024922 0.048686129 2.0713582 0.63389098 4542.6291
37000 1.9933918 0.084026218 2.0752031 0.72269199 4452.0399
38000 2.0286434 0.05351806 2.0799074 0.73016095 4351.0179
39000 2.0047353 0.070614231 2.073122 0.80274462 4289.5501
40000 2.0379085 0.038227025 2.0738712 0.71338936 4246.7929
41000 1.9952571 0.088622162 2.0816623 0.81307645 4200.0671
42000 2.0042363 0.073467747 2.0754771 0.79982857 4148.4054
43000 2.0189089 0.066082632 2.0827483 0.7951291 4081.3285
44000 2.0380445 0.051364672 2.0871447 0.77601424 4031.596
45000 2.0176888 0.071201051 2.086648 0.8814278 3973.177
46000 2.0315294 0.062175754 2.0914479 0.80448793 3920.2923
47000 1.999217 0.091219176 2.0882149 0.97776147 3870.1695
48000 2.0031904 0.091014449 2.0919791 0.9661011 3813.1611
49000 1.9880642 0.10889214 2.0947474 1.0234859 3760.5992
50000 2.0236194 0.078957514 2.1003284 0.99741945 3720.1333
Loop time of 8.99595 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 4.17826 (46.446)
Neigh time (%) = 1.11062 (12.3457)
Comm time (%) = 0.42667 (4.74291)
Outpt time (%) = 0.171033 (1.90122)
Other time (%) = 3.10937 (34.5641)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 564 ave 564 max 564 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6061 ave 6061 max 6061 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6061
Ave neighs/atom = 6.73444
Neighbor list builds = 3122
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.87079 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076739854 2.1127279 0.09765736 21544.21
7000 2.084383 -0.002011532 2.0800555 0.11035732 17791.249
8000 2.0697462 -0.0035908236 2.0638557 0.12727264 15495.564
9000 2.0565713 0.005100289 2.0593865 0.14847835 13885.03
10000 2.0498621 0.0063267281 2.0539112 0.15879624 12601.99
11000 2.0438679 0.018955755 2.0605527 0.18959409 11490.646
12000 2.053458 0.0044167998 2.0555932 0.19336438 10572.921
13000 2.0429256 0.013698073 2.0543538 0.21707695 9791.7501
14000 2.0132501 0.042422704 2.0534359 0.27926827 9147.46
15000 2.0501152 0.0064708164 2.0543081 0.25954559 8659.5624
16000 2.0371395 0.017291634 2.0521676 0.27240923 8172.3226
17000 2.0267747 0.025623672 2.0501464 0.32046495 7767.5953
18000 2.0422824 0.014182115 2.0541954 0.30856342 7387.0945
19000 2.002713 0.050847562 2.0513354 0.3943075 7044.3881
20000 2.028578 0.02503956 2.0513636 0.35569094 6770.0283
21000 2.0222359 0.033814924 2.0538039 0.42126528 6523.5394
22000 2.0312713 0.024739786 2.0537541 0.41123899 6289.3329
23000 1.9999306 0.055831167 2.0535396 0.46845747 6092.6534
24000 2.0082371 0.050865049 2.0568708 0.45467368 5945.5344
25000 2.0184402 0.039542114 2.0557396 0.46077228 5776.9458
26000 2.0197538 0.046732692 2.0642423 0.57349226 5587.6764
27000 2.0225605 0.036043629 2.0563569 0.48998661 5465.5575
28000 2.0282806 0.029362245 2.0553892 0.46801488 5344.7841
29000 2.025716 0.035993945 2.0594592 0.53066607 5238.028
30000 2.0121673 0.054545747 2.0644773 0.62001526 5107.2201
31000 2.0208128 0.048119988 2.0666874 0.54439146 4994.3653
32000 2.0272104 0.045076806 2.0700348 0.63197584 4872.4903
33000 2.0107761 0.060072558 2.0686144 0.63025398 4766.141
34000 1.9980266 0.075358195 2.0711648 0.67880824 4677.1269
35000 2.0253327 0.048362443 2.0714448 0.64004324 4599.5201
36000 2.0118504 0.058973713 2.0685888 0.67459858 4529.9483
37000 2.0104548 0.065481203 2.0737022 0.80781793 4463.1985
38000 2.0125078 0.066003564 2.0762752 0.78305688 4377.6954
39000 2.0174905 0.063736966 2.0789858 0.70398438 4293.5819
40000 2.0275434 0.05243574 2.0777263 0.78595198 4236.8235
41000 1.9680044 0.10509725 2.070915 0.84301968 4224.0137
42000 2.0169009 0.071278882 2.0859388 0.78081027 4160.3455
43000 2.0404682 0.05026415 2.0884652 0.75914083 4061.9873
44000 2.016673 0.068784573 2.0832168 0.80476991 3996.8686
45000 1.9857998 0.10014888 2.0837422 0.90863992 3939.2325
46000 2.0071737 0.075441094 2.0803846 0.86595933 3918.6894
47000 2.0371945 0.055594532 2.0905255 0.88572726 3889.3681
48000 1.9981195 0.097729669 2.093629 1.0507251 3846.1939
49000 2.0047164 0.089245076 2.091734 0.96126669 3809.5319
50000 2.0028203 0.1069487 2.1075437 1.0114594 3741.7317
Loop time of 4.07413 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.10861 (27.2108)
Neigh time (%) = 0.293286 (7.19874)
Comm time (%) = 0.97903 (24.0304)
Outpt time (%) = 0.13185 (3.23627)
Other time (%) = 1.56136 (38.3238)
Nlocal: 225 ave 241 max 200 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 301 ave 311 max 289 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 1463 ave 1565 max 1310 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 5852
Ave neighs/atom = 6.50222
Neighbor list builds = 3126
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 384.277 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -8.502354 -8.5036544 -8.5036544 0 -870253.95 3023.4645 14.46 14.46 14.46 0
1 10.099586 -8.502354 -8.5036544 -8.5036544 0 -870253.93 3023.4645 14.46 14.46 14.46 0
2 10.098343 -8.502354 -8.5036542 -8.5036542 0 -870253.88 3023.4645 14.46 14.46 14.46 0
3 10.096272 -8.502354 -8.5036539 -8.5036539 0 -870253.79 3023.4645 14.46 14.46 14.46 0
4 10.093374 -8.502354 -8.5036536 -8.5036536 0 -870253.67 3023.4645 14.46 14.46 14.46 0
5 10.089648 -8.502354 -8.5036531 -8.5036531 0 -870253.51 3023.4645 14.46 14.46 14.46 0
6 10.085096 -8.502354 -8.5036525 -8.5036525 0 -870253.31 3023.4645 14.46 14.46 14.46 0
7 10.079718 -8.502354 -8.5036518 -8.5036518 0 -870253.08 3023.4645 14.46 14.46 14.46 0
8 10.073516 -8.502354 -8.503651 -8.503651 0 -870252.82 3023.4645 14.46 14.46 14.46 0
9 10.06649 -8.502354 -8.5036501 -8.5036501 0 -870252.52 3023.4645 14.46 14.46 14.46 0
10 10.058642 -8.502354 -8.5036491 -8.5036491 0 -870252.18 3023.4645 14.46 14.46 14.46 0
Loop time of 0.174859 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.174268 (99.6621)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000328779 (0.188025)
Outpt time (%) = 0.000133038 (0.0760827)
Other time (%) = 0.000128984 (0.0737648)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 383.77 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -8.502354 -8.5036544 -8.5036544 0 -870253.95 3023.4645 14.46 14.46 14.46 0
1 10.09959 -8.502354 -8.5036544 -8.5036544 0 -870253.93 3023.4645 14.46 14.46 14.46 0
2 10.098359 -8.502354 -8.5036542 -8.5036542 0 -870253.88 3023.4645 14.46 14.46 14.46 0
3 10.096308 -8.502354 -8.5036539 -8.5036539 0 -870253.79 3023.4645 14.46 14.46 14.46 0
4 10.093437 -8.502354 -8.5036536 -8.5036536 0 -870253.66 3023.4645 14.46 14.46 14.46 0
5 10.089747 -8.502354 -8.5036531 -8.5036531 0 -870253.49 3023.4645 14.46 14.46 14.46 0
6 10.085238 -8.502354 -8.5036525 -8.5036525 0 -870253.29 3023.4645 14.46 14.46 14.46 0
7 10.079911 -8.502354 -8.5036518 -8.5036518 0 -870253.06 3023.4645 14.46 14.46 14.46 0
8 10.073767 -8.502354 -8.503651 -8.503651 0 -870252.79 3023.4645 14.46 14.46 14.46 0
9 10.066807 -8.502354 -8.5036501 -8.5036501 0 -870252.48 3023.4645 14.46 14.46 14.46 0
10 10.059033 -8.502354 -8.5036491 -8.5036491 0 -870252.13 3023.4645 14.46 14.46 14.46 0
Loop time of 0.0476552 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.0449591 (94.3424)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0022549 (4.7317)
Outpt time (%) = 0.000302732 (0.635255)
Other time (%) = 0.000138521 (0.290674)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 492.454 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -5.307041 -5.3071702 -2.6165358 -2.6906344 0.65426811 -1.3085362 25.62 25.62 25.62 16816.568
1 1.0009873 -5.3550555 -5.3551848 -2.9567646 -2.3984202 0.65426879 -1.3085376 25.62 25.62 25.62 16816.568
2 1.0026929 -5.3550537 -5.3551832 -2.9567602 -2.3984231 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
Loop time of 0.759578 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.101777 (13.3992)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00014329 (0.0188644)
Outpt time (%) = 6.62804e-05 (0.00872595)
Other time (%) = 0.657591 (86.5732)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 493.751 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0026929 -5.3334035 -5.333533 -2.9696799 -2.3638531 0.65426936 -1.3085387 25.62 25.62 25.62 16816.568
3 1.0026929 -5.3366561 -5.3367856 -2.9701261 -2.3666596 0.65426936 -1.3085387 25.594382 25.59438 25.59438 16766.17
4 1.0026929 -5.3398622 -5.3399917 -2.9705203 -2.3694714 0.65426936 -1.3085387 25.568763 25.56876 25.56876 16715.873
5 1.0026929 -5.3430214 -5.3431509 -2.9708622 -2.3722886 0.65426936 -1.3085387 25.543145 25.543141 25.54314 16665.677
6 1.0026929 -5.346133 -5.3462625 -2.9711512 -2.3751113 0.65426936 -1.3085387 25.517527 25.517521 25.51752 16615.581
7 1.0026929 -5.3491964 -5.349326 -2.9713866 -2.3779393 0.65426936 -1.3085387 25.491909 25.491901 25.4919 16565.585
8 1.0026929 -5.3522113 -5.3523408 -2.971568 -2.3807728 0.65426936 -1.3085387 25.46629 25.466281 25.46628 16515.69
9 1.0026929 -5.3660227 -5.3661522 -2.9825701 -2.3835821 0.65426936 -1.3085387 25.440672 25.440662 25.44066 16465.896
10 1.0026929 -5.4362377 -5.4363673 -3.0499986 -2.3863686 0.65426936 -1.3085387 25.415054 25.415042 25.41504 16416.201
11 1.0026929 -5.5662016 -5.5663312 -3.1771711 -2.3891601 0.65426936 -1.3085387 25.389436 25.389422 25.38942 16366.607
12 1.0026929 -5.7519309 -5.7520604 -3.360104 -2.3919564 0.65426936 -1.3085387 25.363818 25.363802 25.3638 16317.113
13 1.0026929 -5.9874068 -5.9875363 -3.5927786 -2.3947577 0.65426936 -1.3085387 25.3382 25.338183 25.33818 16267.718
14 1.0026929 -6.2647792 -6.2649087 -3.8673448 -2.3975639 0.65426936 -1.3085387 25.312582 25.312563 25.31256 16218.423
15 1.0026929 -6.5746359 -6.5747654 -4.1743903 -2.400375 0.65426936 -1.3085387 25.286963 25.286943 25.28694 16169.228
16 1.0026929 -6.9063303 -6.9064598 -4.5032687 -2.4031911 0.65426936 -1.3085387 25.261343 25.261323 25.26132 16120.131
17 1.0026929 -7.2483579 -7.2484874 -4.8424753 -2.4060121 0.65426936 -1.3085387 25.235723 25.235703 25.2357 16071.134
18 1.0026929 -7.5887656 -7.5888951 -5.1800571 -2.408838 0.65426936 -1.3085387 25.210104 25.210083 25.21008 16022.236
19 1.0026929 -7.9155773 -7.9157068 -5.504038 -2.4116688 0.65426936 -1.3085387 25.184484 25.184463 25.18446 15973.438
20 1.0026929 -8.217244 -8.2173735 -5.8028522 -2.4145213 0.65426936 -1.3085387 25.158864 25.158844 25.15884 15924.739
21 1.0026929 -8.4831885 -8.483318 -6.0657645 -2.4175535 0.65426936 -1.3085387 25.133244 25.133224 25.133221 15876.139
22 1.0026929 -8.7037271 -8.7038566 -6.2832612 -2.4205954 0.65426936 -1.3085387 25.107624 25.107605 25.107602 15827.639
23 1.0026929 -8.8709155 -8.8710451 -6.4474006 -2.4236444 0.65426936 -1.3085387 25.082004 25.081986 25.081984 15779.238
24 1.0026929 -8.978681 -8.9788105 -6.55211 -2.4267005 0.65426936 -1.3085387 25.056384 25.056368 25.056366 15730.937
25 1.0026929 -9.0230511 -9.0231807 -6.593417 -2.4297637 0.65426936 -1.3085387 25.030764 25.030751 25.030749 15682.736
26 1.0026929 -9.0240292 -9.0241587 -6.5940118 -2.430147 0.65426936 -1.3085387 25.027561 25.027551 25.027549 15676.72
27 1.0026929 -9.0241357 -9.0242652 -6.5939267 -2.4303385 0.65426936 -1.3085387 25.02596 25.025952 25.025951 15673.715
28 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.65426936 -1.3085387 25.026059 25.026052 25.026051 15673.902
Loop time of 5.88834 on 1 procs for 27 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.33353304985 -9.02426597894 -9.02426597894
Force two-norm initial, final = 2433.53 179.132
Force max component initial, final = 1405.03 103.699
Final line search alpha, max atom move = 2.94289e-10 3.05176e-08
Iterations, force evaluations = 27 57
Pair time (%) = 5.50607 (93.508)
Neigh time (%) = 0.363057 (6.16569)
Comm time (%) = 0.00463033 (0.0786355)
Outpt time (%) = 0.000666857 (0.011325)
Other time (%) = 0.0139146 (0.236307)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 4
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 492.631 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
29 1.0026929 -9.0241365 -9.024266 -6.5939394 -2.4303265 0.63678555 -1.2735711 25.026059 25.026052 25.026051 15673.902
30 0.88741647 -9.0386219 -9.0387365 -6.7151088 -2.3236278 0.63678579 -1.2735716 25.026059 25.026052 25.026051 15673.902
Loop time of 0.476254 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.100822 (21.1698)
Neigh time (%) = 0 (0)
Comm time (%) = 6.79493e-05 (0.0142674)
Outpt time (%) = 2.69413e-05 (0.00565692)
Other time (%) = 0.375337 (78.8103)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 492.89 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
30 25.026059 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
31 25.026309 25.026052 25.026051 0 0 0 -1.504334e+08 -1.5326204e+08 -1.5372549e+08 1064068.9 -599765.62 414723.34
32 25.026559 25.026052 25.026051 0 0 0 65979938 -45173439 -45636876 1064082.2 -599660.21 414715.59
33 25.02681 25.026052 25.026051 0 0 0 2.8240082e+08 62914604 62451183 1064095.4 -599554.81 414707.84
34 25.02706 25.026052 25.026051 0 0 0 4.98829e+08 1.7100197e+08 1.7053856e+08 1064108.6 -599449.41 414700.08
35 25.02731 25.026052 25.026051 0 0 0 7.1526424e+08 2.7908854e+08 2.7862515e+08 1064121.9 -599344.01 414692.33
36 25.02756 25.026052 25.026051 0 0 0 9.3170631e+08 3.8717419e+08 3.8671082e+08 1064135.1 -599238.61 414684.58
37 25.027811 25.026052 25.026051 0 0 0 1.148155e+09 4.9525881e+08 4.9479545e+08 1064148.4 -599133.22 414676.83
38 25.028061 25.026052 25.026051 0 0 0 1.36461e+09 6.0334227e+08 6.0287893e+08 1064161.6 -599027.84 414669.08
39 25.028311 25.026052 25.026051 0 0 0 1.5810711e+09 7.1142446e+08 7.1096114e+08 1064174.9 -598922.45 414661.33
40 25.028561 25.026052 25.026051 0 0 0 1.7975381e+09 8.1950525e+08 8.1904196e+08 1064188.2 -598817.07 414653.58
Loop time of 1.1738 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16988 (99.6661)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000679731 (0.0579088)
Outpt time (%) = 0.00296259 (0.252394)
Other time (%) = 0.000277042 (0.0236022)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 493.407 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
40 25.028561 25.026052 25.026051 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
41 25.028561 25.026052 25.026302 0 0 0 2.0140107e+09 9.2758454e+08 9.2712126e+08 1064201.4 -598711.69 414645.83
42 25.028561 25.026052 25.026552 0 0 0 2.1220992e+09 1.0356731e+09 1.1435342e+09 1064179.7 -598601.58 414637.81
43 25.028561 25.026052 25.026802 0 0 0 2.2301859e+09 1.1437611e+09 1.3599535e+09 1064158 -598491.46 414629.79
44 25.028561 25.026052 25.027052 0 0 0 2.3382708e+09 1.2518485e+09 1.576379e+09 1064136.3 -598381.35 414621.77
45 25.028561 25.026052 25.027303 0 0 0 2.4463536e+09 1.359935e+09 1.7928103e+09 1064114.7 -598271.25 414613.74
46 25.028561 25.026052 25.027553 0 0 0 2.5544344e+09 1.4680207e+09 2.0092472e+09 1064093 -598161.15 414605.7
47 25.028561 25.026052 25.027803 0 0 0 2.662513e+09 1.5761053e+09 2.2256896e+09 1064071.3 -598051.06 414597.67
48 25.028561 25.026052 25.028053 0 0 0 2.7705891e+09 1.6841887e+09 2.4421371e+09 1064049.6 -597940.97 414589.63
49 25.028561 25.026052 25.028304 0 0 0 2.8786629e+09 1.7922709e+09 2.6585895e+09 1064027.9 -597830.89 414581.58
50 25.028561 25.026052 25.028554 0 0 0 2.986734e+09 1.9003517e+09 2.8750466e+09 1064006.2 -597720.81 414573.53
Loop time of 1.17224 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16836 (99.6691)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000671864 (0.0573147)
Outpt time (%) = 0.00293803 (0.250635)
Other time (%) = 0.000269175 (0.0229625)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 493.924 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
50 25.028561 25.026052 25.028554 0 0 0 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
51 25.028561 25.026052 25.028554 0 0 5.0057108e-07 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.74 414565.48
52 25.028561 25.026052 25.028554 0 0 1.0011422e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.79 631065.93
53 25.028561 25.026052 25.028554 0 0 1.5017132e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.83 847566.39
54 25.028561 25.026052 25.028554 0 0 2.0022843e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.5 -597610.88 1064066.8
55 25.028561 25.026052 25.028554 0 0 2.5028554e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.93 1280567.3
56 25.028561 25.026052 25.028554 0 0 3.0034265e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597610.97 1497067.7
57 25.028561 25.026052 25.028554 0 0 3.5039975e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.02 1713568.2
58 25.028561 25.026052 25.028554 0 0 4.0045686e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.06 1930068.7
59 25.028561 25.026052 25.028554 0 0 4.5051397e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.11 2146569.1
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.16 2363069.6
Loop time of 1.17218 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16831 (99.6701)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000669956 (0.0571549)
Outpt time (%) = 0.00293446 (0.250342)
Other time (%) = 0.000262737 (0.0224145)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 494.441 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
60 25.028561 25.026052 25.028554 0 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
61 25.028561 25.026052 25.028554 5.0052105e-07 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1063984.6 -597611.2 2579570
62 25.028561 25.026052 25.028554 1.0010421e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1280463.3 -597611.17 2579570
63 25.028561 25.026052 25.028554 1.5015631e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1496942 -597611.15 2579570
64 25.028561 25.026052 25.028554 2.0020842e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1713420.7 -597611.12 2579570.1
65 25.028561 25.026052 25.028554 2.5026052e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 1929899.5 -597611.09 2579570.1
66 25.028561 25.026052 25.028554 3.0031263e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2146378.2 -597611.06 2579570.1
67 25.028561 25.026052 25.028554 3.5036473e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2362856.9 -597611.03 2579570.1
68 25.028561 25.026052 25.028554 4.0041684e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2579335.6 -597611 2579570.1
69 25.028561 25.026052 25.028554 4.5046894e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 2795814.4 -597610.97 2579570.1
70 25.028561 25.026052 25.028554 5.0052105e-06 0 5.0057108e-06 3.0948025e+09 2.008431e+09 3.0915082e+09 3012293.1 -597610.95 2579570.1
Loop time of 1.17232 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.16846 (99.6703)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000672817 (0.0573919)
Outpt time (%) = 0.00292802 (0.249763)
Other time (%) = 0.000264168 (0.0225338)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb.Cu2O.elastic.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 412.257 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -5.307041 -5.3071702 -2.6165358 -2.6906344 0.65350507 -1.3070101 25.62 25.62 25.62 16816.568
1 1.0020305 -5.3673359 -5.3674653 -2.9542297 -2.4132356 0.65350576 -1.3070115 25.62 25.62 25.62 16816.568
2 1.0060932 -5.3673341 -5.367464 -2.9542249 -2.4132391 0.65350631 -1.3070126 25.62 25.62 25.62 16816.568
Loop time of 0.199257 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.025626 (12.8608)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000734687 (0.368714)
Outpt time (%) = 6.24657e-05 (0.0313494)
Other time (%) = 0.172834 (86.7391)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 413.442 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0060932 -5.3330786 -5.3332085 -2.974622 -2.3585866 0.65350631 -1.3070126 25.62 25.62 25.62 16816.568
3 1.0060932 -5.3363314 -5.3364614 -2.9750737 -2.3613876 0.65350631 -1.3070126 25.594384 25.59438 25.594381 16766.172
4 1.0060932 -5.3395378 -5.3396678 -2.9754737 -2.3641941 0.65350631 -1.3070126 25.568768 25.56876 25.568762 16715.877
5 1.0060932 -5.3426973 -5.3428272 -2.9758213 -2.3670059 0.65350631 -1.3070126 25.543152 25.54314 25.543143 16665.683
6 1.0060932 -5.3458091 -5.3459391 -2.976116 -2.3698231 0.65350631 -1.3070126 25.517536 25.51752 25.517525 16615.589
7 1.0060932 -5.3488729 -5.3490029 -2.9763572 -2.3726457 0.65350631 -1.3070126 25.49192 25.4919 25.491906 16565.596
8 1.0060932 -5.3518881 -5.352018 -2.9765443 -2.3754737 0.65350631 -1.3070126 25.466304 25.46628 25.466287 16515.703
9 1.0060932 -5.3656903 -5.3658203 -2.9875426 -2.3782777 0.65350631 -1.3070126 25.440688 25.44066 25.440668 16465.91
10 1.0060932 -5.4358893 -5.4360193 -3.0549604 -2.3810589 0.65350631 -1.3070126 25.415072 25.41504 25.415049 16416.218
11 1.0060932 -5.5658375 -5.5659675 -3.1821225 -2.383845 0.65350631 -1.3070126 25.389457 25.38942 25.389431 16366.626
12 1.0060932 -5.7515526 -5.7516825 -3.3650465 -2.386636 0.65350631 -1.3070126 25.363842 25.3638 25.363812 16317.134
13 1.0060932 -5.9870179 -5.9871478 -3.5977159 -2.389432 0.65350631 -1.3070126 25.338226 25.33818 25.338193 16267.742
14 1.0060932 -6.2643867 -6.2645166 -3.8722838 -2.3922328 0.65350631 -1.3070126 25.312609 25.31256 25.312574 16218.448
15 1.0060932 -6.5742496 -6.5743796 -4.1793409 -2.3950387 0.65350631 -1.3070126 25.286991 25.28694 25.286955 16169.253
16 1.0060932 -6.9059598 -6.9060897 -4.5082402 -2.3978495 0.65350631 -1.3070126 25.261372 25.26132 25.261335 16120.158
17 1.0060932 -7.2480121 -7.248142 -4.8474768 -2.4006652 0.65350631 -1.3070126 25.235753 25.2357 25.235715 16071.161
18 1.0060932 -7.5884527 -7.5885827 -5.1850968 -2.4034859 0.65350631 -1.3070126 25.210133 25.21008 25.210095 16022.263
19 1.0060932 -7.9153023 -7.9154322 -5.5091208 -2.4063115 0.65350631 -1.3070126 25.184513 25.18446 25.184476 15973.465
20 1.0060932 -8.2170093 -8.2171392 -5.8079805 -2.4091587 0.65350631 -1.3070126 25.158893 25.158841 25.158856 15924.766
21 1.0060932 -8.4829952 -8.4831252 -6.0709401 -2.4121851 0.65350631 -1.3070126 25.133273 25.133223 25.133237 15876.167
22 1.0060932 -8.7035764 -8.7037064 -6.2884852 -2.4152212 0.65350631 -1.3070126 25.107653 25.107605 25.107619 15827.668
23 1.0060932 -8.8708084 -8.8709383 -6.4526739 -2.4182644 0.65350631 -1.3070126 25.082033 25.081988 25.082001 15779.269
24 1.0060932 -8.9786185 -8.9787484 -6.5574338 -2.4213146 0.65350631 -1.3070126 25.056413 25.056373 25.056384 15730.97
25 1.0060932 -9.0230363 -9.0231663 -6.5987945 -2.4243718 0.65350631 -1.3070126 25.030793 25.030761 25.03077 15682.774
26 1.0060932 -9.0240207 -9.0241507 -6.5993965 -2.4247541 0.65350631 -1.3070126 25.027591 25.027564 25.027572 15676.761
27 1.0060932 -9.0241307 -9.0242606 -6.5993156 -2.424945 0.65350631 -1.3070126 25.02599 25.02597 25.025976 15673.76
28 1.0060932 -9.0241311 -9.024261 -6.5993219 -2.4249391 0.65350631 -1.3070126 25.026038 25.02602 25.026025 15673.853
29 1.0060932 -9.0241311 -9.0242611 -6.5993235 -2.4249376 0.65350631 -1.3070126 25.02605 25.026033 25.026038 15673.876
30 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.65350631 -1.3070126 25.026056 25.026039 25.026044 15673.888
31 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.65350631 -1.3070126 25.026056 25.026039 25.026044 15673.888
Loop time of 2.31824 on 4 procs for 29 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.33320852891 -9.02426111934 -9.02426111934
Force two-norm initial, final = 2433.86 193.581
Force max component initial, final = 1405.28 113.287
Final line search alpha, max atom move = 2.69382e-10 3.05176e-08
Iterations, force evaluations = 29 83
Pair time (%) = 2.07482 (89.4999)
Neigh time (%) = 0.173133 (7.46831)
Comm time (%) = 0.0567805 (2.44929)
Outpt time (%) = 0.000948668 (0.0409219)
Other time (%) = 0.0125538 (0.541521)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 4
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 412.415 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
31 1.0060932 -9.0241312 -9.0242611 -6.5993242 -2.4249369 0.63638209 -1.2727642 25.026056 25.026039 25.026044 15673.888
32 0.89047585 -9.039436 -9.0395511 -6.7149991 -2.3245519 0.63638241 -1.2727648 25.026056 25.026039 25.026044 15673.888
Loop time of 0.12376 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0256067 (20.6905)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000612259 (0.494713)
Outpt time (%) = 9.44734e-05 (0.0763357)
Other time (%) = 0.097447 (78.7384)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 412.652 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
32 25.026056 25.026039 25.026044 0 0 0 -1.6161297e+08 -1.6914237e+08 -1.6702142e+08 1071968.8 1327464.7 391905.86
33 25.026307 25.026039 25.026044 0 0 0 -1.6161297e+08 -1.6914237e+08 -1.6702142e+08 1071968.8 1327464.7 391905.86
34 25.026557 25.026039 25.026044 0 0 0 54810325 -61048772 -58927789 1071982.1 1327546.1 391898.77
35 25.026807 25.026039 25.026044 0 0 0 2.7124117e+08 47044270 49165285 1071995.3 1327627.6 391891.69
36 25.027057 25.026039 25.026044 0 0 0 4.8767934e+08 1.5513664e+08 1.5725769e+08 1072008.6 1327709.1 391884.6
37 25.027308 25.026039 25.026044 0 0 0 7.0412458e+08 2.6322823e+08 2.653493e+08 1072021.8 1327790.5 391877.51
38 25.027558 25.026039 25.026044 0 0 0 9.2057666e+08 3.713189e+08 3.7344e+08 1072035.1 1327872 391870.43
39 25.027808 25.026039 25.026044 0 0 0 1.1370353e+09 4.7940855e+08 4.8152966e+08 1072048.4 1327953.4 391863.34
40 25.028058 25.026039 25.026044 0 0 0 1.3535004e+09 5.8749704e+08 5.8961818e+08 1072061.7 1328034.8 391856.26
41 25.028309 25.026039 25.026044 0 0 0 1.5699715e+09 6.9558428e+08 6.9770543e+08 1072075 1328116.2 391849.18
42 25.028559 25.026039 25.026044 0 0 0 1.7864486e+09 8.0367013e+08 8.057913e+08 1072088.3 1328197.7 391842.09
Loop time of 0.310848 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.299549 (96.3652)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00796747 (2.56314)
Outpt time (%) = 0.00319105 (1.02656)
Other time (%) = 0.00014019 (0.0450993)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 413.126 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
42 25.028559 25.026039 25.026044 0 0 0 2.0029313e+09 9.1175447e+08 9.1387565e+08 1072101.6 1328279.1 391835.01
43 25.028559 25.026039 25.026294 0 0 0 2.0029313e+09 9.1175447e+08 9.1387565e+08 1072101.6 1328279.1 391835.01
44 25.028559 25.026039 25.026544 0 0 0 2.1110248e+09 1.019848e+09 1.1302984e+09 1072079.3 1328365.3 391827.47
45 25.028559 25.026039 25.026795 0 0 0 2.2191166e+09 1.127941e+09 1.3467276e+09 1072057 1328451.5 391819.92
46 25.028559 25.026039 25.027045 0 0 0 2.3272065e+09 1.2360334e+09 1.5631629e+09 1072034.7 1328537.8 391812.38
47 25.028559 25.026039 25.027295 0 0 0 2.4352945e+09 1.3441249e+09 1.7796041e+09 1072012.3 1328624 391804.83
48 25.028559 25.026039 25.027545 0 0 0 2.5433803e+09 1.4522156e+09 1.9960509e+09 1071990 1328710.2 391797.28
49 25.028559 25.026039 25.027796 0 0 0 2.6514639e+09 1.5603052e+09 2.2125031e+09 1071967.7 1328796.4 391789.72
50 25.028559 25.026039 25.028046 0 0 0 2.7595452e+09 1.6683937e+09 2.4289605e+09 1071945.4 1328882.6 391782.17
51 25.028559 25.026039 25.028296 0 0 0 2.867624e+09 1.776481e+09 2.6454229e+09 1071923.1 1328968.8 391774.61
52 25.028559 25.026039 25.028546 0 0 0 2.9757003e+09 1.8845668e+09 2.8618899e+09 1071900.8 1329054.9 391767.05
Loop time of 0.315019 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302888 (96.1492)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00890404 (2.82651)
Outpt time (%) = 0.00307637 (0.976569)
Other time (%) = 0.000150442 (0.0477566)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 413.6 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
52 25.028559 25.026039 25.028546 0 0 0 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.5 1329141.1 391759.48
53 25.028559 25.026039 25.028546 0 0 5.0057093e-07 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.5 1329141.1 391759.48
54 25.028559 25.026039 25.028546 0 0 1.0011419e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.4 1329141.1 608269.82
55 25.028559 25.026039 25.028546 0 0 1.5017128e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.3 1329141 824780.16
56 25.028559 25.026039 25.028546 0 0 2.0022837e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.2 1329141 1041290.5
57 25.028559 25.026039 25.028546 0 0 2.5028546e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.2 1329140.9 1257800.8
58 25.028559 25.026039 25.028546 0 0 3.0034256e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878.1 1329140.9 1474311.2
59 25.028559 25.026039 25.028546 0 0 3.5039965e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878 1329140.8 1690821.5
60 25.028559 25.026039 25.028546 0 0 4.0045674e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071878 1329140.8 1907331.8
61 25.028559 25.026039 25.028546 0 0 4.5051384e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.9 1329140.7 2123842.2
62 25.028559 25.026039 25.028546 0 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.7 2340352.5
Loop time of 0.314847 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302369 (96.0368)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0093742 (2.97739)
Outpt time (%) = 0.00294709 (0.93604)
Other time (%) = 0.00015682 (0.0498083)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 414.075 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
62 25.028559 25.026039 25.028546 0 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.6 2556862.9
63 25.028559 25.026039 25.028546 5.0052078e-07 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1071877.8 1329140.6 2556862.9
64 25.028559 25.026039 25.028546 1.0010416e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1288366.3 1329140.7 2556862.8
65 25.028559 25.026039 25.028546 1.5015623e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1504854.8 1329140.7 2556862.7
66 25.028559 25.026039 25.028546 2.0020831e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1721343.4 1329140.7 2556862.6
67 25.028559 25.026039 25.028546 2.5026039e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 1937831.9 1329140.8 2556862.5
68 25.028559 25.026039 25.028546 3.0031247e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2154320.4 1329140.8 2556862.4
69 25.028559 25.026039 25.028546 3.5036454e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2370809 1329140.8 2556862.3
70 25.028559 25.026039 25.028546 4.0041662e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2587297.5 1329140.8 2556862.2
71 25.028559 25.026039 25.028546 4.504687e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 2803786 1329140.9 2556862.1
72 25.028559 25.026039 25.028546 5.0052078e-06 0 5.0057093e-06 3.0837738e+09 1.9926512e+09 3.0783614e+09 3020274.6 1329140.9 2556862
Loop time of 0.314899 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.302122 (95.9424)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00967807 (3.07338)
Outpt time (%) = 0.00294942 (0.936622)
Other time (%) = 0.000149965 (0.0476232)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 220160 max 213600 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds = 0

193
examples/comb/log.comb.HfO2.9Jan12.linux.1 Normal file
View File

@ -0,0 +1,193 @@
LAMMPS (10 Jan 2012)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 1771.07 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -10.375148 -10.375148 4.2805776 -14.655726 -402517.96 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.120123 on 1 procs for 1 steps with 1500 atoms
Pair time (%) = 0.119944 (99.8509)
Neigh time (%) = 0 (0)
Comm time (%) = 8.41618e-05 (0.070063)
Outpt time (%) = 3.40939e-05 (0.0283825)
Other time (%) = 6.07967e-05 (0.0506121)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 1771.89 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 2.7464939 -1.373247
2 1.2795093 -11.722657 -11.722823 -2.5378829 -9.1849398 -1178231.8 17627.802 25.642 25.957 26.4845 -4.46691 2.7464939 -1.373247
3 3.9305261 -11.722662 -11.72317 -2.5381759 -9.1849941 -1176818.8 17627.802 25.642 25.957 26.4845 -4.46691 2.7464667 -1.3732333
4 8.163283 -11.722618 -11.723672 -2.5386819 -9.1849902 -1174685 17627.802 25.642 25.957 26.4845 -4.46691 2.7464056 -1.3732028
5 13.960256 -11.722526 -11.724329 -2.5394249 -9.1849042 -1171826.4 17627.802 25.642 25.957 26.4845 -4.46691 2.7463184 -1.3731592
6 21.29783 -11.722408 -11.72516 -2.5403916 -9.184768 -1168232.6 17627.802 25.642 25.957 26.4845 -4.46691 2.7462211 -1.3731106
Loop time of 2.40353 on 1 procs for 5 steps with 1500 atoms
Pair time (%) = 0.598113 (24.8847)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000421047 (0.0175178)
Outpt time (%) = 0.000158072 (0.00657663)
Other time (%) = 1.80484 (75.0912)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 1773.36 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 21.29783 -11.670408 -11.673159 -2.8765459 -8.7966134 -1265631.7 17627.802 25.642 25.957 26.4845 -4.46691 2.7462211 -1.3731106
7 21.29783 -11.675131 -11.677882 -2.881099 -8.7967827 -1253486.8 17619.929 25.636872 25.952496 26.482562 -4.46691 2.7462211 -1.3731106
8 21.29783 -11.679808 -11.68256 -2.8856058 -8.7969538 -1240999.6 17612.041 25.631743 25.947989 26.480601 -4.46691 2.7462211 -1.3731106
9 21.29783 -11.684439 -11.68719 -2.8900654 -8.7971248 -1228174.4 17604.137 25.626615 25.943479 26.478617 -4.46691 2.7462211 -1.3731106
10 21.29783 -11.689021 -11.691773 -2.8944766 -8.797296 -1215016.6 17596.218 25.621486 25.938967 26.476607 -4.46691 2.7462211 -1.3731106
11 21.29783 -11.693555 -11.696306 -2.8988384 -8.7974677 -1201528.9 17588.281 25.616358 25.934452 26.474572 -4.46691 2.7462211 -1.3731106
12 21.29783 -11.698037 -11.700788 -2.9031496 -8.7976389 -1187674.4 17580.327 25.61123 25.929934 26.472509 -4.46691 2.7462211 -1.3731106
13 21.29783 -11.70247 -11.705221 -2.9074093 -8.7978121 -1173415.2 17572.353 25.606101 25.925412 26.470418 -4.46691 2.7462211 -1.3731106
14 21.29783 -11.707235 -11.709986 -2.9120023 -8.7979838 -1158172.5 17564.36 25.600973 25.920887 26.468297 -4.46691 2.7462211 -1.3731106
15 21.29783 -11.713863 -11.716614 -2.9184576 -8.7981563 -1142098.6 17556.347 25.595844 25.916358 26.466147 -4.46691 2.7462211 -1.3731106
16 21.29783 -11.722779 -11.72553 -2.9272014 -8.7983285 -1129422 17548.315 25.590716 25.911823 26.463971 -4.46691 2.7462211 -1.3731106
17 21.29783 -11.741011 -11.743762 -2.9452614 -8.7985004 -1124627 17540.249 25.585588 25.90728 26.46175 -4.46691 2.7462211 -1.3731106
18 21.29783 -11.748152 -11.750903 -2.9522304 -8.7986728 -1124520.6 17532.121 25.580459 25.902721 26.459445 -4.46691 2.7462211 -1.3731106
19 21.29783 -11.75378 -11.756532 -2.9576857 -8.7988459 -1119185 17523.917 25.575331 25.898158 26.457028 -4.46691 2.7462211 -1.3731106
20 21.29783 -11.758859 -11.761611 -2.9625911 -8.7990195 -1104339.2 17515.652 25.570202 25.89359 26.45452 -4.46691 2.7462211 -1.3731106
21 21.29783 -11.76349 -11.766241 -2.9670486 -8.7991922 -1076322.1 17507.352 25.565074 25.889017 26.451959 -4.46691 2.7462211 -1.3731106
22 21.29783 -11.767701 -11.770452 -2.9710158 -8.7994367 -1048872.9 17499.053 25.559946 25.884435 26.449405 -4.46691 2.7462211 -1.3731106
23 21.29783 -11.775875 -11.778626 -2.9749154 -8.8037107 -1025626.1 17490.752 25.554817 25.879846 26.446854 -4.46691 2.7462211 -1.3731106
24 21.29783 -11.813826 -11.816577 -2.9785903 -8.8379868 -1008756.2 17482.437 25.549689 25.875251 26.444283 -4.46691 2.7462211 -1.3731106
25 21.29783 -11.910194 -11.912945 -2.982199 -8.9307461 -995245.49 17474.1 25.54456 25.870662 26.441668 -4.46691 2.7462211 -1.3731106
26 21.29783 -11.910731 -11.913482 -2.982422 -8.9310604 -994153.58 17473.579 25.54424 25.870377 26.441502 -4.46691 2.7462211 -1.3731106
27 21.29783 -11.910731 -11.913482 -2.982422 -8.9310604 -994153.58 17473.579 25.54424 25.870377 26.441502 -4.46691 2.7462211 -1.3731106
Loop time of 5.40827 on 1 procs for 21 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-11.6731593188 -11.9134824619 -11.9134824619
Force two-norm initial, final = 25697.5 19505.2
Force max component initial, final = 18706.6 13710.2
Final line search alpha, max atom move = 2.78239e-14 3.8147e-10
Iterations, force evaluations = 21 44
Pair time (%) = 5.39078 (99.6768)
Neigh time (%) = 0 (0)
Comm time (%) = 0.003757 (0.0694677)
Outpt time (%) = 0.000648499 (0.0119909)
Other time (%) = 0.0130765 (0.241788)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
velocity all create 300.1 2398378
run 10
Memory usage per processor = 1771.89 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
27 300.1 -11.874717 -11.913482 -2.982422 -8.9310604 -990851.4 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
28 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
29 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
30 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
31 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
32 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
33 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
34 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
35 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
36 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
37 300.1 -12.178585 -12.21735 -1.7956176 -10.421733 -909695.53 17473.579 25.54424 25.870377 26.441502 -4.46691 3.0600299 -1.5300149
Loop time of 1.66635 on 1 procs for 10 steps with 1500 atoms
Pair time (%) = 1.19877 (71.9397)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000849009 (0.0509501)
Outpt time (%) = 0.00031805 (0.0190866)
Other time (%) = 0.466416 (27.9902)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.045e+06 ave 1.045e+06 max 1.045e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1045000
Ave neighs/atom = 696.667
Neighbor list builds = 0
Dangerous builds = 0

291
examples/comb/log.comb.HfO2.9Jan12.linux.4 Normal file
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@ -0,0 +1,291 @@
LAMMPS (10 Jan 2012)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 2 by 2 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 416.525 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -10.375148 -10.375148 4.2805776 -14.655726 -402517.96 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0318046 on 4 procs for 1 steps with 1500 atoms
Pair time (%) = 0.030692 (96.502)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00102538 (3.224)
Outpt time (%) = 3.89218e-05 (0.122378)
Other time (%) = 4.82202e-05 (0.151614)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 416.923 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.24497526 -10.375149 -10.37518 4.28055 -14.65573 -402368.81 17627.802 25.642 25.957 26.4845 -4.46691 2.480664 -1.240332
2 1.332821 -11.209515 -11.209687 -3.2054666 -8.0042207 -1191111.8 17627.802 25.642 25.957 26.4845 -4.46691 2.480664 -1.240332
3 4.354723 -11.20952 -11.210083 -3.2057752 -8.0043075 -1189669.1 17627.802 25.642 25.957 26.4845 -4.46691 2.4806442 -1.2403221
4 9.3099681 -11.2095 -11.210703 -3.206296 -8.0044071 -1187480.4 17627.802 25.642 25.957 26.4845 -4.46691 2.4805928 -1.2402964
5 16.179541 -11.209458 -11.211548 -3.2070561 -8.0044916 -1184541.9 17627.802 25.642 25.957 26.4845 -4.46691 2.4805273 -1.2402636
6 24.937669 -11.209421 -11.212642 -3.2080101 -8.0046317 -1180839.7 17627.802 25.642 25.957 26.4845 -4.46691 2.4804545 -1.2402272
Loop time of 0.665697 on 4 procs for 5 steps with 1500 atoms
Pair time (%) = 0.150524 (22.6115)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00534689 (0.803202)
Outpt time (%) = 0.000192285 (0.0288847)
Other time (%) = 0.509634 (76.5564)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 417.638 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 24.937669 -11.119392 -11.122613 -3.7917885 -7.3308248 -1331535.2 17627.802 25.642 25.957 26.4845 -4.46691 2.4804545 -1.2402272
7 24.937669 -11.124364 -11.127585 -3.7966203 -7.3309649 -1319068.8 17619.914 25.636872 25.952494 26.482541 -4.46691 2.4804545 -1.2402272
8 24.937669 -11.12929 -11.132511 -3.8014047 -7.3311063 -1306249 17612.011 25.631743 25.947986 26.480559 -4.46691 2.4804545 -1.2402272
9 24.937669 -11.134167 -11.137388 -3.8061404 -7.3312478 -1293080.4 17604.094 25.626615 25.943476 26.478554 -4.46691 2.4804545 -1.2402272
10 24.937669 -11.138994 -11.142216 -3.8108264 -7.3313893 -1279568.8 17596.16 25.621486 25.938963 26.476524 -4.46691 2.4804545 -1.2402272
11 24.937669 -11.143771 -11.146993 -3.8154614 -7.3315313 -1265720.4 17588.21 25.616358 25.934448 26.474468 -4.46691 2.4804545 -1.2402272
12 24.937669 -11.148496 -11.151717 -3.8200446 -7.3316729 -1251540.8 17580.241 25.61123 25.92993 26.472385 -4.46691 2.4804545 -1.2402272
13 24.937669 -11.153513 -11.156734 -3.8249183 -7.3318161 -1237144.2 17572.254 25.606101 25.925408 26.470273 -4.46691 2.4804545 -1.2402272
14 24.937669 -11.16005 -11.163272 -3.8313134 -7.3319582 -1222915.3 17564.247 25.600973 25.920884 26.46813 -4.46691 2.4804545 -1.2402272
15 24.937669 -11.16669 -11.169911 -3.8378099 -7.332101 -1208411.1 17556.216 25.595844 25.916354 26.465954 -4.46691 2.4804545 -1.2402272
16 24.937669 -11.176313 -11.179534 -3.8472905 -7.3322435 -1194529.9 17548.16 25.590716 25.911819 26.463742 -4.46691 2.4804545 -1.2402272
17 24.937669 -11.189963 -11.193184 -3.8607982 -7.3323858 -1181590.6 17540.074 25.585588 25.907276 26.461489 -4.46691 2.4804545 -1.2402272
18 24.937669 -11.198449 -11.20167 -3.8691419 -7.332528 -1166711 17531.951 25.580459 25.902722 26.459188 -4.46691 2.4804545 -1.2402272
19 24.937669 -11.205262 -11.208484 -3.8758138 -7.3326699 -1151023.9 17523.796 25.575331 25.89816 26.456843 -4.46691 2.4804545 -1.2402272
20 24.937669 -11.212314 -11.215535 -3.8827236 -7.3328117 -1135134.5 17515.611 25.570202 25.893592 26.454455 -4.46691 2.4804545 -1.2402272
21 24.937669 -11.218016 -11.221237 -3.8882845 -7.3329526 -1118552.5 17507.392 25.565074 25.889016 26.45202 -4.46691 2.4804545 -1.2402272
22 24.937669 -11.222659 -11.225881 -3.8927875 -7.333093 -1101383.9 17499.139 25.559946 25.884434 26.449538 -4.46691 2.4804545 -1.2402272
23 24.937669 -11.226952 -11.230173 -3.8969397 -7.3332337 -1083865.1 17490.854 25.554817 25.879846 26.447008 -4.46691 2.4804545 -1.2402272
24 24.937669 -11.231023 -11.234244 -3.9008707 -7.3333736 -1066045.2 17482.533 25.549689 25.875252 26.444426 -4.46691 2.4804545 -1.2402272
25 24.937669 -11.235033 -11.238254 -3.9047394 -7.3335144 -1047983.4 17474.175 25.54456 25.870652 26.441792 -4.46691 2.4804545 -1.2402272
26 24.937669 -11.238979 -11.242201 -3.9085455 -7.333655 -1029686.9 17465.779 25.539432 25.866046 26.4391 -4.46691 2.4804545 -1.2402272
27 24.937669 -11.242863 -11.246084 -3.9122887 -7.3337956 -1011163.7 17457.34 25.534304 25.861433 26.436349 -4.46691 2.4804545 -1.2402272
28 24.937669 -11.246686 -11.249907 -3.9159688 -7.3339381 -992422.88 17448.858 25.529175 25.856812 26.433534 -4.46691 2.4804545 -1.2402272
29 24.937669 -11.250446 -11.253668 -3.9195856 -7.3340819 -973472.02 17440.328 25.524047 25.852184 26.430652 -4.46691 2.4804545 -1.2402272
30 24.937669 -11.254146 -11.257367 -3.923139 -7.3342279 -954319.47 17431.749 25.518918 25.847547 26.427699 -4.46691 2.4804545 -1.2402272
31 24.937669 -11.257781 -11.261003 -3.9266292 -7.3343734 -934971.89 17423.116 25.51379 25.842902 26.424669 -4.46691 2.4804545 -1.2402272
32 24.937669 -11.261355 -11.264576 -3.9300563 -7.3345201 -915438.13 17414.426 25.508662 25.838247 26.421559 -4.46691 2.4804545 -1.2402272
33 24.937669 -11.264868 -11.268089 -3.9334206 -7.3346683 -895726.51 17405.675 25.503533 25.833583 26.418362 -4.46691 2.4804545 -1.2402272
34 24.937669 -11.268319 -11.27154 -3.9367223 -7.3348175 -875844.65 17396.86 25.498405 25.828908 26.415072 -4.46691 2.4804545 -1.2402272
35 24.937669 -11.271708 -11.27493 -3.9399621 -7.3349676 -855800.42 17387.974 25.493276 25.824221 26.411684 -4.46691 2.4804545 -1.2402272
36 24.937669 -11.275035 -11.278257 -3.9431406 -7.3351162 -835600.16 17379.014 25.488148 25.819523 26.40819 -4.46691 2.4804545 -1.2402272
37 24.937669 -11.278302 -11.281523 -3.9462585 -7.3352643 -815252.4 17369.973 25.48302 25.814811 26.404583 -4.46691 2.4804545 -1.2402272
38 24.937669 -11.281508 -11.284729 -3.949317 -7.3354119 -794764.78 17360.845 25.477891 25.810085 26.400852 -4.46691 2.4804545 -1.2402272
39 24.937669 -11.284657 -11.287878 -3.9523172 -7.335561 -774146.03 17351.623 25.472763 25.805345 26.396989 -4.46691 2.4804545 -1.2402272
40 24.937669 -11.28775 -11.290971 -3.9552606 -7.3357107 -753402.85 17342.3 25.467634 25.800587 26.392983 -4.46691 2.4804545 -1.2402272
41 24.937669 -11.290789 -11.294011 -3.9581487 -7.3358619 -732542.91 17332.865 25.462506 25.795813 26.388822 -4.46691 2.4804545 -1.2402272
42 24.937669 -11.293778 -11.296999 -3.9609838 -7.3360152 -711573.18 17323.31 25.457378 25.791019 26.384491 -4.46691 2.4804545 -1.2402272
43 24.937669 -11.296716 -11.299937 -3.9637679 -7.3361695 -690499.53 17313.623 25.452249 25.786204 26.379975 -4.46691 2.4804545 -1.2402272
44 24.937669 -11.299611 -11.302832 -3.966504 -7.3363285 -669329.96 17303.791 25.447121 25.781367 26.375256 -4.46691 2.4804545 -1.2402272
45 24.937669 -11.302465 -11.305686 -3.9691953 -7.336491 -648069.16 17293.8 25.441992 25.776504 26.370314 -4.46691 2.4804545 -1.2402272
46 24.937669 -11.30528 -11.308502 -3.9718455 -7.3366562 -626720.99 17283.632 25.436864 25.771614 26.365124 -4.46691 2.4804545 -1.2402272
47 24.937669 -11.307978 -11.311199 -3.9743804 -7.3368185 -605946.37 17273.585 25.431893 25.766844 26.359827 -4.46691 2.4804545 -1.2402272
48 24.937669 -11.310512 -11.313733 -3.9767586 -7.3369747 -586171.83 17263.86 25.427179 25.76229 26.35453 -4.46691 2.4804545 -1.2402272
49 24.937669 -11.312898 -11.31612 -3.978995 -7.3371247 -567358.74 17254.444 25.422709 25.757942 26.349233 -4.46691 2.4804545 -1.2402272
50 24.937669 -11.315151 -11.318372 -3.9811032 -7.337269 -549468.1 17245.321 25.418472 25.753791 26.343936 -4.46691 2.4804545 -1.2402272
51 24.937669 -11.317282 -11.320503 -3.9830955 -7.3374078 -532460.71 17236.477 25.414458 25.749827 26.33864 -4.46691 2.4804545 -1.2402272
52 24.937669 -11.319303 -11.322525 -3.9849831 -7.3375416 -516297.54 17227.899 25.410655 25.746041 26.333343 -4.46691 2.4804545 -1.2402272
53 24.937669 -11.321225 -11.324447 -3.9867761 -7.3376707 -500940.12 17219.573 25.407053 25.742425 26.328046 -4.46691 2.4804545 -1.2402272
54 24.937669 -11.323058 -11.326279 -3.9884836 -7.3377956 -486350.73 17211.488 25.403642 25.738971 26.322749 -4.46691 2.4804545 -1.2402272
55 24.937669 -11.32481 -11.328031 -3.9901141 -7.3379171 -472493.07 17203.631 25.400413 25.735671 26.317452 -4.46691 2.4804545 -1.2402272
56 24.937669 -11.326489 -11.32971 -3.9916749 -7.3380352 -459331.31 17195.991 25.397358 25.732517 26.312155 -4.46691 2.4804545 -1.2402272
57 24.937669 -11.328102 -11.331323 -3.9931729 -7.3381501 -446830.89 17188.558 25.394466 25.729502 26.306858 -4.46691 2.4804545 -1.2402272
58 24.937669 -11.329654 -11.332876 -3.9946142 -7.3382614 -434958.48 17181.322 25.391731 25.72662 26.301561 -4.46691 2.4804545 -1.2402272
59 24.937669 -11.331153 -11.334374 -3.9960043 -7.3383695 -423682.29 17174.272 25.389145 25.723864 26.296264 -4.46691 2.4804545 -1.2402272
60 24.937669 -11.332601 -11.335823 -3.9973482 -7.3384745 -412971.91 17167.399 25.386699 25.721228 26.290967 -4.46691 2.4804545 -1.2402272
61 24.937669 -11.334006 -11.337227 -3.9986504 -7.3385765 -402798.3 17160.695 25.384388 25.718706 26.285671 -4.46691 2.4804545 -1.2402272
62 24.937669 -11.335369 -11.338591 -3.999915 -7.3386757 -393133.76 17154.152 25.382205 25.716293 26.280374 -4.46691 2.4804545 -1.2402272
63 24.937669 -11.336696 -11.339918 -4.0011456 -7.3387722 -383951.94 17147.76 25.380142 25.713983 26.275077 -4.46691 2.4804545 -1.2402272
64 24.937669 -11.33799 -11.341212 -4.0023455 -7.3388662 -375227.79 17141.513 25.378195 25.711772 26.26978 -4.46691 2.4804545 -1.2402272
65 24.937669 -11.339254 -11.342475 -4.0035177 -7.3389578 -366937.52 17135.404 25.376357 25.709653 26.264483 -4.46691 2.4804545 -1.2402272
66 24.937669 -11.340491 -11.343712 -4.0046649 -7.3390471 -359058.56 17129.426 25.374623 25.707624 26.259186 -4.46691 2.4804545 -1.2402272
67 24.937669 -11.341702 -11.344924 -4.0057895 -7.3391342 -351569.51 17123.572 25.372988 25.70568 26.253889 -4.46691 2.4804545 -1.2402272
68 24.937669 -11.342892 -11.346113 -4.0068937 -7.3392192 -344450.1 17117.836 25.371447 25.703816 26.248592 -4.46691 2.4804545 -1.2402272
69 24.937669 -11.344061 -11.347282 -4.0079795 -7.3393023 -337681.13 17112.212 25.369995 25.702029 26.243295 -4.46691 2.4804545 -1.2402272
70 24.937669 -11.345211 -11.348432 -4.0090487 -7.3393835 -331244.45 17106.696 25.368628 25.700315 26.237998 -4.46691 2.4804545 -1.2402272
71 24.937669 -11.346345 -11.349567 -4.0101029 -7.3394638 -325123.5 17101.281 25.367342 25.698671 26.232702 -4.46691 2.4804545 -1.2402272
72 24.937669 -11.347464 -11.350685 -4.0111435 -7.3395417 -319300.89 17095.963 25.366132 25.697093 26.227405 -4.46691 2.4804545 -1.2402272
73 24.937669 -11.34857 -11.351791 -4.0121718 -7.3396197 -313762.69 17090.736 25.364996 25.695578 26.222108 -4.46691 2.4804545 -1.2402272
74 24.937669 -11.349662 -11.352883 -4.0131891 -7.3396939 -308492.11 17085.598 25.363929 25.694123 26.216811 -4.46691 2.4804545 -1.2402272
75 24.937669 -11.350742 -11.353963 -4.0141963 -7.3397671 -303476.96 17080.542 25.362927 25.692725 26.211514 -4.46691 2.4804545 -1.2402272
76 24.937669 -11.351812 -11.355033 -4.0151946 -7.3398386 -298703.85 17075.566 25.361989 25.691382 26.206217 -4.46691 2.4804545 -1.2402272
77 24.937669 -11.352873 -11.356094 -4.0161846 -7.3399096 -294161.04 17070.665 25.36111 25.690091 26.20092 -4.46691 2.4804545 -1.2402272
78 24.937669 -11.353926 -11.357147 -4.0171674 -7.3399796 -289836.52 17065.836 25.360288 25.688849 26.195623 -4.46691 2.4804545 -1.2402272
79 24.937669 -11.35497 -11.358192 -4.0181434 -7.3400483 -285719.12 17061.075 25.35952 25.687655 26.190326 -4.46691 2.4804545 -1.2402272
80 24.937669 -11.356008 -11.35923 -4.0191135 -7.340116 -281798.55 17056.379 25.358803 25.686506 26.185029 -4.46691 2.4804545 -1.2402272
81 24.937669 -11.357041 -11.360262 -4.0200782 -7.340184 -278065.73 17051.745 25.358135 25.685399 26.179733 -4.46691 2.4804545 -1.2402272
82 24.937669 -11.358068 -11.361289 -4.0210379 -7.3402515 -274510.78 17047.17 25.357514 25.684334 26.174436 -4.46691 2.4804545 -1.2402272
83 24.937669 -11.35909 -11.362311 -4.0219933 -7.340318 -271124.57 17042.651 25.356936 25.683307 26.169139 -4.46691 2.4804545 -1.2402272
84 24.937669 -11.360107 -11.363329 -4.0229447 -7.3403841 -267898.97 17038.186 25.356401 25.682318 26.163842 -4.46691 2.4804545 -1.2402272
85 24.937669 -11.36112 -11.364342 -4.0238925 -7.3404492 -264825.72 17033.771 25.355905 25.681365 26.158545 -4.46691 2.4804545 -1.2402272
86 24.937669 -11.362129 -11.36535 -4.0248371 -7.3405133 -261897.31 17029.405 25.355448 25.680445 26.153248 -4.46691 2.4804545 -1.2402272
87 24.937669 -11.363134 -11.366355 -4.0257788 -7.3405765 -259106.64 17025.085 25.355027 25.679558 26.147951 -4.46691 2.4804545 -1.2402272
88 24.937669 -11.364135 -11.367357 -4.0267179 -7.3406387 -256446.95 17020.808 25.35464 25.678702 26.142654 -4.46691 2.4804545 -1.2402272
89 24.937669 -11.365133 -11.368355 -4.0276546 -7.3407001 -253911.89 17016.574 25.354285 25.677875 26.137357 -4.46691 2.4804545 -1.2402272
90 24.937669 -11.366129 -11.36935 -4.0285893 -7.3407607 -251495.4 17012.379 25.353962 25.677076 26.13206 -4.46691 2.4804545 -1.2402272
91 24.937669 -11.367121 -11.370342 -4.029522 -7.3408204 -249191.74 17008.223 25.353669 25.676304 26.126764 -4.46691 2.4804545 -1.2402272
92 24.937669 -11.368111 -11.371333 -4.0304531 -7.3408794 -246995.48 17004.103 25.353403 25.675558 26.121467 -4.46691 2.4804545 -1.2402272
93 24.937669 -11.369099 -11.37232 -4.0313827 -7.3409374 -244901.4 17000.017 25.353165 25.674837 26.11617 -4.46691 2.4804545 -1.2402272
94 24.937669 -11.370084 -11.373306 -4.032311 -7.3409945 -242904.51 16995.964 25.352951 25.674139 26.110873 -4.46691 2.4804545 -1.2402272
95 24.937669 -11.371068 -11.374289 -4.0332381 -7.3410509 -241000.35 16991.942 25.352762 25.673463 26.105576 -4.46691 2.4804545 -1.2402272
96 24.937669 -11.372049 -11.37527 -4.0341641 -7.3411063 -239184.32 16987.95 25.352596 25.672809 26.100279 -4.46691 2.4804545 -1.2402272
97 24.937669 -11.373029 -11.37625 -4.0350892 -7.341161 -237452.42 16983.987 25.352452 25.672175 26.094982 -4.46691 2.4804545 -1.2402272
98 24.937669 -11.374007 -11.377229 -4.0360135 -7.341215 -235800.7 16980.05 25.352329 25.671561 26.089685 -4.46691 2.4804545 -1.2402272
99 24.937669 -11.374985 -11.378206 -4.0369371 -7.3412694 -234226.03 16976.14 25.352225 25.670965 26.084388 -4.46691 2.4804545 -1.2402272
100 24.937669 -11.375963 -11.379184 -4.0378601 -7.341324 -232724.75 16972.254 25.352141 25.670388 26.079091 -4.46691 2.4804545 -1.2402272
101 24.937669 -11.37694 -11.380161 -4.0387826 -7.3413784 -231293.15 16968.391 25.352074 25.669827 26.073795 -4.46691 2.4804545 -1.2402272
102 24.937669 -11.377915 -11.381137 -4.0397046 -7.3414322 -229927.75 16964.551 25.352024 25.669283 26.068498 -4.46691 2.4804545 -1.2402272
103 24.937669 -11.37889 -11.382112 -4.0406262 -7.3414855 -228625.48 16960.733 25.35199 25.668755 26.063201 -4.46691 2.4804545 -1.2402272
104 24.937669 -11.379864 -11.383086 -4.0415475 -7.3415382 -227383.42 16956.934 25.351972 25.668242 26.057904 -4.46691 2.4804545 -1.2402272
105 24.937669 -11.380838 -11.384059 -4.0424685 -7.3415903 -226198.79 16953.155 25.351968 25.667743 26.052607 -4.46691 2.4804545 -1.2402272
106 24.937669 -11.38181 -11.385031 -4.0433894 -7.3416419 -225068.97 16949.395 25.351978 25.667258 26.04731 -4.46691 2.4804545 -1.2402272
107 24.937669 -11.382783 -11.386004 -4.0443101 -7.3416939 -223992.05 16945.652 25.352001 25.666786 26.042013 -4.46691 2.4804545 -1.2402272
108 24.937669 -11.383755 -11.386976 -4.0452307 -7.3417454 -222965.04 16941.926 25.352037 25.666326 26.036716 -4.46691 2.4804545 -1.2402272
109 24.937669 -11.384727 -11.387948 -4.0461513 -7.3417972 -221986.16 16938.216 25.352084 25.665879 26.031419 -4.46691 2.4804545 -1.2402272
110 24.937669 -11.385699 -11.38892 -4.0470718 -7.3418485 -221052.74 16934.521 25.352143 25.665444 26.026122 -4.46691 2.4804545 -1.2402272
111 24.937669 -11.38667 -11.389892 -4.0479923 -7.3418993 -220162.75 16930.841 25.352212 25.665019 26.020826 -4.46691 2.4804545 -1.2402272
112 24.937669 -11.387641 -11.390863 -4.048913 -7.3419496 -219314.21 16927.174 25.352291 25.664605 26.015529 -4.46691 2.4804545 -1.2402272
113 24.937669 -11.388612 -11.391833 -4.0498336 -7.3419995 -218505.28 16923.521 25.35238 25.664202 26.010232 -4.46691 2.4804545 -1.2402272
114 24.937669 -11.389582 -11.392803 -4.0507545 -7.3420489 -217734.19 16919.88 25.352478 25.663808 26.004935 -4.46691 2.4804545 -1.2402272
115 24.937669 -11.390553 -11.393774 -4.0516754 -7.3420988 -216999.89 16916.252 25.352585 25.663424 25.999638 -4.46691 2.4804545 -1.2402272
116 24.937669 -11.391524 -11.394745 -4.0525965 -7.3421486 -216300.32 16912.635 25.3527 25.663049 25.994341 -4.46691 2.4804545 -1.2402272
117 24.937669 -11.39201 -11.395231 -4.0530571 -7.3421737 -215967.06 16910.832 25.352761 25.662866 25.991693 -4.46691 2.4804545 -1.2402272
118 24.937669 -11.392232 -11.395453 -4.0532686 -7.3421844 -215803.49 16909.932 25.352792 25.662775 25.990368 -4.46691 2.4804545 -1.2402272
119 24.937669 -11.392243 -11.395465 -4.0532786 -7.342186 -215784.41 16909.819 25.352796 25.662764 25.990203 -4.46691 2.4804545 -1.2402272
120 24.937669 -11.392247 -11.395468 -4.0532822 -7.3421862 -215782.06 16909.805 25.352797 25.662763 25.990182 -4.46691 2.4804545 -1.2402272
121 24.937669 -11.392249 -11.39547 -4.053284 -7.3421863 -215780.89 16909.798 25.352797 25.662762 25.990172 -4.46691 2.4804545 -1.2402272
122 24.937669 -11.392249 -11.395471 -4.0532845 -7.3421863 -215780.6 16909.796 25.352797 25.662762 25.990169 -4.46691 2.4804545 -1.2402272
123 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.45 16909.796 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
124 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.41 16909.795 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
125 24.937669 -11.39225 -11.395471 -4.0532847 -7.3421863 -215780.41 16909.795 25.352797 25.662762 25.990168 -4.46691 2.4804545 -1.2402272
Loop time of 6.48088 on 4 procs for 119 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-11.1226132511 -11.3954710611 -11.3954710611
Force two-norm initial, final = 27009.2 6698.47
Force max component initial, final = 19644.3 6673.92
Final line search alpha, max atom move = 2.28633e-13 1.52588e-09
Iterations, force evaluations = 119 198
Pair time (%) = 6.18186 (95.3861)
Neigh time (%) = 0.13631 (2.10326)
Comm time (%) = 0.121525 (1.87513)
Outpt time (%) = 0.00443709 (0.0684643)
Other time (%) = 0.0367464 (0.566998)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 268488 ave 268492 max 268483 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 1073950
Ave neighs/atom = 715.967
Neighbor list builds = 2
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
velocity all create 300.1 2398378
run 10
Memory usage per processor = 416.923 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
125 300.1 -11.356706 -11.395471 -4.0532847 -7.3421863 -212412.69 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
126 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
127 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
128 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
129 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
130 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
131 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
132 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
133 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
134 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
135 300.1 -11.883805 -11.92257 -2.247232 -9.6753381 -131419.33 16909.795 25.352797 25.662762 25.990168 -4.46691 3.011271 -1.5056355
Loop time of 0.445023 on 4 procs for 10 steps with 1500 atoms
Pair time (%) = 0.314639 (70.7017)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00810659 (1.82161)
Outpt time (%) = 0.000411868 (0.0925499)
Other time (%) = 0.121866 (27.3841)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 271875 ave 271875 max 271875 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1087500
Ave neighs/atom = 725
Neighbor list builds = 0
Dangerous builds = 0

69
examples/comb/log.comb.Si.9Jan12.linux.1 Normal file
View File

@ -0,0 +1,69 @@
LAMMPS (10 Jan 2012)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 384.657 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -5.2974091 -5.2987121 -5.2987121 0 -71570.238 10246.592 21.72 21.72 21.72 0
1 10.098269 -5.2974091 -5.2987119 -5.2987119 0 -71570.213 10246.592 21.72 21.72 21.72 0
2 10.093077 -5.2974091 -5.2987112 -5.2987112 0 -71570.137 10246.592 21.72 21.72 21.72 0
3 10.08443 -5.2974091 -5.2987101 -5.2987101 0 -71570.011 10246.592 21.72 21.72 21.72 0
4 10.072338 -5.2974091 -5.2987085 -5.2987085 0 -71569.835 10246.592 21.72 21.72 21.72 0
5 10.056815 -5.2974091 -5.2987065 -5.2987065 0 -71569.609 10246.592 21.72 21.72 21.72 0
6 10.037878 -5.2974091 -5.2987041 -5.2987041 0 -71569.334 10246.592 21.72 21.72 21.72 0
7 10.015548 -5.2974091 -5.2987012 -5.2987012 0 -71569.01 10246.592 21.72 21.72 21.72 0
8 9.9898514 -5.2974091 -5.2986979 -5.2986979 0 -71568.636 10246.592 21.72 21.72 21.72 0
9 9.9608163 -5.2974091 -5.2986941 -5.2986941 0 -71568.215 10246.592 21.72 21.72 21.72 0
10 9.9284757 -5.2974091 -5.29869 -5.29869 0 -71567.746 10246.592 21.72 21.72 21.72 0
Loop time of 0.131721 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.131023 (99.47)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000367165 (0.278744)
Outpt time (%) = 0.000140667 (0.106792)
Other time (%) = 0.000190258 (0.14444)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 383.808 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -5.2974091 -5.2987121 -5.2987121 0 -71570.238 10246.592 21.72 21.72 21.72 0
1 10.098254 -5.2974091 -5.2987119 -5.2987119 0 -71570.212 10246.592 21.72 21.72 21.72 0
2 10.093019 -5.2974091 -5.2987112 -5.2987112 0 -71570.136 10246.592 21.72 21.72 21.72 0
3 10.0843 -5.2974091 -5.2987101 -5.2987101 0 -71570.008 10246.592 21.72 21.72 21.72 0
4 10.072108 -5.2974091 -5.2987085 -5.2987085 0 -71569.83 10246.592 21.72 21.72 21.72 0
5 10.056457 -5.2974091 -5.2987065 -5.2987065 0 -71569.601 10246.592 21.72 21.72 21.72 0
6 10.037364 -5.2974091 -5.298704 -5.298704 0 -71569.322 10246.592 21.72 21.72 21.72 0
7 10.014852 -5.2974091 -5.2987011 -5.2987011 0 -71568.993 10246.592 21.72 21.72 21.72 0
8 9.9889464 -5.2974091 -5.2986978 -5.2986978 0 -71568.614 10246.592 21.72 21.72 21.72 0
9 9.9596766 -5.2974091 -5.298694 -5.298694 0 -71568.187 10246.592 21.72 21.72 21.72 0
10 9.927076 -5.2974091 -5.2986898 -5.2986898 0 -71567.712 10246.592 21.72 21.72 21.72 0
Loop time of 0.0353957 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0332664 (93.9841)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00170434 (4.81509)
Outpt time (%) = 0.000266969 (0.754241)
Other time (%) = 0.000158072 (0.446583)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 385.344 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -5.298087 -5.298216 -5.298216 0
1 1 -5.3007406 -5.3008696 -5.3008696 0
2 1 -5.3032941 -5.3034231 -5.3034231 0
3 1 -5.3057463 -5.3058753 -5.3058753 0
4 1 -5.3080963 -5.3082253 -5.3082253 0
5 1 -5.310343 -5.310472 -5.310472 0
6 1 -5.3124852 -5.3126142 -5.3126142 0
7 1 -5.3145219 -5.3146509 -5.3146509 0
8 1 -5.316452 -5.3165811 -5.3165811 0
9 1 -5.3182744 -5.3184034 -5.3184034 0
10 1 -5.319988 -5.320117 -5.320117 0
11 1 -5.3215916 -5.3217206 -5.3217206 0
12 1 -5.3230841 -5.3232131 -5.3232131 0
13 1 -5.3244643 -5.3245933 -5.3245933 0
14 1 -5.3257312 -5.3258602 -5.3258602 0
15 1 -5.3268835 -5.3270126 -5.3270126 0
16 1 -5.3279202 -5.3280492 -5.3280492 0
17 1 -5.3288399 -5.3289689 -5.3289689 0
18 1 -5.3296416 -5.3297706 -5.3297706 0
19 1 -5.330324 -5.330453 -5.330453 0
20 1 -5.3308859 -5.3310149 -5.3310149 0
21 1 -5.3313261 -5.3314551 -5.3314551 0
22 1 -5.3316434 -5.3317725 -5.3317725 0
23 1 -5.3318366 -5.3319656 -5.3319656 0
24 1 -5.3319044 -5.3320335 -5.3320335 0
25 1 -5.3319045 -5.3320335 -5.3320335 0
26 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.641141 on 1 procs for 26 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.29821600825 -5.33203354013 -5.33203354013
Force two-norm initial, final = 799.113 0.221963
Force max component initial, final = 461.368 0.12815
Final line search alpha, max atom move = 0.000121927 1.5625e-05
Iterations, force evaluations = 26 37
Pair time (%) = 0.512635 (79.9566)
Neigh time (%) = 0.121496 (18.95)
Comm time (%) = 0.00175428 (0.273619)
Outpt time (%) = 0.00022912 (0.0357363)
Other time (%) = 0.00502706 (0.78408)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 3
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
Memory usage per processor = 384.352 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
26 1 -5.3319045 -5.3320335 -5.3320335 0
27 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.0137792 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0137219 (99.5847)
Neigh time (%) = 0 (0)
Comm time (%) = 3.69549e-05 (0.268194)
Outpt time (%) = 9.77516e-06 (0.0709416)
Other time (%) = 1.04904e-05 (0.0761325)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 384.81 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 21.201945 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -8.8447721e-06 -8.4498844e-06 -3.4721654e-06
28 21.202157 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -9.2168914e-06 -8.6256272e-06 -2.98407e-06
29 21.202369 21.201945 21.201945 0 0 0 310358.27 310352.06 310352.06 -8.4833253e-06 -7.9020222e-06 -2.5493378e-06
30 21.202581 21.201945 21.201945 0 0 0 420331.84 420315.03 420315.03 -8.8006585e-06 -8.0215558e-06 -3.3761116e-06
31 21.202793 21.201945 21.201945 0 0 0 530306.27 530274.45 530274.45 -8.5096512e-06 -7.6252451e-06 -5.0268132e-06
32 21.203005 21.201945 21.201945 0 0 0 640281.55 640230.33 640230.33 -8.1652807e-06 -8.8525987e-06 -6.7073981e-06
33 21.203217 21.201945 21.201945 0 0 0 750257.69 750182.67 750182.67 -8.0727845e-06 -7.9112719e-06 -5.5575991e-06
34 21.203429 21.201945 21.201945 0 0 0 860234.68 860131.46 860131.46 -8.7195464e-06 -8.420001e-06 -3.5539889e-06
35 21.203641 21.201945 21.201945 0 0 0 970212.53 970076.71 970076.71 -9.1912771e-06 -8.7423147e-06 -6.3680082e-06
36 21.203853 21.201945 21.201945 0 0 0 1080191.2 1080018.4 1080018.4 -8.7416032e-06 -8.6889515e-06 -6.1602475e-06
37 21.204065 21.201945 21.201945 0 0 0 1190170.8 1189956.6 1189956.6 -8.263469e-06 -8.460557e-06 -2.753541e-06
Loop time of 0.165838 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163672 (98.694)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000379562 (0.228875)
Outpt time (%) = 0.00165892 (1.00032)
Other time (%) = 0.000127316 (0.076771)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 385.268 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 21.204065 21.201945 21.201945 0 0 0 1300151.2 1299891.2 1299891.2 -8.5068051e-06 -8.341735e-06 -1.0682601e-05
38 21.204065 21.201945 21.202157 0 0 0 1300151.2 1299891.2 1299891.2 -8.6917976e-06 -8.5608798e-06 -9.949746e-06
39 21.204065 21.201945 21.202369 0 0 0 1410093.3 1409811.3 1409839.5 -3.943896e-06 -5.7881281e-06 -1.2222307e-05
40 21.204065 21.201945 21.202581 0 0 0 1520031.8 1519727.8 1519788.6 5.9268724e-07 -7.7433557e-06 -1.0823479e-05
41 21.204065 21.201945 21.202793 0 0 0 1629966.8 1629640.8 1629738.6 -4.0790828e-06 -7.9582315e-06 -8.9045388e-06
42 21.204065 21.201945 21.203005 0 0 0 1739898.2 1739550.3 1739689.4 -7.4637325e-06 -7.3819089e-06 -1.0844825e-05
43 21.204065 21.201945 21.203217 0 0 0 1849826.1 1849456.2 1849641.1 -1.3091771e-07 -7.8351404e-06 -1.0877554e-05
44 21.204065 21.201945 21.203429 0 0 0 1959750.5 1959358.6 1959593.7 5.9909083e-06 -6.7621843e-06 -1.1562738e-05
45 21.204065 21.201945 21.203641 0 0 0 2069671.3 2069257.4 2069547.1 5.3697607e-06 -7.5476906e-06 -1.0171025e-05
46 21.204065 21.201945 21.203853 0 0 0 2179588.5 2179152.7 2179501.4 7.4559059e-06 -8.3858486e-06 -1.0113393e-05
47 21.204065 21.201945 21.204065 0 0 0 2289502.3 2289044.4 2289456.5 8.1389548e-06 -7.1328807e-06 -1.1707174e-05
Loop time of 0.1659 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163715 (98.6829)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000379801 (0.228934)
Outpt time (%) = 0.00167823 (1.01159)
Other time (%) = 0.000127077 (0.0765986)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 385.725 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 21.204065 21.201945 21.204065 0 0 0 2399412.4 2398932.6 2399412.4 1.2782265e-05 -8.2784107e-06 -1.164883e-05
48 21.204065 21.201945 21.204065 0 0 4.2408131e-07 2399412.4 2398932.6 2399412.4 1.2881164e-05 -7.8749849e-06 -1.141759e-05
49 21.204065 21.201945 21.204065 0 0 8.4816261e-07 2399412.4 2398932.6 2399412.4 1.3132327e-05 -8.5857827e-06 219.84282
50 21.204065 21.201945 21.204065 0 0 1.2722439e-06 2399412.4 2398932.6 2399412.4 1.3429026e-05 -6.4875418e-06 439.68565
51 21.204065 21.201945 21.204065 0 0 1.6963252e-06 2399412.4 2398932.6 2399412.4 1.3087502e-05 -5.472218e-06 659.52848
52 21.204065 21.201945 21.204065 0 0 2.1204065e-06 2399412.4 2398932.6 2399412.4 1.331305e-05 -1.5510903e-07 879.37131
53 21.204065 21.201945 21.204065 0 0 2.5444878e-06 2399412.4 2398932.6 2399412.4 1.3029158e-05 1.0452072e-06 1099.2141
54 21.204065 21.201945 21.204065 0 0 2.9685691e-06 2399412.4 2398932.6 2399412.4 1.245497e-05 3.791633e-06 1319.057
55 21.204065 21.201945 21.204065 0 0 3.3926505e-06 2399412.4 2398932.6 2399412.4 1.2748824e-05 8.154608e-06 1538.8998
56 21.204065 21.201945 21.204065 0 0 3.8167318e-06 2399412.4 2398932.6 2399412.4 1.3488082e-05 1.0240753e-05 1758.7426
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2915317e-05 1.3717899e-05 1978.5855
Loop time of 0.165923 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.163732 (98.6796)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000390053 (0.235081)
Outpt time (%) = 0.00167251 (1.008)
Other time (%) = 0.000128269 (0.0773065)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 386.183 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2363897e-05 1.9987719e-05 2198.4283
58 21.204065 21.201945 21.204065 4.240389e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1.2859108e-05 1.9237788e-05 2198.4283
59 21.204065 21.201945 21.204065 8.480778e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 219.84283 -0.00012237462 2198.4283
60 21.204065 21.201945 21.204065 1.2721167e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 439.68565 -0.00026263658 2198.4283
61 21.204065 21.201945 21.204065 1.6961556e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 659.52847 -0.00040342648 2198.4283
62 21.204065 21.201945 21.204065 2.1201945e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 879.37129 -0.00054391257 2198.4283
63 21.204065 21.201945 21.204065 2.5442334e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1099.2141 -0.00068552355 2198.4283
64 21.204065 21.201945 21.204065 2.9682723e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1319.0569 -0.00082718719 2198.4283
65 21.204065 21.201945 21.204065 3.3923112e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1538.8998 -0.00096788602 2198.4283
66 21.204065 21.201945 21.204065 3.8163501e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1758.7426 -0.0011099011 2198.4283
67 21.204065 21.201945 21.204065 4.240389e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1978.5854 -0.0012526114 2198.4283
Loop time of 0.166279 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.164098 (98.6882)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000380278 (0.228698)
Outpt time (%) = 0.00167036 (1.00455)
Other time (%) = 0.000130653 (0.0785748)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225280 ave 225280 max 225280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0

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@ -0,0 +1,296 @@
LAMMPS (10 Jan 2012)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 384.499 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -5.298087 -5.298216 -5.298216 0
1 1 -5.3007406 -5.3008696 -5.3008696 0
2 1 -5.3032941 -5.3034231 -5.3034231 0
3 1 -5.3057463 -5.3058753 -5.3058753 0
4 1 -5.3080963 -5.3082253 -5.3082253 0
5 1 -5.310343 -5.310472 -5.310472 0
6 1 -5.3124852 -5.3126142 -5.3126142 0
7 1 -5.3145219 -5.3146509 -5.3146509 0
8 1 -5.316452 -5.3165811 -5.3165811 0
9 1 -5.3182744 -5.3184034 -5.3184034 0
10 1 -5.319988 -5.320117 -5.320117 0
11 1 -5.3215916 -5.3217206 -5.3217206 0
12 1 -5.3230841 -5.3232131 -5.3232131 0
13 1 -5.3244643 -5.3245933 -5.3245933 0
14 1 -5.3257312 -5.3258602 -5.3258602 0
15 1 -5.3268835 -5.3270126 -5.3270126 0
16 1 -5.3279202 -5.3280492 -5.3280492 0
17 1 -5.3288399 -5.3289689 -5.3289689 0
18 1 -5.3296416 -5.3297706 -5.3297706 0
19 1 -5.330324 -5.330453 -5.330453 0
20 1 -5.3308859 -5.3310149 -5.3310149 0
21 1 -5.3313261 -5.3314551 -5.3314551 0
22 1 -5.3316434 -5.3317725 -5.3317725 0
23 1 -5.3318366 -5.3319656 -5.3319656 0
24 1 -5.3319044 -5.3320335 -5.3320335 0
25 1 -5.3319045 -5.3320335 -5.3320335 0
26 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.250753 on 4 procs for 26 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-5.29821600825 -5.33203354012 -5.33203354012
Force two-norm initial, final = 799.113 0.221963
Force max component initial, final = 461.368 0.12815
Final line search alpha, max atom move = 0.000121927 1.5625e-05
Iterations, force evaluations = 26 37
Pair time (%) = 0.132469 (52.8283)
Neigh time (%) = 0.0654684 (26.1087)
Comm time (%) = 0.0481624 (19.2071)
Outpt time (%) = 0.000469863 (0.187381)
Other time (%) = 0.00418389 (1.66853)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 3
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
Memory usage per processor = 383.507 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
26 1 -5.3319045 -5.3320335 -5.3320335 0
27 1 -5.3319045 -5.3320335 -5.3320335 0
Loop time of 0.00479984 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.00358206 (74.6287)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00118113 (24.6076)
Outpt time (%) = 2.31266e-05 (0.48182)
Other time (%) = 1.35303e-05 (0.28189)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:471)
run 10
Memory usage per processor = 383.965 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 21.201945 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -7.7070687e-06 -3.8058632e-06 -1.3983292e-05
28 21.202157 21.201945 21.201945 0 0 0 200385.55 200385.55 200385.55 -7.6074574e-06 -3.7702878e-06 -1.3585558e-05
29 21.202369 21.201945 21.201945 0 0 0 310358.27 310352.06 310352.06 -6.6668421e-06 -3.6792146e-06 -7.5669014e-06
30 21.202581 21.201945 21.201945 0 0 0 420331.84 420315.03 420315.03 -7.1762828e-06 -3.9709334e-06 -8.7117198e-06
31 21.202793 21.201945 21.201945 0 0 0 530306.27 530274.45 530274.45 -7.4146384e-06 -3.7098095e-06 -8.0407666e-06
32 21.203005 21.201945 21.201945 0 0 0 640281.55 640230.33 640230.33 -6.9144473e-06 -3.671388e-06 -9.8821526e-06
33 21.203217 21.201945 21.201945 0 0 0 750257.69 750182.67 750182.67 -6.8219511e-06 -3.598814e-06 -9.722063e-06
34 21.203429 21.201945 21.201945 0 0 0 860234.68 860131.46 860131.46 -5.8386453e-06 -4.1658869e-06 -1.1708597e-05
35 21.203641 21.201945 21.201945 0 0 0 970212.53 970076.71 970076.71 -6.7991828e-06 -4.0449303e-06 -1.4273588e-05
36 21.203853 21.201945 21.201945 0 0 0 1080191.2 1080018.4 1080018.4 -6.9471768e-06 -4.0342577e-06 -6.4647735e-06
37 21.204065 21.201945 21.201945 0 0 0 1190170.8 1189956.6 1189956.6 -6.5373474e-06 -3.5354897e-06 -7.4680016e-06
Loop time of 0.0582895 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0428118 (73.4468)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0132927 (22.8047)
Outpt time (%) = 0.00210714 (3.61496)
Other time (%) = 7.78437e-05 (0.133547)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 384.423 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 21.204065 21.201945 21.201945 0 0 0 1300151.2 1299891.2 1299891.2 -7.732683e-06 -3.9915672e-06 -1.0324e-05
38 21.204065 21.201945 21.202157 0 0 0 1300151.2 1299891.2 1299891.2 -7.6593976e-06 -3.7304432e-06 -1.0456341e-05
39 21.204065 21.201945 21.202369 0 0 0 1410093.3 1409811.3 1409839.5 -8.7024702e-06 -2.759233e-06 -1.2029488e-05
40 21.204065 21.201945 21.202581 0 0 0 1520031.8 1519727.8 1519788.6 -1.2521141e-05 -3.7197706e-06 -1.131869e-05
41 21.204065 21.201945 21.202793 0 0 0 1629966.8 1629640.8 1629738.6 -1.5294604e-05 -4.3451873e-06 -1.0193082e-05
42 21.204065 21.201945 21.203005 0 0 0 1739898.2 1739550.3 1739689.4 -2.1207246e-05 -2.4511495e-06 -1.127173e-05
43 21.204065 21.201945 21.203217 0 0 0 1849826.1 1849456.2 1849641.1 -2.2560537e-05 -4.0741022e-06 -1.0863324e-05
44 21.204065 21.201945 21.203429 0 0 0 1959750.5 1959358.6 1959593.7 -2.5883997e-05 -3.9545687e-06 -9.4637851e-06
45 21.204065 21.201945 21.203641 0 0 0 2069671.3 2069257.4 2069547.1 -3.1642953e-05 -3.5852953e-06 -1.0898899e-05
46 21.204065 21.201945 21.203853 0 0 0 2179588.5 2179152.7 2179501.4 -2.3043652e-05 -4.3067658e-06 -9.9049209e-06
47 21.204065 21.201945 21.204065 0 0 0 2289502.3 2289044.4 2289456.5 -2.4092416e-05 -3.0054153e-06 -1.0928783e-05
Loop time of 0.0580854 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0426171 (73.3696)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0133364 (22.96)
Outpt time (%) = 0.00205803 (3.54311)
Other time (%) = 7.39098e-05 (0.127243)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 384.88 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 21.204065 21.201945 21.204065 0 0 0 2399412.4 2398932.6 2399412.4 -2.394798e-05 -4.7607087e-06 -9.6708344e-06
48 21.204065 21.201945 21.204065 0 0 4.2408131e-07 2399412.4 2398932.6 2399412.4 -2.4658066e-05 -3.597391e-06 -1.0876843e-05
49 21.204065 21.201945 21.204065 0 0 8.4816261e-07 2399412.4 2398932.6 2399412.4 -2.4053995e-05 -6.6063638e-06 219.84282
50 21.204065 21.201945 21.204065 0 0 1.2722439e-06 2399412.4 2398932.6 2399412.4 -2.4549205e-05 -9.9312468e-06 439.68565
51 21.204065 21.201945 21.204065 0 0 1.6963252e-06 2399412.4 2398932.6 2399412.4 -2.4068225e-05 -1.3762013e-05 659.52848
52 21.204065 21.201945 21.204065 0 0 2.1204065e-06 2399412.4 2398932.6 2399412.4 -2.4051149e-05 -1.3256841e-05 879.37131
53 21.204065 21.201945 21.204065 0 0 2.5444878e-06 2399412.4 2398932.6 2399412.4 -2.387754e-05 -1.4584518e-05 1099.2141
54 21.204065 21.201945 21.204065 0 0 2.9685691e-06 2399412.4 2398932.6 2399412.4 -2.4606126e-05 -1.4511944e-05 1319.057
55 21.204065 21.201945 21.204065 0 0 3.3926505e-06 2399412.4 2398932.6 2399412.4 -2.4684392e-05 -1.3372817e-05 1538.8998
56 21.204065 21.201945 21.204065 0 0 3.8167318e-06 2399412.4 2398932.6 2399412.4 -2.4492996e-05 -1.3092483e-05 1758.7426
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.4132261e-05 -1.5846735e-05 1978.5855
Loop time of 0.0582204 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0425564 (73.0954)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0134656 (23.1287)
Outpt time (%) = 0.00212365 (3.64761)
Other time (%) = 7.46846e-05 (0.128279)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 44000 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 385.338 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 21.204065 21.201945 21.204065 0 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.3903155e-05 -1.5495249e-05 2198.4283
58 21.204065 21.201945 21.204065 4.240389e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 -2.4564147e-05 -1.6061611e-05 2198.4283
59 21.204065 21.201945 21.204065 8.480778e-07 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 219.8428 -0.00015851218 2198.4283
60 21.204065 21.201945 21.204065 1.2721167e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 439.68561 -0.0003005522 2198.4283
61 21.204065 21.201945 21.204065 1.6961556e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 659.52844 -0.00044221512 2198.4283
62 21.204065 21.201945 21.204065 2.1201945e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 879.37126 -0.0005848827 2198.4283
63 21.204065 21.201945 21.204065 2.5442334e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1099.2141 -0.00072538515 2198.4283
64 21.204065 21.201945 21.204065 2.9682723e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1319.0569 -0.00086665461 2198.4283
65 21.204065 21.201945 21.204065 3.3923112e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1538.8997 -0.0010079945 2198.4283
66 21.204065 21.201945 21.204065 3.8163501e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1758.7425 -0.0011483945 2198.4283
67 21.204065 21.201945 21.204065 4.240389e-06 0 4.2408131e-06 2399412.4 2398932.6 2399412.4 1978.5854 -0.0012892271 2198.4283
Loop time of 0.0581976 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0426993 (73.3695)
Neigh time (%) = 0 (0)
Comm time (%) = 0.013256 (22.7775)
Outpt time (%) = 0.00216591 (3.72165)
Other time (%) = 7.64728e-05 (0.131402)
Nlocal: 128 ave 164 max 104 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 3073 ave 3097 max 3037 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 56320 ave 72160 max 45760 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 225280
Ave neighs/atom = 440
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 2.06456 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065651733 -3.2595015 0 -3.1987287 -0.03625351 8602.1883
200 0.060086376 -3.2531936 0 -3.1975725 -0.23134158 8635.4
400 0.060533553 -3.2509973 0 -3.1949623 -0.43071023 8675.8283
600 0.06082965 -3.2466949 0 -3.1903858 -0.6030901 8713.3314
800 0.061677224 -3.2413215 0 -3.1842278 -0.74856841 8752.7927
1000 0.062383731 -3.2349273 0 -3.1771796 -0.87459354 8789.671
1200 0.063709246 -3.2276094 0 -3.1686347 -0.98058454 8825.4386
1400 0.065404552 -3.2196608 0 -3.1591168 -1.0699554 8863.034
1600 0.067579602 -3.2110378 0 -3.1484804 -1.1460845 8897.2152
1800 0.069324241 -3.2018536 0 -3.1376812 -1.2025669 8929.5485
2000 0.071014927 -3.1921108 0 -3.1263733 -1.2434925 8960.5106
2200 0.072992881 -3.1818701 0 -3.1143017 -1.2706212 9000.9309
2400 0.075000723 -3.1712313 0 -3.1018043 -1.2835822 9031.5102
2600 0.076843477 -3.1601004 0 -3.0889675 -1.2797332 9068.6361
2800 0.078671706 -3.1487747 0 -3.0759495 -1.2664476 9100.45
3000 0.080713586 -3.1373277 0 -3.0626123 -1.2445454 9131.0432
3200 0.08309469 -3.1260242 0 -3.0491047 -1.2150129 9165.4844
3400 0.085424766 -3.1146623 0 -3.0355859 -1.1843858 9203.3855
3600 0.087396485 -3.1029493 0 -3.0220477 -1.1438492 9230.2539
3800 0.089007987 -3.090822 0 -3.0084286 -1.1004992 9255.5005
4000 0.089813071 -3.0794078 0 -2.9962692 -1.0632524 9278.281
4200 0.08584753 -3.0668559 0 -2.9873882 -1.0383674 9305.2666
4400 0.086197517 -3.0559678 0 -2.9761761 -1.0292345 9325.4174
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0212664 9358.4367
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0275959 9392.0495
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0219203 9432.5928
Loop time of 6.90229 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 5.71184 (82.7529)
Neigh time (%) = 0.270525 (3.91935)
Comm time (%) = 0.00593114 (0.0859301)
Outpt time (%) = 0.063314 (0.91729)
Other time (%) = 0.850676 (12.3246)
Nlocal: 8141 ave 8141 max 8141 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 71389 ave 71389 max 71389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 71389
Ave neighs/atom = 8.76907
Neighbor list builds = 100
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 2.06601 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065993465 -3.2595015 0 -3.1984123 -0.035954133 8602.1883
200 0.060035253 -3.2531886 0 -3.1976149 -0.22766671 8635.1231
400 0.06054278 -3.2510706 0 -3.1950271 -0.42828601 8674.411
600 0.060576995 -3.246816 0 -3.1907408 -0.60041241 8714.1874
800 0.060802753 -3.2413477 0 -3.1850635 -0.7452853 8753.0178
1000 0.061812114 -3.2349942 0 -3.1777756 -0.87164178 8793.5161
1200 0.06317147 -3.2277552 0 -3.1692783 -0.98048929 8819.7022
1400 0.065125405 -3.2198031 0 -3.1595175 -1.0694348 8855.382
1600 0.06725411 -3.2111272 0 -3.148871 -1.1445446 8889.2003
1800 0.069389572 -3.2019689 0 -3.137736 -1.1995438 8930.2905
2000 0.071276448 -3.1921621 0 -3.1261826 -1.2400335 8965.5706
2200 0.073243486 -3.1818809 0 -3.1140805 -1.2653286 8994.1745
2400 0.075063494 -3.1711703 0 -3.1016851 -1.2777211 9035.0036
2600 0.076789207 -3.1600658 0 -3.0889832 -1.275987 9070.0031
2800 0.07875979 -3.1487143 0 -3.0758075 -1.2642789 9102.7214
3000 0.080591853 -3.1372361 0 -3.0626334 -1.2393582 9139.2757
3200 0.08227693 -3.125423 0 -3.0492605 -1.2059907 9165.9163
3400 0.084289444 -3.1136554 0 -3.03563 -1.1676892 9201.2975
3600 0.086720297 -3.1021183 0 -3.0218427 -1.1268117 9229.7367
3800 0.089264018 -3.0909262 0 -3.0082959 -1.0903935 9261.8789
4000 0.091377688 -3.0795096 0 -2.9949227 -1.0584261 9294.1379
4200 0.092665135 -3.0678736 0 -2.9820949 -1.0394077 9328.0647
4400 0.09055434 -3.0560482 0 -2.9722234 -1.0327663 9358.6524
4600 0.088763719 -3.0446018 0 -2.9624346 -1.0280829 9388.1338
4800 0.089467982 -3.0337452 0 -2.950926 -1.0235966 9423.847
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0178644 9448.4573
Loop time of 1.91453 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 1.43427 (74.9148)
Neigh time (%) = 0.0727076 (3.79767)
Comm time (%) = 0.107613 (5.62085)
Outpt time (%) = 0.051915 (2.71163)
Other time (%) = 0.248028 (12.955)
Nlocal: 2035.25 ave 2064 max 2015 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 198 ave 248 max 150 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 17850 ave 18250 max 17601 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 71400
Ave neighs/atom = 8.77042
Neighbor list builds = 106
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.28198 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019973 -2.7914873 0.22407026 -2.4032386 -0.40914143
2500 0.40242274 -2.8142159 0.24281467 -2.4138053 -0.3391299
3000 0.42771065 -2.8535488 0.25848739 -2.4279767 -0.2500108
3500 0.44706195 -2.7890555 0.18446345 -2.3442289 -0.1005632
4000 0.4041733 -2.7741037 0.22161024 -2.3719512 -0.13373446
4500 0.47549052 -2.8368758 0.21740299 -2.3637627 -0.14246916
5000 0.42071015 -2.7518085 0.20821432 -2.3332019 -0.047522754
5500 0.43520504 -2.8042986 0.24366805 -2.3712696 -0.22180582
6000 0.42802195 -2.7822398 0.24060881 -2.3563579 -0.35350862
6500 0.4479767 -2.8175363 0.25806495 -2.3717994 0.07885849
7000 0.39538519 -2.7246562 0.23766993 -2.331248 -0.098542228
7500 0.40716663 -2.7115371 0.21917238 -2.3064063 -0.14844207
8000 0.42814546 -2.7318282 0.23188976 -2.3058235 -0.37209482
8500 0.46175735 -2.7607768 0.23020837 -2.3013282 -0.33381513
9000 0.48360992 -2.758533 0.21927619 -2.2773411 -0.016767257
9500 0.47646809 -2.7812073 0.24046809 -2.3071216 -0.12582235
10000 0.48207466 -2.7437285 0.20973254 -2.2640642 0.51612253
Loop time of 1.0464 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 0.83996 (80.2713)
Neigh time (%) = 0.0338588 (3.23573)
Comm time (%) = 0.0464656 (4.44051)
Outpt time (%) = 0.0178115 (1.70217)
Other time (%) = 0.108306 (10.3503)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1673 ave 1673 max 1673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1673
Ave neighs/atom = 8.365
Neighbor list builds = 679
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
dump 1 all custom 200 dump.dipole id type x y z mux muy muz
run 10000
Memory usage per processor = 3.28129 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019968 -2.7914873 0.22407029 -2.4032386 -0.4091395
2500 0.40237391 -2.8138968 0.24276582 -2.4135348 -0.33901619
3000 0.42595202 -2.8621684 0.26812111 -2.4383462 -0.19493812
3500 0.41153448 -2.8070419 0.23860803 -2.397565 -0.032395966
4000 0.40867238 -2.7790568 0.22331133 -2.3724278 0.014462986
4500 0.39803378 -2.7718651 0.23536245 -2.3758215 -0.25429533
5000 0.42736901 -2.8476039 0.2824171 -2.4223718 0.12187395
5500 0.41115816 -2.7810177 0.24508517 -2.3719153 -0.1925336
6000 0.43184788 -2.8015292 0.24726776 -2.3718406 -0.014489672
6500 0.45955478 -2.8340069 0.26105652 -2.3767499 -0.16015969
7000 0.43826613 -2.7488226 0.20031236 -2.3127478 0.071480756
7500 0.45738321 -2.7892162 0.23337255 -2.3341199 -0.17245012
8000 0.46107991 -2.7322063 0.18569571 -2.2734318 -0.21563894
8500 0.40367385 -2.7623279 0.27023252 -2.3606724 -0.038576129
9000 0.43104207 -2.7672424 0.25452132 -2.3383555 0.044351007
9500 0.38924411 -2.7231541 0.24926613 -2.3358562 -0.21910634
10000 0.44421944 -2.7677489 0.23376321 -2.3257506 0.034770807
Loop time of 0.446674 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.213113 (47.7111)
Neigh time (%) = 0.00897831 (2.01004)
Comm time (%) = 0.149779 (33.532)
Outpt time (%) = 0.0130295 (2.91701)
Other time (%) = 0.0617741 (13.8298)
Nlocal: 50 ave 55 max 41 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 87.75 ave 92 max 78 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 415 ave 481 max 301 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 1660
Ave neighs/atom = 8.3
Neighbor list builds = 671
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
4 = max bonds/atom
6 = max angles/atom
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
384 atoms
320 bonds
448 angles
192 dihedrals
0 impropers
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:216)
G vector = 0.142075
grid = 3 3 3
stencil order = 5
RMS precision = 0.000329493
using double precision FFTs
brick FFT buffer size/proc = 512 27 576
Memory usage per processor = 7.9487 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723443 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723443 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.224193 E_long = -361.169476 E_hbond = -69.322152
C_hbond = 235.000000 Press = -847.552598 Volume = 7447.236335
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 2.14577e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 203708 ave 203708 max 203708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
4 = max bonds/atom
6 = max angles/atom
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
384 atoms
320 bonds
448 angles
192 dihedrals
0 impropers
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:216)
G vector = 0.142075
grid = 3 3 3
stencil order = 5
RMS precision = 0.000329493
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.143211
grid = 3 3 3
stencil order = 4
RMS precision = 0.000315601
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.140124
grid = 3 3 3
stencil order = 3
RMS precision = 0.000354326
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.127333
grid = 3 3 3
stencil order = 2
RMS precision = 0.00055716
using double precision FFTs
WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:228)
G vector = 0.113516
grid = 9 9 9
stencil order = 1
RMS precision = 0.000864991
using double precision FFTs
brick FFT buffer size/proc = 360 243 360
Memory usage per processor = 6.52575 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 118.484313 KinEng = 0.000000 Temp = 0.000000
PotEng = 118.484313 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 529.430008 E_long = -288.614421 E_hbond = -69.322152
C_hbond = 235.000000 Press = -803.848888 Volume = 7447.236335
Loop time of 1.09673e-05 on 4 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 1.09673e-05 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 50927 ave 55516 max 46073 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 1 by 1 MPI processor grid
2000 atoms
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Memory usage per processor = 2.19122 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5774.4337 865.73356 874.29837 679.99459 888.89401
100 -5752.6028 652.10345 601.94922 670.57848 780.52664
Loop time of 1.19197 on 1 procs for 100 steps with 2000 atoms
Pair time (%) = 1.05228 (88.2801)
Neigh time (%) = 0.119006 (9.98397)
Comm time (%) = 0.00567245 (0.475887)
Outpt time (%) = 6.00815e-05 (0.0050405)
Other time (%) = 0.0149598 (1.25504)
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4144 ave 4144 max 4144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99875 ave 99875 max 99875 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99875
Ave neighs/atom = 49.9375
Neighbor list builds = 30
Dangerous builds = 10

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LAMMPS (10 Jan 2012)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 2 by 2 MPI processor grid
2000 atoms
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Memory usage per processor = 1.87326 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5774.4337 865.73356 874.29837 679.99459 888.89401
100 -5752.6028 652.10345 601.94922 670.57848 780.52664
Loop time of 0.324442 on 4 procs for 100 steps with 2000 atoms
Pair time (%) = 0.275492 (84.9125)
Neigh time (%) = 0.0300437 (9.26011)
Comm time (%) = 0.0126455 (3.89763)
Outpt time (%) = 5.33462e-05 (0.0164424)
Other time (%) = 0.00620759 (1.91331)
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2149.75 ave 2152 max 2148 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 24968.8 ave 25028 max 24876 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 99875
Ave neighs/atom = 49.9375
Neighbor list builds = 30
Dangerous builds = 10

161
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LAMMPS (10 Jan 2012)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
#pair_style resquared 4.0
#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.71598 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
Loop time of 0.744775 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.5056 (67.8863)
Neigh time (%) = 0.0121155 (1.62673)
Comm time (%) = 0.0133355 (1.79054)
Outpt time (%) = 0.0179069 (2.40434)
Other time (%) = 0.195817 (26.2921)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 232 ave 232 max 232 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2868 ave 2868 max 2868 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.72613 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981976 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720135 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222385 1187.4615
2400 2.1323063 -3.3152815 -1.1669962 0.76099867 1187.4615
2500 2.0866912 -3.269205 -1.176606 0.67971578 1187.4615
2600 2.0982825 -3.2774432 -1.1869918 0.90454676 1187.4615
2700 2.0482779 -3.2229456 -1.1928884 0.69425859 1187.4615
2800 1.9676351 -3.1400429 -1.1685864 0.7577946 1187.4615
2900 2.0421413 -3.2182319 -1.1866955 0.79375204 1187.4615
3000 2.1074018 -3.2869882 -1.2013002 0.18882145 1187.4615
3100 2.0467315 -3.2228162 -1.1821143 0.70508986 1187.4615
3200 2.1165018 -3.2983333 -1.1590455 0.5195734 1187.4615
3300 2.1523232 -3.3384994 -1.1803176 0.45229381 1187.4615
3400 2.0966131 -3.2797219 -1.1608863 0.75030508 1187.4615
3500 2.0623035 -3.2433952 -1.1409405 0.78443505 1187.4615
3600 2.0110509 -3.1874756 -1.1629634 0.54103399 1187.4615
3700 2.0105927 -3.1835726 -1.1894401 0.27445727 1187.4615
3800 1.9528229 -3.1230718 -1.1908005 0.53926039 1187.4615
3900 2.0657038 -3.2420623 -1.1608259 0.56113492 1187.4615
4000 2.0354627 -3.2069944 -1.2073941 0.5668484 1187.4615
Loop time of 0.780395 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.622527 (79.7707)
Neigh time (%) = 0.00560331 (0.71801)
Comm time (%) = 0.0139475 (1.78723)
Outpt time (%) = 0.0179484 (2.29991)
Other time (%) = 0.120369 (15.4241)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 222 ave 222 max 222 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2914 ave 2914 max 2914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2914
Ave neighs/atom = 7.285
Neighbor list builds = 47
Dangerous builds = 0

161
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LAMMPS (10 Jan 2012)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
#pair_style resquared 4.0
#pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.70503 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.49491311 1187.4615
Loop time of 0.276916 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.13188 (47.6245)
Neigh time (%) = 0.00327903 (1.18413)
Comm time (%) = 0.0477025 (17.2263)
Outpt time (%) = 0.0184636 (6.66759)
Other time (%) = 0.0755909 (27.2974)
Nlocal: 100 ave 113 max 79 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 139.75 ave 151 max 132 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 717 ave 880 max 487 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.70587 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.49491311 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981977 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720134 1187.4615
2300 2.0160348 -3.1912829 -1.1652127 0.98222397 1187.4615
2400 2.1323061 -3.3152813 -1.1669962 0.76099924 1187.4615
2500 2.0866909 -3.2692047 -1.1766059 0.67971739 1187.4615
2600 2.0982828 -3.2774435 -1.1869916 0.90454525 1187.4615
2700 2.0482779 -3.2229456 -1.1928882 0.69426441 1187.4615
2800 1.9676376 -3.1400474 -1.1685904 0.7577817 1187.4615
2900 2.0421364 -3.2182286 -1.1866999 0.79377489 1187.4615
3000 2.1074314 -3.2870216 -1.2013314 0.18876892 1187.4615
3100 2.0467964 -3.2228886 -1.1821044 0.70505639 1187.4615
3200 2.1167631 -3.298607 -1.1590547 0.51900634 1187.4615
3300 2.1528874 -3.339087 -1.1804887 0.45092936 1187.4615
3400 2.0979325 -3.2807362 -1.1607408 0.75035729 1187.4615
3500 2.0604373 -3.2416646 -1.1425421 0.7913285 1187.4615
3600 2.013392 -3.1897322 -1.1643385 0.56365647 1187.4615
3700 1.9922643 -3.1651575 -1.1883771 0.3074551 1187.4615
3800 1.9456148 -3.1160905 -1.1794166 0.73639236 1187.4615
3900 2.0237054 -3.1999536 -1.1869795 0.77500395 1187.4615
4000 2.0613642 -3.2364067 -1.2375068 0.53583637 1187.4615
Loop time of 0.294889 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.158921 (53.8917)
Neigh time (%) = 0.00147468 (0.500079)
Comm time (%) = 0.0758675 (25.7275)
Outpt time (%) = 0.0184799 (6.26672)
Other time (%) = 0.0401463 (13.614)
Nlocal: 100 ave 120 max 68 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 136 ave 151 max 126 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 732.5 ave 972 max 402 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2930
Ave neighs/atom = 7.325
Neighbor list builds = 47
Dangerous builds = 0

161
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LAMMPS (10 Jan 2012)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
#pair_style gayberne 1.0 3.0 1.0 4.0
#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
dump 1 all custom 100 dump.ellipse.resquared id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.71598 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 1.45024 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.21183 (83.5607)
Neigh time (%) = 0.0117629 (0.811095)
Comm time (%) = 0.00985646 (0.679641)
Outpt time (%) = 0.0178938 (1.23385)
Other time (%) = 0.198897 (13.7147)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 207 ave 207 max 207 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1886 ave 1886 max 1886 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.718 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
2800 1.9512215 0.15099708 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279164 2.0994516 1.3620722 1657.9242
3000 1.9067873 0.19775142 2.0931298 1.4157494 1657.9242
3100 1.9114596 0.19296349 2.1126573 1.411347 1657.9242
3200 1.9427389 0.15998518 2.0865326 1.3075167 1657.9242
3300 1.9111615 0.19317456 2.1216596 1.4309787 1657.9242
3400 1.9538371 0.14833029 2.1210138 1.2276245 1657.9242
3500 1.9244333 0.17929251 2.082515 1.3186851 1657.9242
3600 1.9511825 0.15107526 2.1197982 1.2271872 1657.9242
3700 1.9369717 0.16601219 2.0970211 1.2812847 1657.9242
3800 1.9418085 0.16093887 2.1231359 1.2354724 1657.9242
3900 1.9450402 0.15760907 2.139479 1.2392343 1657.9242
4000 1.9350094 0.16819308 2.1142355 1.2676502 1657.9242
Loop time of 2.46236 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 2.30114 (93.4523)
Neigh time (%) = 0.00465512 (0.189051)
Comm time (%) = 0.0134063 (0.544447)
Outpt time (%) = 0.0178988 (0.726895)
Other time (%) = 0.125267 (5.08728)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 209 ave 209 max 209 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

161
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LAMMPS (10 Jan 2012)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
#pair_style gayberne 1.0 3.0 1.0 4.0
#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
dump 1 all custom 100 dump.ellipse.resquared id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.70503 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 0.700645 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.315776 (45.0694)
Neigh time (%) = 0.00318927 (0.45519)
Comm time (%) = 0.202914 (28.961)
Outpt time (%) = 0.0198641 (2.83512)
Other time (%) = 0.158901 (22.6793)
Nlocal: 100 ave 109 max 96 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 116 ave 120 max 109 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 471.5 ave 499 max 455 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.70587 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384026 1657.9242
2800 1.9512215 0.15099708 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279165 2.0994516 1.3620722 1657.9242
3000 1.9067873 0.19775135 2.0931298 1.4157491 1657.9242
3100 1.9114597 0.19296344 2.1126573 1.4113468 1657.9242
3200 1.942739 0.15998509 2.0865326 1.3075162 1657.9242
3300 1.9111617 0.19317434 2.1216595 1.4309773 1657.9242
3400 1.9538374 0.14833002 2.121014 1.2276232 1657.9242
3500 1.9244329 0.17929295 2.0825158 1.3186873 1657.9242
3600 1.9511828 0.1510749 2.1197985 1.227186 1657.9242
3700 1.9369672 0.16601695 2.0970237 1.2813052 1657.9242
3800 1.9418088 0.16093858 2.1231366 1.2354749 1657.9242
3900 1.9450382 0.15761114 2.1394772 1.2392412 1657.9242
4000 1.9350119 0.16819038 2.1142388 1.2676423 1657.9242
Loop time of 0.718566 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.588593 (81.9121)
Neigh time (%) = 0.00123084 (0.171291)
Comm time (%) = 0.0711493 (9.90156)
Outpt time (%) = 0.0183669 (2.55604)
Other time (%) = 0.0392267 (5.45902)
Nlocal: 100 ave 107 max 97 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 117.5 ave 121 max 115 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 475.75 ave 511 max 446 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 2.05834 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.5232453 571.43371
500 1.0644427 -0.31382888 0 0.44395296 3.0018809 571.43371
1000 1 -0.42965445 0 0.28225032 2.9617821 571.43371
1500 1.0739874 -0.41189772 0 0.35267901 2.5626845 571.43371
2000 1 -0.40814279 0 0.30376197 2.923516 571.43371
2500 1.1930756 -0.38494744 0 0.46440874 2.8344861 571.43371
3000 1 -0.45104936 0 0.2608554 2.6581476 571.43371
3500 1.1157229 -0.42511668 0 0.36917176 2.548283 571.43371
4000 0.99847156 -0.38248232 0 0.32833434 2.7743789 571.43371
4500 0.99986482 -0.40537662 0 0.30643191 2.5662059 571.43371
5000 0.98699088 -0.42972933 0 0.27291418 2.8700314 571.43371
5500 0.99529887 -0.4099323 0 0.2986257 2.6108218 571.43371
6000 1 -0.37315745 0 0.33874731 2.6162108 571.43371
6500 1.0875953 -0.43070589 0 0.34355841 2.4212644 571.43371
7000 1 -0.37770812 0 0.33419664 2.3471175 571.43371
7500 1.0225134 -0.39148836 0 0.33644382 2.3372521 571.43371
8000 1 -0.4303298 0 0.28157496 2.6649863 571.43371
8500 1.0059281 -0.47968607 0 0.23643894 2.2977497 571.43371
9000 1 -0.47706517 0 0.23483959 2.3965332 571.43371
9500 1.034152 -0.43908184 0 0.29713592 2.0674205 571.43371
10000 1 -0.42405289 0 0.28785187 2.0333283 571.43371
Loop time of 0.345332 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.123751 (35.8355)
Neigh time (%) = 0.0470059 (13.6118)
Comm time (%) = 0.00936413 (2.71163)
Outpt time (%) = 0.0644042 (18.6499)
Other time (%) = 0.100806 (29.1912)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 50 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 955 ave 955 max 955 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 955
Ave neighs/atom = 2.27381
Neighbor list builds = 992
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 2.06205 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.5232453 571.43371
500 1.0951876 -0.33403931 0 0.44562996 3.2508527 571.43371
1000 1 -0.3731019 0 0.33880286 2.856717 571.43371
1500 1.0366879 -0.36031105 0 0.37771198 3.0202123 571.43371
2000 1 -0.41052955 0 0.30137522 2.8657413 571.43371
2500 1.1228407 -0.37042187 0 0.4289338 2.945087 571.43371
3000 1 -0.38445437 0 0.32745039 2.5940132 571.43371
3500 0.98347805 -0.45261096 0 0.24753175 2.7993099 571.43371
4000 1 -0.4065517 0 0.30535307 2.6210066 571.43371
4500 1.1209102 -0.40962998 0 0.38835132 2.4000886 571.43371
5000 1 -0.41496008 0 0.29694469 2.4655161 571.43371
5500 0.97933303 -0.39271136 0 0.30448049 2.7152128 571.43371
6000 1 -0.3939977 0 0.31790706 2.4334363 571.43371
6500 1.0519775 -0.50040975 0 0.24849803 2.5037073 571.43371
7000 1 -0.42318431 0 0.28872046 2.467848 571.43371
7500 1.1143879 -0.41498175 0 0.37835632 2.4540473 571.43371
8000 1 -0.46010124 0 0.25180353 2.5558114 571.43371
8500 1.0240867 -0.45394562 0 0.27510657 2.4271829 571.43371
9000 1 -0.4381772 0 0.27372756 2.4112541 571.43371
9500 1.0233668 -0.40460424 0 0.32393546 2.4071091 571.43371
10000 1 -0.4130336 0 0.29887116 2.3859891 571.43371
Loop time of 0.240091 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0312895 (13.0323)
Neigh time (%) = 0.0124956 (5.20452)
Comm time (%) = 0.0893214 (37.2031)
Outpt time (%) = 0.0469025 (19.5353)
Other time (%) = 0.0600821 (25.0247)
Nlocal: 105 ave 113 max 93 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 41.5 ave 48 max 34 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 235.25 ave 295 max 177 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 941
Ave neighs/atom = 2.24048
Neighbor list builds = 964
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 2.05834 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.5232453 571.43371
500 1.0990751 -0.36396768 0 0.41846911 2.5229954 575.44891
1000 1 -0.34609791 0 0.36580685 1.9739861 584.56264
1500 1.2112861 -0.39062708 0 0.47169327 1.5221639 587.13863
2000 1 -0.39956949 0 0.31233527 1.2499009 582.89761
2500 1.2236323 -0.40128446 0 0.46982521 1.4279626 569.92814
3000 1 -0.48849341 0 0.22341135 1.5094342 553.53722
3500 1.2404531 -0.63017461 0 0.25290984 1.7684919 535.11692
4000 1 -0.71551408 0 -0.0036093194 2.2079801 516.62236
4500 1.2253142 -0.76279403 0 0.10951296 2.6160527 503.09551
5000 1 -0.79031676 0 -0.078411998 3.0921313 499.00007
5500 1.2025712 -0.74032174 0 0.11579442 2.5892112 502.06255
6000 1 -0.6581062 0 0.053798563 2.0984473 510.32132
6500 1.2126636 -0.65632165 0 0.20697931 2.0771501 515.46227
7000 1 -0.68607157 0 0.02583319 1.9548014 518.03757
7500 1.2318514 -0.64168507 0 0.23527579 1.8621166 515.41686
8000 1 -0.69622159 0 0.015683171 2.1564483 508.61671
8500 1.2204376 -0.74071986 0 0.12811549 2.3967887 501.80266
9000 1 -0.79193368 0 -0.080028922 2.4413256 499.77059
9500 1.2151255 -0.75195108 0 0.11310255 2.4315907 500.33116
10000 1 -0.76066018 0 -0.048755416 2.4113886 502.50751
Loop time of 0.440015 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.136467 (31.0142)
Neigh time (%) = 0.0267653 (6.08282)
Comm time (%) = 0.00789261 (1.79371)
Outpt time (%) = 0.128578 (29.2214)
Other time (%) = 0.140311 (31.8879)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 50 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1124 ave 1124 max 1124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1124
Ave neighs/atom = 2.67619
Neighbor list builds = 562
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 2.06205 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.5232453 571.43371
500 1.0758737 -0.36090417 0 0.40501541 2.782759 574.95676
1000 1 -0.35701441 0 0.35489035 2.0579148 585.60492
1500 1.2368663 -0.37709732 0 0.50343367 1.4868643 587.08385
2000 1 -0.39362939 0 0.31827537 1.4238684 578.83266
2500 1.2272957 -0.423819 0 0.44989866 1.4547395 570.04942
3000 1 -0.49143403 0 0.22047073 1.5348969 554.87718
3500 1.2444908 -0.597618 0 0.2883409 1.8757604 536.90691
4000 1 -0.70133089 0 0.010573874 2.1399937 521.35928
4500 1.2212572 -0.74525028 0 0.12416857 2.7605953 507.52559
5000 1 -0.77887442 0 -0.066969662 2.9849792 501.10169
5500 1.2118683 -0.76479769 0 0.097937148 2.7555194 505.25255
6000 1 -0.64166654 0 0.070238224 2.4653816 510.17292
6500 1.2230732 -0.66072614 0 0.20998549 2.0855543 517.97007
7000 1 -0.61750407 0 0.094400687 1.9316563 520.97755
7500 1.2289276 -0.68159213 0 0.19328728 2.0003789 520.18556
8000 1 -0.69786226 0 0.014042499 2.1485637 517.24977
8500 1.2206044 -0.75028089 0 0.11867321 2.3924356 513.28362
9000 1 -0.75191705 0 -0.040012285 2.521768 509.91505
9500 1.2149548 -0.71491732 0 0.15001477 2.3827722 508.86228
10000 1 -0.71239141 0 -0.00048664424 2.3193862 508.75244
Loop time of 0.334578 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.034201 (10.2221)
Neigh time (%) = 0.00749511 (2.24017)
Comm time (%) = 0.0808396 (24.1616)
Outpt time (%) = 0.0899565 (26.8865)
Other time (%) = 0.122086 (36.4895)
Nlocal: 105 ave 107 max 104 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 43.5 ave 45 max 42 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 279.5 ave 296 max 265 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 1118
Ave neighs/atom = 2.6619
Neighbor list builds = 565
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 112 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
862 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 2.05873 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1440102 2444.4558
1000 0.1 -3.0915465 0 -3.0503052 0.010017516 2444.4558
2000 0.1 -3.0826487 0 -3.0414074 -0.42021097 2444.4558
3000 0.089819692 -3.07584 0 -3.0387972 -0.25257042 2444.4558
4000 0.098489874 -3.0667093 0 -3.0260907 -0.25511521 2444.4558
5000 0.11379986 -3.0557087 0 -3.0087762 -0.080886978 2444.4558
6000 0.11269179 -3.04532 0 -2.9988445 -0.33387724 2444.4558
7000 0.1 -3.0380598 0 -2.9968185 -0.32430244 2444.4558
8000 0.1 -3.0346458 0 -2.9934045 -0.38022997 2444.4558
9000 0.1 -3.0323928 0 -2.9911515 -0.42944097 2444.4558
10000 0.1 -3.0354969 0 -2.9942556 -0.3547036 2444.4558
11000 0.11248007 -3.0371526 0 -2.9907643 -0.42222237 2444.4558
12000 0.10241295 -3.0422315 0 -2.9999951 -0.24193736 2444.4558
13000 0.11139984 -3.044969 0 -2.9990263 -0.32692165 2444.4558
14000 0.099297055 -3.0415792 0 -3.0006278 -0.34441013 2444.4558
15000 0.11494243 -3.045278 0 -2.9978742 -0.26868839 2444.4558
16000 0.11211716 -3.0460201 0 -2.9997815 -0.27620024 2444.4558
17000 0.11246574 -3.0461857 0 -2.9998034 -0.31782055 2444.4558
18000 0.11194476 -3.0440786 0 -2.9979112 -0.35902467 2444.4558
19000 0.11200621 -3.0473992 0 -3.0012064 -0.25540459 2444.4558
20000 0.10818968 -3.0456459 0 -3.0010271 -0.29452342 2444.4558
Loop time of 5.76747 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 4.63048 (80.2861)
Neigh time (%) = 0.297429 (5.15701)
Comm time (%) = 0.0432248 (0.749459)
Outpt time (%) = 0.0548413 (0.950872)
Other time (%) = 0.741497 (12.8565)
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 145 ave 145 max 145 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14369 ave 14369 max 14369 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14369
Ave neighs/atom = 8.33469
Neighbor list builds = 717
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
2 by 2 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 112 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
862 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 2.06212 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1440102 2444.4558
1000 0.081958665 -3.0927273 0 -3.0589265 -0.021850399 2444.4558
2000 0.082641883 -3.0850764 0 -3.0509938 -0.44968978 2444.4558
3000 0.092293442 -3.0748001 0 -3.0367371 -0.25358115 2444.4558
4000 0.096012911 -3.0565129 0 -3.0169159 -0.027674947 2444.4558
5000 0.1 -3.0465555 0 -3.0053142 -0.09934336 2444.4558
6000 0.11642983 -3.0390782 0 -2.991061 -0.21038719 2444.4558
7000 0.11597773 -3.0331763 0 -2.9853456 -0.46354952 2444.4558
8000 0.11937909 -3.0305563 0 -2.9813228 -0.30779188 2444.4558
9000 0.11109992 -3.0274146 0 -2.9815956 -0.52451724 2444.4558
10000 0.11600378 -3.0164577 0 -2.9686163 -0.35721513 2444.4558
11000 0.11403444 -3.0138385 0 -2.9668092 -0.45128937 2444.4558
12000 0.11732466 -3.0220572 0 -2.973671 -0.26756468 2444.4558
13000 0.10909933 -3.0270216 0 -2.9820276 -0.39570586 2444.4558
14000 0.10530217 -3.0326565 0 -2.9892285 -0.1708647 2444.4558
15000 0.11252086 -3.0326775 0 -2.9862724 -0.41750799 2444.4558
16000 0.10635548 -3.0310857 0 -2.9872233 -0.27111401 2444.4558
17000 0.11718463 -3.036313 0 -2.9879845 -0.34485392 2444.4558
18000 0.11632659 -3.0376748 0 -2.9897002 -0.2781061 2444.4558
19000 0.11302219 -3.0324168 0 -2.985805 -0.35512798 2444.4558
20000 0.11916746 -3.0379931 0 -2.9888469 -0.30162295 2444.4558
Loop time of 1.9566 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 1.17991 (60.3041)
Neigh time (%) = 0.0769351 (3.93207)
Comm time (%) = 0.391056 (19.9865)
Outpt time (%) = 0.0432984 (2.21293)
Other time (%) = 0.265402 (13.5644)
Nlocal: 431 ave 486 max 376 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 95 ave 119 max 75 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 3599 ave 4160 max 3136 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 14396
Ave neighs/atom = 8.35035
Neighbor list builds = 708
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 46.8382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865618 -5.760326 0 -4.6223462 0.19586078
200 0.75643081 -5.7572862 0 -4.6226445 0.22641252
300 0.74927357 -5.7463992 0 -4.6224932 0.2973801
400 0.7404924 -5.7329247 0 -4.6221905 0.37767073
500 0.73092032 -5.7182616 0 -4.6218854 0.46900679
600 0.72315678 -5.706314 0 -4.621583 0.5348031
700 0.71597165 -5.6952207 0 -4.6212675 0.59549602
800 0.71194748 -5.6889042 0 -4.6209871 0.63784817
900 0.70596464 -5.6796285 0 -4.6206857 0.68573109
1000 0.70323336 -5.67534 0 -4.6204941 0.7069076
Loop time of 20.1772 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 12.8361 (63.6167)
Neigh time (%) = 7.34329e-05 (0.00036394)
Comm time (%) = 1.08434 (5.3741)
Outpt time (%) = 0.0102942 (0.051019)
Other time (%) = 6.24641 (30.9578)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69905 ave 69905 max 69905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 14.5128 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865619 -5.7603258 0 -4.622346 0.19586113
200 0.75643076 -5.7572857 0 -4.6226439 0.22641355
300 0.74927365 -5.7463989 0 -4.6224928 0.29738053
400 0.74049513 -5.7329265 0 -4.6221881 0.37765479
500 0.73092165 -5.7182628 0 -4.6218846 0.46899675
600 0.72307341 -5.7061845 0 -4.6215786 0.53536825
700 0.71593631 -5.6951696 0 -4.6212694 0.59644919
800 0.71106107 -5.6875486 0 -4.6209611 0.6450072
900 0.70789378 -5.6825117 0 -4.6206752 0.67079907
1000 0.70324302 -5.6753075 0 -4.6204471 0.71004301
Loop time of 8.45152 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 5.1208 (60.5903)
Neigh time (%) = 5.52535e-05 (0.00065377)
Comm time (%) = 1.60643 (19.0076)
Outpt time (%) = 0.032979 (0.390213)
Other time (%) = 1.69126 (20.0113)
Nlocal: 64000 ave 64090 max 63900 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 30521 ave 30604 max 30461 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 58.5637 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.7599844 -6.1430228 0 -5.0030506 -0.43702259
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563905
300 0.7502998 -6.1286575 0 -5.0032122 -0.33104598
400 0.73999173 -6.1132483 0 -5.003265 -0.24002836
500 0.73224837 -6.101694 0 -5.0033257 -0.16523366
600 0.72448052 -6.0900828 0 -5.0033662 -0.099466624
700 0.71878723 -6.0815904 0 -5.0034138 -0.044361885
800 0.71444388 -6.0751019 0 -5.0034403 -0.0083893389
900 0.70949961 -6.0676978 0 -5.0034525 0.032534654
1000 0.70480647 -6.0606748 0 -5.0034693 0.067358025
Loop time of 43.8997 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 35.1574 (80.0858)
Neigh time (%) = 8.29697e-05 (0.000188998)
Comm time (%) = 1.61756 (3.68467)
Outpt time (%) = 0.011915 (0.0271413)
Other time (%) = 7.1127 (16.2022)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 141753 ave 141753 max 141753 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 20.3741 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.75998442 -6.1430228 0 -5.0030506 -0.4370226
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563885
300 0.75029998 -6.1286577 0 -5.0032121 -0.33104745
400 0.73999268 -6.1132497 0 -5.003265 -0.24002923
500 0.73223459 -6.1016733 0 -5.0033257 -0.16512674
600 0.72450196 -6.0901153 0 -5.0033666 -0.099408327
700 0.71915302 -6.0821406 0 -5.0034153 -0.045922554
800 0.71398822 -6.0744174 0 -5.0034392 -0.0064880998
900 0.70918338 -6.0672194 0 -5.0034485 0.032885247
1000 0.70513415 -6.0611556 0 -5.0034585 0.063293271
Loop time of 20.8409 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 14.4203 (69.1925)
Neigh time (%) = 5.91874e-05 (0.000283997)
Comm time (%) = 4.66054 (22.3625)
Outpt time (%) = 0.0455028 (0.218335)
Other time (%) = 1.71444 (8.22633)
Nlocal: 64000 ave 64103 max 63848 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 64409.2 ave 64479 max 64338 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 1 by 1 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
1 by 1 by 1 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector = 0.210111
grid = 108 108 108
stencil order = 5
RMS precision = 8.76251e-06
using double precision FFTs
brick FFT buffer size/proc = 1520875 1259712 158700
Memory usage per processor = 266.913 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.5 0 -2366643.7 -449.93537 4242016.4
100 411.69679 -2392428.5 0 -2376695.2 7046.7022 4308883.6
200 401.28406 -2394152.4 0 -2378817.1 3243.2514 4334284.6
Loop time of 174.691 on 1 procs for 200 steps with 295650 atoms
Pair time (%) = 12.053 (6.89962)
Kspce time (%) = 80.9936 (46.3638)
Neigh time (%) = 0.013356 (0.00764546)
Comm time (%) = 0.347907 (0.199155)
Outpt time (%) = 0.00172615 (0.000988114)
Other time (%) = 81.2818 (46.5288)
FFT time (% of Kspce) = 56.1923 (69.3786)
FFT Gflps 3d (1d only) = 1.25956 2.99555
Nlocal: 295650 ave 295650 max 295650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 226982 ave 226982 max 226982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

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LAMMPS (10 Jan 2012)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 2 by 2 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
2 by 1 by 2 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector = 0.210111
grid = 108 108 108
stencil order = 5
RMS precision = 8.76251e-06
using double precision FFTs
brick FFT buffer size/proc = 427915 314928 84180
Memory usage per processor = 80.0627 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.5 0 -2366643.7 -449.93522 4242016.4
100 411.69683 -2392428.5 0 -2376695.2 7046.7136 4308883.6
200 401.28395 -2394152.4 0 -2378817.1 3243.2713 4334284.6
Loop time of 62.4573 on 4 procs for 200 steps with 295650 atoms
Pair time (%) = 5.04743 (8.08141)
Kspce time (%) = 35.3904 (56.6633)
Neigh time (%) = 0.00620693 (0.00993788)
Comm time (%) = 0.473388 (0.757939)
Outpt time (%) = 0.000503302 (0.000805833)
Other time (%) = 21.5394 (34.4866)
FFT time (% of Kspce) = 22.1085 (62.4703)
FFT Gflps 3d (1d only) = 3.20138 11.8522
Nlocal: 73912.5 ave 74223 max 73638 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 105257 ave 105797 max 104698 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

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LAMMPS (10 Jan 2012)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 1 by 1 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 237705 184320 40365
Memory usage per processor = 757.714 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0401 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5754 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3907 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.8336 (sec) ----------------
TotEng = -233301.4802 KinEng = 123222.6026 Temp = 214.7785
PotEng = -356524.0828 E_bond = 13098.4631 E_angle = 56766.9481
E_dihed = 45556.8121 E_impro = 1313.9420 E_vdwl = -40863.8988
E_coul = 1705023.3608 E_long = -2137419.7102 Press = -1634.3633
Volume = 2522232.7977
---------------- Step 200 ----- CPU = 72.2618 (sec) ----------------
TotEng = -308340.6857 KinEng = 108944.3257 Temp = 189.8913
PotEng = -417285.0114 E_bond = 9579.0680 E_angle = 47373.8383
E_dihed = 39847.6180 E_impro = 967.6100 E_vdwl = -23634.8218
E_coul = 1646565.2623 E_long = -2137983.5863 Press = -1185.9778
Volume = 2554683.5150
Loop time of 72.2618 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.1078 (13.9878)
Bond time (%) = 29.9182 (41.4025)
Kspce time (%) = 7.29844 (10.1)
Neigh time (%) = 1.64225 (2.27264)
Comm time (%) = 0.614946 (0.850997)
Outpt time (%) = 0.00137877 (0.00190803)
Other time (%) = 22.6787 (31.3841)
FFT time (% of Kspce) = 5.23688 (71.7535)
FFT Gflps 3d (1d only) = 1.70695 3.00498
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161678 ave 161678 max 161678 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

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LAMMPS (10 Jan 2012)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 2 by 2 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 68635 46080 17649
Memory usage per processor = 249.821 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.2605 (sec) ----------------
TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785
PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463
E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548
E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527
Volume = 2522232.7976
---------------- Step 200 ----- CPU = 23.7724 (sec) ----------------
TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871
PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551
E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292
E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181
Volume = 2554683.4248
Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.55113 (19.1446)
Bond time (%) = 7.43137 (31.2604)
Kspce time (%) = 3.8699 (16.2789)
Neigh time (%) = 0.51208 (2.15409)
Comm time (%) = 0.544156 (2.28902)
Outpt time (%) = 0.000452995 (0.00190555)
Other time (%) = 6.86337 (28.8711)
FFT time (% of Kspce) = 1.94085 (50.1524)
FFT Gflps 3d (1d only) = 4.60577 11.8123
Nlocal: 64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 70640.8 ave 70645 max 70636 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

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LAMMPS (10 Jan 2012)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.80047 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4422116e-13 -4.919366e-13 -4.9777247e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.082279 on 1 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.78407e-10
Force max component initial, final = 1960.27 3.42777e-10
Final line search alpha, max atom move = 1 3.42777e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0646594 (78.5855)
Neigh time (%) = 0.00100803 (1.22514)
Comm time (%) = 0.00203061 (2.46796)
Outpt time (%) = 2.09808e-05 (0.0254996)
Other time (%) = 0.01456 (17.6959)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

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LAMMPS (10 Jan 2012)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.77702 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.5540246e-13 -4.9541511e-13 -5.0200254e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0306363 on 4 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.85569e-10
Force max component initial, final = 1960.27 3.45689e-10
Final line search alpha, max atom move = 1 3.45689e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0165715 (54.0909)
Neigh time (%) = 0.000261545 (0.85371)
Comm time (%) = 0.00607055 (19.8149)
Outpt time (%) = 2.06828e-05 (0.0675108)
Other time (%) = 0.00771207 (25.173)
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6350 max 4305 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

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LAMMPS (10 Jan 2012)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.8492869 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 2.05409 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.4364576 444.44898
1000 0.11974254 -3.0876892 0 -2.9853378 -0.037066341 440.70336
2000 0.12086797 -3.0886512 0 -2.9853378 -0.39890862 444.27124
3000 0.11671309 -3.0840074 0 -2.9842455 -0.34866631 442.86992
4000 0.12339115 -3.1000529 0 -2.9945828 -0.049706317 438.90862
5000 0.10860594 -3.0866045 0 -2.9937722 -0.47982999 443.91419
6000 0.11839788 -3.0929689 0 -2.9917669 -0.033460572 442.61903
7000 0.12194527 -3.0835584 0 -2.9793242 -0.13984271 443.27826
8000 0.11671309 -3.0862884 0 -2.9865265 0.073966694 441.62891
9000 0.12449823 -3.0880806 0 -2.9816643 0.286535 439.19731
10000 0.12475263 -3.0830722 0 -2.9764384 0.38108754 440.41873
11000 0.11198118 -3.0743549 0 -2.9786377 0.67596956 438.41816
12000 0.10823034 -3.0621355 0 -2.9696244 0.6649774 441.05346
13000 0.11942981 -3.0579575 0 -2.9558734 1.0886185 437.64369
14000 0.12310404 -3.051382 0 -2.9461573 0.8709419 445.45575
15000 0.11148461 -3.0402208 0 -2.944928 1.0042519 451.82353
16000 0.12322343 -3.0415521 0 -2.9362254 0.75832833 456.81935
17000 0.12311138 -3.0300343 0 -2.9248034 1.0485025 452.83229
18000 0.12062553 -3.0261658 0 -2.9230597 1.3986216 451.63454
19000 0.11959722 -3.01431 0 -2.9120828 1.3963118 457.84103
20000 0.1223325 -3.001585 0 -2.8970199 1.1239303 470.04007
21000 0.12083113 -3.0284422 0 -2.9251604 0.76695976 472.84172
22000 0.12468602 -3.0235245 0 -2.9169477 0.63519991 474.9289
23000 0.1121845 -3.033121 0 -2.93723 0.50655931 470.8489
24000 0.12205846 -3.0311794 0 -2.9268485 0.86936481 470.95605
25000 0.11671309 -3.0309847 0 -2.9312228 0.79942435 469.32518
26000 0.11557645 -3.0148577 0 -2.9160673 1.1178134 474.47516
27000 0.10570593 -3.0092032 0 -2.9188498 1.16049 472.48381
28000 0.11149859 -3.0023437 0 -2.907039 1.3034926 476.52895
29000 0.12150147 -2.9856999 0 -2.8818451 1.576077 476.13435
30000 0.11570444 -2.9624626 0 -2.8635628 1.5924214 479.30483
Loop time of 2.37765 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.74991 (73.5984)
Neigh time (%) = 0.0673277 (2.83169)
Comm time (%) = 0.0314863 (1.32426)
Outpt time (%) = 0.041635 (1.7511)
Other time (%) = 0.487288 (20.4945)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 110 ave 110 max 110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3711 ave 3711 max 3711 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3711
Ave neighs/atom = 8.83571
Neighbor list builds = 621
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.05417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11570444 -2.9624626 0 -2.8635628 1.5928299 479.18192
31000 0.11127312 -3.0236091 0 -2.928497 -0.42641663 488.03115
32000 0.11671309 -3.0403133 0 -2.9405514 -0.61477383 482.6357
33000 0.1064338 -3.0543214 0 -2.9633459 0.05053527 477.25528
34000 0.11379897 -3.0605823 0 -2.9633112 -0.35440488 480.63527
35000 0.11347154 -3.0266072 0 -2.929616 -0.63550997 492.44164
36000 0.11559268 -3.0426571 0 -2.9438529 0.10866887 480.22106
37000 0.11536103 -3.0427298 0 -2.9441236 -0.22501835 487.22831
38000 0.11408836 -3.0413739 0 -2.9438555 -0.43474089 483.01876
39000 0.12197337 -3.0486194 0 -2.9443612 0.00099966915 482.72141
40000 0.10928369 -3.037574 0 -2.9441625 -0.16523601 481.54733
41000 0.11891319 -3.0458468 0 -2.9442043 -0.41056942 485.92683
42000 0.11869627 -3.0456605 0 -2.9442035 -0.039105165 481.87338
43000 0.12196802 -3.0483028 0 -2.9440492 -0.36036 485.66289
44000 0.11136469 -3.0393148 0 -2.9441245 -0.45635454 484.16586
45000 0.1143683 -3.0421148 0 -2.9443571 -0.060706621 486.97264
46000 0.1066384 -3.035115 0 -2.9439646 -0.25781902 481.22702
47000 0.11688473 -3.0440763 0 -2.9441677 -0.28936877 481.73579
48000 0.11710026 -3.0545023 0 -2.9544095 -0.039191015 480.77901
49000 0.11164285 -3.0497188 0 -2.9542907 -0.16529304 481.95614
50000 0.11585744 -3.0417673 0 -2.9427368 -0.23962959 483.62182
51000 0.12149422 -3.0465877 0 -2.942739 -0.20755029 481.20963
52000 0.11812513 -3.0435892 0 -2.9426203 -0.32437686 485.36167
53000 0.1124516 -3.03874 0 -2.9426207 -0.23019183 484.21046
54000 0.1144055 -3.040525 0 -2.9427355 -0.16004524 483.89709
55000 0.11932966 -3.0447354 0 -2.9427369 -0.30835161 484.4687
56000 0.1217659 -3.0468199 0 -2.942739 -0.23163285 482.61402
57000 0.11522266 -3.0516101 0 -2.9531222 -0.17640213 484.37016
58000 0.11424257 -3.0506964 0 -2.9530462 -0.24886576 481.40236
59000 0.11626176 -3.0423269 0 -2.9429508 -0.3377255 484.34589
60000 0.11322673 -3.0398445 0 -2.9430626 -0.0027517474 481.19045
Loop time of 2.15946 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.73037 (80.1299)
Neigh time (%) = 0.067282 (3.11568)
Comm time (%) = 0.0314145 (1.45474)
Outpt time (%) = 0.039238 (1.81703)
Other time (%) = 0.291153 (13.4827)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3581 ave 3581 max 3581 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3581
Ave neighs/atom = 8.52619
Neighbor list builds = 627
Dangerous builds = 0

172
examples/indent/log.indent.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.8492869 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 2.06073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.4364576 444.44898
1000 0.11573595 -3.0964873 0 -2.9975606 -0.20452577 441.75296
2000 0.11519605 -3.0960246 0 -2.9975594 -0.38140765 442.24623
3000 0.11367906 -3.0839597 0 -2.9867912 -0.42587846 444.50683
4000 0.11618844 -3.0860897 0 -2.9867762 -0.041588892 439.76178
5000 0.11327789 -3.0848614 0 -2.9880358 -0.48908114 446.10767
6000 0.12058424 -3.0869438 0 -2.983873 0.011479332 440.48452
7000 0.11772522 -3.0833477 0 -2.9827207 -0.090395475 442.48351
8000 0.12533514 -3.0970033 0 -2.9898715 0.13265726 441.15042
9000 0.1198683 -3.0867062 0 -2.9842473 0.340532 439.38624
10000 0.12234014 -3.0835007 0 -2.9789291 0.28405153 441.85872
11000 0.11082436 -3.0754796 0 -2.9807511 0.62206175 441.23576
12000 0.10842719 -3.0646379 0 -2.9719584 0.65396032 442.56232
13000 0.11686417 -3.0600388 0 -2.9601477 1.0043055 438.41699
14000 0.12557378 -3.0570017 0 -2.949666 0.85725525 442.01753
15000 0.11934084 -3.0498848 0 -2.9478768 1.039414 451.6596
16000 0.12576913 -3.045218 0 -2.9377154 1.3482054 441.18584
17000 0.11546547 -3.0348364 0 -2.9361409 1.6321324 439.40029
18000 0.12148737 -3.0221156 0 -2.9182728 1.6092057 449.17017
19000 0.11883764 -3.0036776 0 -2.9020997 1.5204069 447.04095
20000 0.1116568 -3.0038165 0 -2.9083766 1.4080056 461.66692
21000 0.11344555 -2.9898881 0 -2.8929192 1.134675 473.88035
22000 0.11948255 -3.0240618 0 -2.9219327 0.8071654 473.3811
23000 0.1167118 -3.012886 0 -2.9131252 1.1366688 470.07014
24000 0.1139144 -3.0145927 0 -2.9172231 0.75037492 475.10421
25000 0.11524573 -3.0017351 0 -2.9032274 1.056555 470.50461
26000 0.11964798 -3.0134647 0 -2.9111942 1.4494695 466.24739
27000 0.12346176 -3.0083111 0 -2.9027807 1.5494444 469.95245
28000 0.12260647 -2.9956772 0 -2.8908779 1.7319832 470.55197
29000 0.12231691 -2.9866104 0 -2.8820586 1.9114487 468.06771
30000 0.1134125 -2.9719856 0 -2.8750449 1.735366 474.78395
Loop time of 1.0663 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.451498 (42.3424)
Neigh time (%) = 0.0176335 (1.6537)
Comm time (%) = 0.308133 (28.8973)
Outpt time (%) = 0.0310341 (2.91044)
Other time (%) = 0.258004 (24.1961)
Nlocal: 105 ave 116 max 91 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 94 ave 100 max 86 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 925.75 ave 1100 max 749 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3703
Ave neighs/atom = 8.81667
Neighbor list builds = 611
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.06079 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.1134125 -2.9719856 0 -2.8750449 1.7378746 474.09862
31000 0.11671309 -3.0217195 0 -2.9219576 -0.50572599 490.27459
32000 0.11261625 -2.9897143 0 -2.8934542 -0.70997911 493.98951
33000 0.11498233 -3.0201655 0 -2.921883 0.38808051 478.58058
34000 0.11444975 -3.0198659 0 -2.9220386 0.14411722 480.00811
35000 0.11671309 -3.0101633 0 -2.9104013 -0.31038903 489.29194
36000 0.11832748 -3.033948 0 -2.9328062 0.28268025 485.97741
37000 0.12386678 -3.0497535 0 -2.9438769 -0.096409691 481.17214
38000 0.10970544 -3.0368866 0 -2.9431146 -0.57192593 488.84185
39000 0.11752117 -3.0438396 0 -2.9433869 -0.13110937 481.57511
40000 0.1278535 -3.0527156 0 -2.9434313 -0.020633536 480.95061
41000 0.11847117 -3.0444569 0 -2.9431922 -0.32009068 483.3596
42000 0.10998018 -3.0371983 0 -2.9431914 -0.11913829 485.08859
43000 0.12322652 -3.0486827 0 -2.9433534 -0.018180953 480.95501
44000 0.1165669 -3.0437041 0 -2.9440672 -0.22685911 483.00453
45000 0.12003564 -3.046557 0 -2.9439551 -0.24287632 485.55689
46000 0.11627326 -3.0433775 0 -2.9439916 0.0072953137 481.95676
47000 0.12002477 -3.0467416 0 -2.944149 -0.33751499 484.3466
48000 0.11111324 -3.0390436 0 -2.9440683 -0.077328891 479.23853
49000 0.12033918 -3.0470467 0 -2.9441854 -0.092900033 482.77182
50000 0.12148513 -3.0361756 0 -2.9323348 -0.29588104 483.00856
51000 0.11671309 -3.044055 0 -2.9442931 -0.15159 481.04897
52000 0.12315525 -3.0496811 0 -2.9444127 -0.18861076 484.19046
53000 0.11997084 -3.0468807 0 -2.9443342 -0.28251306 484.17158
54000 0.1213341 -3.0480047 0 -2.9442929 -0.35292761 488.50849
55000 0.11788218 -3.045133 0 -2.9443718 -0.18025658 482.13662
56000 0.12296487 -3.049555 0 -2.9444493 -0.139658 483.25481
57000 0.11729933 -3.0447115 0 -2.9444485 -0.24740079 482.47832
58000 0.11901212 -3.0460985 0 -2.9443714 -0.2523838 484.38143
59000 0.11452134 -3.0424137 0 -2.9445252 -0.13008427 481.35053
60000 0.1121022 -3.0402301 0 -2.9444094 -0.21943641 488.19161
Loop time of 0.960824 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.445671 (46.3843)
Neigh time (%) = 0.0183511 (1.90994)
Comm time (%) = 0.31143 (32.4128)
Outpt time (%) = 0.030867 (3.21255)
Other time (%) = 0.154504 (16.0804)
Nlocal: 105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 91.25 ave 98 max 83 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 895.25 ave 1042 max 713 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3581
Ave neighs/atom = 8.52619
Neighbor list builds = 633
Dangerous builds = 0

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examples/indent/log.indent.min.9Jan12.linux.1 Normal file
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LAMMPS (10 Jan 2012)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1801584 0 -3.1801584 -1.3058039 441.04528
20 0 -3.1831474 0 -3.1831474 -1.2345239 438.53563
30 0 -3.1861452 0 -3.1861452 -1.0910037 438.78112
40 0 -3.1901049 0 -3.1901049 -0.84865219 435.53833
50 0 -3.1904808 0 -3.1904808 -0.81510177 435.53833
60 0 -3.1906458 0 -3.1906458 -0.78391531 435.53833
70 0 -3.190782 0 -3.190782 -0.75177925 435.53833
74 0 -3.1908431 0 -3.1908431 -0.73891705 435.53833
Loop time of 0.0452979 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058073 -3.19084306284
Force two-norm initial, final = 6.74302 0.560627
Force max component initial, final = 1.46877 0.0659033
Final line search alpha, max atom move = 0.00643442 0.00042405
Iterations, force evaluations = 74 411
Pair time (%) = 0.0378823 (83.6294)
Neigh time (%) = 0.0004251 (0.938456)
Comm time (%) = 0.00039506 (0.872137)
Outpt time (%) = 0.0027256 (6.01706)
Other time (%) = 0.00386977 (8.54295)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.246435 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624129 -0.73821499 435.95254
80 0 -3.1521235 0 -3.1418193 -0.2610823 435.95258
90 0 -3.172501 0 -3.1715058 -0.36505563 436.10565
100 0 -3.1770944 0 -3.1759303 -0.36789247 436.07336
110 0 -3.179003 0 -3.1778726 -0.34166118 435.98826
120 0 -3.1801576 0 -3.1792109 -0.29566094 435.68693
130 0 -3.1806637 0 -3.1798826 -0.25109465 435.29031
140 0 -3.1811622 0 -3.180374 -0.18867263 434.93784
150 0 -3.1811721 0 -3.1804507 -0.17763419 433.08677
156 0 -3.1811921 0 -3.1804771 -0.17272768 433.95891
Loop time of 0.050761 on 1 procs for 82 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241291014 -3.18047400548 -3.18047707458
Force two-norm initial, final = 1731.02 0.522006
Force max component initial, final = 1265.65 0.163418
Final line search alpha, max atom move = 0.00298294 0.000487467
Iterations, force evaluations = 82 418
Pair time (%) = 0.0383368 (75.5241)
Neigh time (%) = 0.00255942 (5.04211)
Comm time (%) = 0.000461578 (0.909317)
Outpt time (%) = 0.00308037 (6.06838)
Other time (%) = 0.00632286 (12.4561)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3590 ave 3590 max 3590 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3590
Ave neighs/atom = 8.54762
Neighbor list builds = 24
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
156 0 -3.1811921 0 -0.18185886 -0.17245392 434.6478
160 0 -3.0132059 0 -2.1460246 1.2550302 434.64724
170 0 -3.0137792 0 -2.9636783 1.6528322 434.64063
180 0 -3.0743259 0 -3.0588429 1.3080533 434.60386
190 0 -3.0950888 0 -3.0847726 1.180783 434.74413
200 0 -3.1004681 0 -3.0919512 1.1557783 434.83863
210 0 -3.1023546 0 -3.0946252 1.2001339 432.54115
220 0 -3.1026809 0 -3.0951731 1.2181969 432.54115
230 0 -3.1038605 0 -3.0963027 1.2945176 431.63227
240 0 -3.1039956 0 -3.0965499 1.310294 431.25237
250 0 -3.1041599 0 -3.0968021 1.3296476 432.71979
251 0 -3.1041297 0 -3.0968045 1.3346958 431.22872
Loop time of 0.0553658 on 1 procs for 95 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.181858864004 -3.09680212193 -3.09680447766
Force two-norm initial, final = 1765.16 0.902559
Force max component initial, final = 924.657 0.24895
Final line search alpha, max atom move = 0.00129143 0.0003215
Iterations, force evaluations = 95 443
Pair time (%) = 0.0411718 (74.3632)
Neigh time (%) = 0.00282073 (5.09472)
Comm time (%) = 0.000554085 (1.00077)
Outpt time (%) = 0.0038321 (6.92142)
Other time (%) = 0.00698709 (12.6199)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 107 ave 107 max 107 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3652 ave 3652 max 3652 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3652
Ave neighs/atom = 8.69524
Neighbor list builds = 26
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
251 0 -3.1041297 0 2.0179509 1.3331076 431.74246
260 0 -2.4519149 0 -2.2477274 6.6083811 432.289
270 0 -2.8311972 0 -2.7410091 4.0667972 439.44435
280 0 -2.9064388 0 -2.8740571 3.5711821 443.61256
290 0 -2.9442479 0 -2.9277565 3.2265202 448.51793
300 0 -2.9590906 0 -2.9459633 3.1004821 452.45083
310 0 -2.9633194 0 -2.9509764 3.0506152 453.58916
320 0 -2.9656103 0 -2.9548573 3.0261904 453.95834
328 0 -2.9669235 0 -2.9563046 3.008729 453.95834
Loop time of 0.0352268 on 1 procs for 77 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.0179508962 -2.95630432347 -2.95630458026
Force two-norm initial, final = 2330.77 8.17726
Force max component initial, final = 1037.35 1.89183
Final line search alpha, max atom move = 1.61036e-06 3.04651e-06
Iterations, force evaluations = 77 268
Pair time (%) = 0.0257685 (73.1503)
Neigh time (%) = 0.00191307 (5.43072)
Comm time (%) = 0.000335932 (0.953625)
Outpt time (%) = 0.00268078 (7.61005)
Other time (%) = 0.00452852 (12.8553)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3865 ave 3865 max 3865 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3865
Ave neighs/atom = 9.20238
Neighbor list builds = 17
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
328 0 -2.9669235 0 7.5568154 3.0093541 453.86405
330 0 -2.7876408 0 4.0929345 4.3904808 453.51058
340 0 -2.2554147 0 -1.8086972 8.9255431 452.26883
350 0 -2.5599367 0 -2.4765088 7.0889392 454.95321
360 0 -2.708787 0 -2.6627879 6.0591926 454.89369
370 0 -2.751066 0 -2.7115599 5.7322256 455.39303
380 0 -2.7670072 0 -2.732598 5.5174796 457.45078
390 0 -2.7837505 0 -2.7575583 5.287488 460.89613
400 0 -2.8496447 0 -2.8327475 4.6744698 465.68651
410 0 -2.8950235 0 -2.8846868 4.3330565 466.43586
420 0 -2.931656 0 -2.9211571 4.012274 467.72774
430 0 -2.9439208 0 -2.9333319 3.879408 468.74511
440 0 -2.9490042 0 -2.9392223 3.7981242 469.94173
450 0 -2.9671462 0 -2.9593828 3.5669612 473.90143
460 0 -2.9790249 0 -2.9714639 3.4729198 475.09937
470 0 -2.9841414 0 -2.9765515 3.4091179 476.63384
480 0 -2.9908553 0 -2.9840059 3.3524674 477.60218
490 0 -2.9932915 0 -2.9866901 3.2209929 480.5305
500 0 -2.9943854 0 -2.9875383 3.1955071 480.5305
510 0 -2.9952148 0 -2.9880037 3.1698354 480.5305
517 0 -2.9952859 0 -2.9880707 3.1663812 480.5305
Loop time of 0.0913372 on 1 procs for 189 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.55681544322 -2.98806903 -2.98807070853
Force two-norm initial, final = 3597.73 1.65251
Force max component initial, final = 1510.6 0.260453
Final line search alpha, max atom move = 0.000217837 5.67363e-05
Iterations, force evaluations = 189 705
Pair time (%) = 0.0679402 (74.384)
Neigh time (%) = 0.0040462 (4.42996)
Comm time (%) = 0.00089097 (0.975474)
Outpt time (%) = 0.0072484 (7.93587)
Other time (%) = 0.0112114 (12.2747)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3735 ave 3735 max 3735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3735
Ave neighs/atom = 8.89286
Neighbor list builds = 35
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
517 0 -2.9952859 0 -2.4853146 3.1725652 479.59385
520 0 -2.9198 0 -2.7938547 3.8651798 479.59991
530 0 -2.914821 0 -2.8819122 4.0567315 479.50228
540 0 -2.9117576 0 -2.8945547 4.1585549 479.05261
550 0 -2.9145342 0 -2.8968377 4.1285617 479.54524
560 0 -2.9216524 0 -2.9064011 4.094412 479.31375
570 0 -2.932897 0 -2.9173028 4.0230624 479.29658
580 0 -2.9354268 0 -2.920867 4.0170383 478.94399
590 0 -2.937095 0 -2.9221659 4.0054303 479.27795
600 0 -2.9380766 0 -2.923016 4.001867 479.8173
610 0 -2.9388105 0 -2.9239198 4.0019078 480.98557
620 0 -2.9388078 0 -2.9241639 3.9989421 481.07316
630 0 -2.9389523 0 -2.9243365 4.0118887 479.60846
640 0 -2.9389486 0 -2.9244942 3.9965251 481.89847
647 0 -2.9390355 0 -2.9245617 4.0040398 480.57245
Loop time of 0.0892859 on 1 procs for 130 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.48531461147 -2.92455912822 -2.92456171264
Force two-norm initial, final = 487.558 0.783854
Force max component initial, final = 232.369 0.142477
Final line search alpha, max atom move = 0.000879757 0.000125345
Iterations, force evaluations = 130 703
Pair time (%) = 0.068279 (76.4724)
Neigh time (%) = 0.00469089 (5.25378)
Comm time (%) = 0.000895262 (1.00269)
Outpt time (%) = 0.00496078 (5.55606)
Other time (%) = 0.0104599 (11.7151)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 114 ave 114 max 114 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3922 ave 3922 max 3922 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3922
Ave neighs/atom = 9.3381
Neighbor list builds = 41
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
647 0 -2.9390355 0 -2.2881675 4.004627 480.50198
650 0 -2.8179859 0 -2.6482515 5.0256592 480.50335
660 0 -2.816781 0 -2.7646371 5.2249994 480.47728
670 0 -2.8136395 0 -2.7841907 5.3222105 479.85834
680 0 -2.8198172 0 -2.790435 5.2808396 480.19766
690 0 -2.8223412 0 -2.7932491 5.3024888 478.66784
700 0 -2.822621 0 -2.7942434 5.296465 479.60866
710 0 -2.8227778 0 -2.7959249 5.3042755 479.89149
720 0 -2.8247184 0 -2.8014216 5.2239378 485.98615
730 0 -2.8282652 0 -2.8044889 5.1538112 487.69349
740 0 -2.8300796 0 -2.8088105 5.0797415 490.56397
750 0 -2.8330076 0 -2.8115118 5.0273392 490.56397
760 0 -2.8428407 0 -2.8208753 4.8380767 496.43781
770 0 -2.8532495 0 -2.8317146 4.7355181 498.18312
780 0 -2.8577608 0 -2.8359443 4.6826343 499.33933
790 0 -2.8613609 0 -2.8396361 4.6517266 497.55084
800 0 -2.8652079 0 -2.8432245 4.5853809 499.07467
810 0 -2.87249 0 -2.849878 4.5097768 498.3913
820 0 -2.8761105 0 -2.8534683 4.4503024 498.27677
830 0 -2.8779811 0 -2.8560281 4.425496 498.32955
840 0 -2.8817086 0 -2.8605554 4.3476382 499.26253
850 0 -2.8846306 0 -2.8640867 4.2891586 499.70114
860 0 -2.8891911 0 -2.8698441 4.2003836 499.39278
866 0 -2.8894083 0 -2.870152 4.2061476 498.42046
Loop time of 0.125655 on 1 procs for 219 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.28816747895 -2.87014946015 -2.87015196056
Force two-norm initial, final = 540.634 3.99773
Force max component initial, final = 239.896 0.750875
Final line search alpha, max atom move = 6.43213e-05 4.82973e-05
Iterations, force evaluations = 219 962
Pair time (%) = 0.0958545 (76.2839)
Neigh time (%) = 0.00576615 (4.58888)
Comm time (%) = 0.00116706 (0.928781)
Outpt time (%) = 0.0083425 (6.63922)
Other time (%) = 0.0145247 (11.5592)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 112 ave 112 max 112 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3989 ave 3989 max 3989 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3989
Ave neighs/atom = 9.49762
Neighbor list builds = 49
Dangerous builds = 0

386
examples/indent/log.indent.min.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1801584 0 -3.1801584 -1.3058039 441.04528
20 0 -3.1831474 0 -3.1831474 -1.2345239 438.53563
30 0 -3.1861452 0 -3.1861452 -1.0910037 438.78112
40 0 -3.1901049 0 -3.1901049 -0.84865219 435.53833
50 0 -3.1904808 0 -3.1904808 -0.81510177 435.53833
60 0 -3.1906458 0 -3.1906458 -0.78391528 435.53833
70 0 -3.190782 0 -3.190782 -0.75177926 435.53833
74 0 -3.1908431 0 -3.1908431 -0.73891675 435.53833
Loop time of 0.0206316 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058192 -3.19084306553
Force two-norm initial, final = 6.74302 0.560405
Force max component initial, final = 1.46877 0.0658777
Final line search alpha, max atom move = 0.00643452 0.000423891
Iterations, force evaluations = 74 411
Pair time (%) = 0.00988287 (47.9017)
Neigh time (%) = 0.000116825 (0.566245)
Comm time (%) = 0.00376642 (18.2556)
Outpt time (%) = 0.00290936 (14.1015)
Other time (%) = 0.00395608 (19.1749)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 84 ave 90 max 79 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 895 ave 909 max 887 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.246435 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624137 -0.73821469 435.95253
80 0 -3.1521235 0 -3.1418193 -0.261082 435.95257
90 0 -3.1725009 0 -3.1715057 -0.36505507 436.10564
100 0 -3.1770919 0 -3.1759284 -0.36787366 436.0732
110 0 -3.1795983 0 -3.1785044 -0.32332683 435.97859
120 0 -3.180806 0 -3.1800339 -0.20962981 435.13284
130 0 -3.1810339 0 -3.1803164 -0.19436655 434.96509
140 0 -3.1811242 0 -3.1804145 -0.1823656 433.48453
150 0 -3.1812451 0 -3.1805047 -0.16049814 432.87389
154 0 -3.1812423 0 -3.1805491 -0.15211702 432.87389
Loop time of 0.024414 on 4 procs for 80 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241374146 -3.18054712963 -3.18054912974
Force two-norm initial, final = 1731.02 0.603655
Force max component initial, final = 1265.65 0.194416
Final line search alpha, max atom move = 0.00540441 0.0010507
Iterations, force evaluations = 80 406
Pair time (%) = 0.00969785 (39.7225)
Neigh time (%) = 0.000582635 (2.38648)
Comm time (%) = 0.00488079 (19.9917)
Outpt time (%) = 0.00335246 (13.7317)
Other time (%) = 0.00590026 (24.1675)
Nlocal: 105 ave 111 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 85.5 ave 89 max 81 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 897.5 ave 1001 max 804 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3590
Ave neighs/atom = 8.54762
Neighbor list builds = 20
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
154 0 -3.1812423 0 -0.19846921 -0.15159029 434.378
160 0 -2.9587626 0 -2.5389232 1.7767479 434.37743
170 0 -3.0234014 0 -2.994039 1.6447519 434.36678
180 0 -3.0796519 0 -3.0631136 1.2885477 434.3441
190 0 -3.0942895 0 -3.0828558 1.2001972 434.53434
200 0 -3.1004103 0 -3.0919048 1.1644668 434.96021
210 0 -3.1018559 0 -3.0939737 1.1821125 432.91523
220 0 -3.1031993 0 -3.0959548 1.2692205 432.35082
230 0 -3.1038581 0 -3.0964047 1.2903845 431.99861
240 0 -3.1040414 0 -3.0967671 1.3400158 431.31375
250 0 -3.1041911 0 -3.0968745 1.3470137 430.97789
260 0 -3.1041223 0 -3.0970712 1.386564 430.92355
262 0 -3.1041329 0 -3.0970762 1.3846332 431.51763
Loop time of 0.032465 on 4 procs for 108 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.198469207811 -3.09707484463 -3.09707619592
Force two-norm initial, final = 1759.88 0.734387
Force max component initial, final = 924.476 0.262782
Final line search alpha, max atom move = 0.00390625 0.00102649
Iterations, force evaluations = 108 532
Pair time (%) = 0.0128388 (39.5466)
Neigh time (%) = 0.00085789 (2.64251)
Comm time (%) = 0.00652206 (20.0895)
Outpt time (%) = 0.00459975 (14.1683)
Other time (%) = 0.0076465 (23.5531)
Nlocal: 105 ave 111 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 94 ave 96 max 93 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 916.25 ave 1004 max 830 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3665
Ave neighs/atom = 8.72619
Neighbor list builds = 29
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
262 0 -3.1041329 0 1.9882182 1.3862425 431.01668
270 0 -2.5008708 0 -2.1274702 6.2192521 431.43485
280 0 -2.8266381 0 -2.7256392 4.1305111 439.06864
290 0 -2.8948399 0 -2.8501454 3.6910353 442.62509
300 0 -2.9370293 0 -2.9162661 3.3306144 447.16569
310 0 -2.9581655 0 -2.9440078 3.1533891 450.48484
320 0 -2.9634122 0 -2.950379 3.1003819 452.48876
330 0 -2.9673602 0 -2.9574433 2.9726812 457.22624
340 0 -2.9713345 0 -2.9621124 2.9040639 457.22624
350 0 -2.9861765 0 -2.9769147 2.6936716 458.29899
360 0 -3.0073392 0 -2.9985921 2.3803852 464.10283
370 0 -3.0466409 0 -3.0398575 1.7948406 466.90897
380 0 -3.0758597 0 -3.0700028 1.5090443 467.56199
390 0 -3.093661 0 -3.0898261 1.3095249 470.06302
400 0 -3.1036401 0 -3.1004924 1.2216848 469.7629
410 0 -3.1132635 0 -3.1105323 1.0773999 469.945
418 0 -3.1149693 0 -3.1123334 1.0362325 472.71946
Loop time of 0.0366988 on 4 procs for 156 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
1.98821816295 -3.11233083453 -3.11233344792
Force two-norm initial, final = 2323.34 6.44773
Force max component initial, final = 1036.14 3.71983
Final line search alpha, max atom move = 2.56426e-05 9.5386e-05
Iterations, force evaluations = 156 527
Pair time (%) = 0.0129628 (35.322)
Neigh time (%) = 0.00114769 (3.12731)
Comm time (%) = 0.00773114 (21.0665)
Outpt time (%) = 0.00628912 (17.1371)
Other time (%) = 0.00856811 (23.3471)
Nlocal: 105 ave 119 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 89 ave 94 max 81 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 901.25 ave 1077 max 709 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3605
Ave neighs/atom = 8.58333
Neighbor list builds = 38
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74738 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
418 0 -3.1149693 0 3.9695775 1.0398804 471.06117
420 0 -3.0639124 0 1.5556717 1.5540598 470.92114
430 0 -2.7329444 0 -2.4617667 4.5830122 470.34088
440 0 -2.8674448 0 -2.7961604 3.8042496 473.94741
450 0 -2.9194372 0 -2.8988557 3.452036 479.04769
460 0 -2.9540818 0 -2.9365384 3.0756579 483.80479
470 0 -2.966952 0 -2.9520341 2.898389 487.89422
480 0 -2.9765545 0 -2.964481 2.6876987 489.82166
490 0 -2.9800876 0 -2.970126 2.6458351 491.68343
500 0 -2.9870857 0 -2.9778018 2.5301258 493.51842
510 0 -3.0037082 0 -2.9957281 2.3017972 495.1069
520 0 -3.0447086 0 -3.0397584 1.911385 496.66926
530 0 -3.0523184 0 -3.0470425 1.8129976 496.40855
540 0 -3.0565959 0 -3.0511846 1.7331627 496.91534
550 0 -3.0631725 0 -3.0572614 1.6135296 498.59311
560 0 -3.0681437 0 -3.0620609 1.5829711 497.34497
570 0 -3.0754999 0 -3.068936 1.5508329 495.84223
580 0 -3.0791924 0 -3.0725672 1.5199839 497.9288
589 0 -3.0795685 0 -3.0729707 1.5102713 497.95469
Loop time of 0.044094 on 4 procs for 171 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
3.96957753316 -3.07297035788 -3.07297073814
Force two-norm initial, final = 2831.94 1.62478
Force max component initial, final = 1369.84 0.405516
Final line search alpha, max atom move = 6.02041e-05 2.44137e-05
Iterations, force evaluations = 171 578
Pair time (%) = 0.0140276 (31.8129)
Neigh time (%) = 0.001252 (2.83938)
Comm time (%) = 0.0106812 (24.2237)
Outpt time (%) = 0.00707901 (16.0543)
Other time (%) = 0.0110542 (25.0696)
Nlocal: 105 ave 124 max 88 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 96 ave 106 max 87 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 906.75 ave 1112 max 701 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3627
Ave neighs/atom = 8.63571
Neighbor list builds = 42
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74743 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
589 0 -3.0795685 0 -2.5645649 1.5134157 496.92009
590 0 -3.0451965 0 -2.7444051 1.8088174 496.92009
600 0 -2.9961727 0 -2.9643999 2.3950616 496.97053
610 0 -3.0044844 0 -2.9857066 2.376008 497.00209
620 0 -3.0140073 0 -2.9967979 2.3299437 496.80141
630 0 -3.0162496 0 -3.0004658 2.3321472 496.68198
640 0 -3.0163782 0 -3.0017964 2.3448435 496.43329
650 0 -3.0170272 0 -3.0035125 2.3710061 495.40836
Loop time of 0.0185835 on 4 procs for 61 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.56456488251 -3.00351081845 -3.0035124756
Force two-norm initial, final = 485.265 2.93819
Force max component initial, final = 232.267 0.739278
Final line search alpha, max atom move = 6.69976e-05 4.95299e-05
Iterations, force evaluations = 61 252
Pair time (%) = 0.00620061 (33.3662)
Neigh time (%) = 0.000388563 (2.0909)
Comm time (%) = 0.00460953 (24.8043)
Outpt time (%) = 0.00249505 (13.4261)
Other time (%) = 0.00488979 (26.3125)
Nlocal: 105 ave 122 max 88 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 98.5 ave 108 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 949 ave 1171 max 711 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3796
Ave neighs/atom = 9.0381
Neighbor list builds = 13
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.8492869 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:167)
Memory usage per processor = 2.74743 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
650 0 -3.0170272 0 -2.3648009 2.3681511 496.00561
660 0 -2.8919518 0 -2.8405212 3.5522447 495.98613
670 0 -2.9005277 0 -2.863283 3.5344449 495.86556
680 0 -2.9028036 0 -2.874857 3.5600205 495.73432
690 0 -2.9040138 0 -2.8811237 3.5847696 495.73432
695 0 -2.9044182 0 -2.8814536 3.5808985 495.92978
Loop time of 0.0143149 on 4 procs for 45 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.36480087899 -2.88145342509 -2.88145356187
Force two-norm initial, final = 544.106 3.08132
Force max component initial, final = 243.974 0.504739
Final line search alpha, max atom move = 6.0444e-06 3.05084e-06
Iterations, force evaluations = 45 198
Pair time (%) = 0.00502551 (35.1068)
Neigh time (%) = 0.00018084 (1.2633)
Comm time (%) = 0.00382853 (26.7451)
Outpt time (%) = 0.00163871 (11.4476)
Other time (%) = 0.00364131 (25.4372)
Nlocal: 105 ave 125 max 85 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 98 ave 110 max 86 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 992.75 ave 1273 max 709 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3971
Ave neighs/atom = 9.45476
Neighbor list builds = 6
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 MPI processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 5.10825 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0790551 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.0747664 (94.5751)
Neigh time (%) = 0.00214291 (2.71065)
Comm time (%) = 0.000567198 (0.717472)
Outpt time (%) = 0.0012064 (1.52602)
Other time (%) = 0.000372171 (0.470775)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 543 ave 543 max 543 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1526 ave 1526 max 1526 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3052 ave 3052 max 3052 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

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LAMMPS (10 Jan 2012)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 MPI processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.99306 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.03332 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.0281992 (84.6316)
Neigh time (%) = 0.000612736 (1.83895)
Comm time (%) = 0.00279725 (8.39511)
Outpt time (%) = 0.00148147 (4.44621)
Other time (%) = 0.000229299 (0.688174)
Nlocal: 32 ave 36 max 30 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 293.75 ave 305 max 285 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 381.5 ave 413 max 334 min
Histogram: 1 0 0 0 1 0 0 0 0 2
FullNghs: 763 ave 866 max 678 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 6.77655 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346
50 300 -8149.7654 0 -8096.1353 10637.302 19676.681
75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029
100 300 -8173.6884 0 -8120.0584 5954.839 19878.848
Loop time of 1.46607 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 1.44517 (98.5743)
Neigh time (%) = 0.0143578 (0.979338)
Comm time (%) = 0.00156951 (0.107055)
Outpt time (%) = 6.38962e-05 (0.00435832)
Other time (%) = 0.00490999 (0.334908)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23806 ave 23806 max 23806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47612 ave 47612 max 47612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47612
Ave neighs/atom = 24.9017
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 6.95314 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
100 292.0799 -8177.7235 0 -8142.9266 2567.6871 19863.778
200 306.71233 -8177.1504 0 -8140.6103 873.12617 20039.427
300 295.7806 -8172.9505 0 -8137.7127 -1054.1773 20083.875
400 309.18439 -8169.6374 0 -8132.8028 -1785.2352 20114.391
500 304.51122 -8163.9147 0 -8127.6369 -160.33189 20175.64
600 300 -8158.55 0 -8122.8096 1555.8342 20272.069
700 304.32794 -8149.4746 0 -8113.2185 3702.0205 20422.656
800 304.79621 -8138.8368 0 -8102.5249 3723.0289 20502.876
900 303.87706 -8128.16 0 -8091.9576 4388.821 20631.103
1000 300 -8113.4908 0 -8077.7503 6189.061 20747.117
1100 306.13486 -8097.1731 0 -8060.7018 8908.048 20871.68
1200 309.15672 -8081.8589 0 -8045.0276 10527.674 20988.916
1300 304.48415 -8064.5597 0 -8028.2851 10066.833 21118.364
1400 300 -8046.7607 0 -8011.0202 10976.596 21230.714
1500 300 -8041.3546 0 -8005.6141 11944.043 21366.268
1600 309.60321 -8035.2271 0 -7998.3426 11344.414 21522.036
1700 300 -8029.1687 0 -7993.4283 11303.058 21627.405
1800 300 -8034.2245 0 -7998.4841 9635.5534 21728.966
1900 307.86145 -8037.1072 0 -8000.4302 6167.8738 21849.865
2000 307.81899 -8029.9421 0 -7993.2701 3170.0159 22004.862
2100 300 -8032.7539 0 -7997.0135 1311.0313 22098.991
2200 300 -8042.5128 0 -8006.7724 1644.7181 22223.554
2300 309.60919 -8041.3003 0 -8004.415 3447.4419 22344.453
2400 303.51436 -8036.8571 0 -8000.698 5476.9727 22461.689
2500 309.82464 -8036.3148 0 -7999.4039 6946.3833 22589.915
2600 308.45257 -8038.9157 0 -8002.1683 9164.9017 22713.257
2700 306.90752 -8041.0584 0 -8004.495 8144.5283 22836.599
2800 308.64671 -8042.8933 0 -8006.1228 8314.2343 22957.498
2900 300 -8044.2363 0 -8008.4959 6534.6291 23077.176
3000 308.55125 -8045.1049 0 -8008.3457 2319.2124 23193.191
Loop time of 46.7216 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 45.8546 (98.1444)
Neigh time (%) = 0.622606 (1.33259)
Comm time (%) = 0.0498846 (0.10677)
Outpt time (%) = 0.0463471 (0.0991986)
Other time (%) = 0.148106 (0.316996)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1658 ave 1658 max 1658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23394 ave 23394 max 23394 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46788 ave 46788 max 46788 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46788
Ave neighs/atom = 24.4707
Neighbor list builds = 222
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 5.96949 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346
50 300 -8152.0635 0 -8098.4335 10060.658 19678.279
75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8
100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128
Loop time of 0.400293 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.387236 (96.7382)
Neigh time (%) = 0.00367391 (0.917806)
Comm time (%) = 0.00746405 (1.86465)
Outpt time (%) = 9.32813e-05 (0.0233033)
Other time (%) = 0.00182539 (0.456014)
Nlocal: 478 ave 486 max 469 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 809 ave 818 max 801 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 5932.75 ave 6076 max 5807 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 11865.5 ave 12111 max 11653 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 47462
Ave neighs/atom = 24.8232
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.meam
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 6.01016 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
100 301.02661 -8174.1628 0 -8138.3 441.39614 19947.951
200 290.97251 -8175.7136 0 -8141.0487 -438.32628 19981.719
300 304.4239 -8173.5555 0 -8137.288 -2447.7976 20067.185
400 305.76192 -8168.2982 0 -8131.8713 -814.70984 20153.166
500 304.73368 -8164.7296 0 -8128.4252 -963.99012 20227.497
600 300.12426 -8157.4957 0 -8121.7405 39.926198 20299.368
700 301.07583 -8150.7214 0 -8114.8528 2178.1731 20419.159
800 297.37471 -8139.56 0 -8104.1323 4209.733 20518.203
900 304.4007 -8127.6685 0 -8091.4038 6132.0576 20631.103
1000 306.98916 -8112.2064 0 -8075.6333 8585.8087 20758.108
1100 303.05268 -8097.0258 0 -8060.9217 9885.1628 20871.68
1200 300.37461 -8081.159 0 -8045.3739 9988.7374 20999.907
1300 307.55251 -8065.2275 0 -8028.5873 10516.036 21126.912
1400 303.2639 -8051.2915 0 -8015.1623 11668.072 21235.599
1500 300 -8039.6298 0 -8003.8893 12498.158 21361.383
1600 300 -8032.3339 0 -7996.5935 13558.654 21487.167
1700 300 -8021.6093 0 -7985.8689 13720.956 21608.067
1800 300 -8013.5338 0 -7977.7933 10671.997 21727.745
1900 300 -8014.5801 0 -7978.8396 6968.6386 21849.865
2000 300 -8026.6571 0 -7990.9167 3269.4443 21974.428
2100 300 -8033.1013 0 -7997.3609 1537.4207 22102.655
2200 307.36281 -8028.6497 0 -7992.0321 3817.5435 22222.333
2300 300 -8027.913 0 -7992.1726 3488.2549 22348.117
2400 300 -8035.0837 0 -7999.3433 2982.0314 22465.353
2500 304.59101 -8038.8331 0 -8002.5457 1690.5828 22581.367
2600 300 -8038.555 0 -8002.8146 1526.8827 22699.824
2700 300 -8040.1447 0 -8004.4043 736.6537 22824.387
2800 308.16594 -8041.4384 0 -8004.7252 -602.64831 22948.95
2900 300 -8038.5929 0 -8002.8524 -884.13202 23067.406
3000 300 -8037.9149 0 -8002.1744 -1850.8904 23201.739
Loop time of 13.031 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 12.489 (95.8408)
Neigh time (%) = 0.16103 (1.23574)
Comm time (%) = 0.275773 (2.11628)
Outpt time (%) = 0.049704 (0.381428)
Other time (%) = 0.0554834 (0.425779)
Nlocal: 478 ave 511 max 445 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 789 ave 828 max 753 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 5745.75 ave 6118 max 5418 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 11491.5 ave 12238 max 10833 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 45966
Ave neighs/atom = 24.0408
Neighbor list builds = 222
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 2.35378 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.734027 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 0.608454 (82.8925)
Neigh time (%) = 0.0777593 (10.5935)
Comm time (%) = 0.0137377 (1.87155)
Outpt time (%) = 0.0153244 (2.08771)
Other time (%) = 0.0187521 (2.55469)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 50 dump.melt
thermo 50
run 250
Memory usage per processor = 1.88302 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.233054 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.160472 (68.8563)
Neigh time (%) = 0.0206246 (8.84973)
Comm time (%) = 0.0306477 (13.1505)
Outpt time (%) = 0.0157282 (6.74875)
Other time (%) = 0.00558102 (2.39473)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.47141 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.163739 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.104032 (63.5352)
Bond time (%) = 0.00943089 (5.75971)
Neigh time (%) = 0.0185628 (11.3368)
Comm time (%) = 0.00374722 (2.28854)
Outpt time (%) = 0.000244856 (0.14954)
Other time (%) = 0.0277214 (16.9302)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 500 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 2.62399 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727748 0.058613381 -1.4645364 1.9980607
2000 0.45568658 -2.0037656 0.074778215 -1.4736806 1.6979005
3000 0.43671047 -2.0101721 0.066612232 -1.5072134 1.3631017
4000 0.45419638 -2.0139494 0.064399825 -1.4957317 1.3952686
5000 0.45368357 -2.0268297 0.065024202 -1.5085 1.3128018
6000 0.44241657 -2.0508715 0.065291859 -1.5435318 1.1631984
7000 0.44036478 -2.0343729 0.066010146 -1.5283649 1.3395296
8000 0.45870389 -2.0491085 0.064635438 -1.5261514 1.1153148
9000 0.45 -2.0737557 0.070248782 -1.5538819 1.0579445
10000 0.46139552 -2.0614311 0.054305268 -1.5461148 1.040611
11000 0.44754946 -2.0536429 0.0571427 -1.5493237 1.170479
12000 0.43858048 -2.0504687 0.061823314 -1.5504304 1.2423332
13000 0.46060343 -2.0809383 0.062536551 -1.5581822 0.99462586
14000 0.46550804 -2.068068 0.059087308 -1.5438606 1.0492141
15000 0.4579624 -2.0768414 0.064313259 -1.5549474 0.83362407
16000 0.44360024 -2.0691464 0.065649722 -1.5602661 1.1220055
17000 0.44503208 -2.09618 0.063717133 -1.5878016 0.98900539
18000 0.461234 -2.0784927 0.057483485 -1.5601596 0.80401226
19000 0.44546608 -2.090735 0.061518829 -1.5841213 0.76355309
20000 0.44633986 -2.0927653 0.062315089 -1.5844823 0.83608229
21000 0.450372 -2.0755249 0.053057162 -1.5724711 0.86811182
22000 0.44345039 -2.0858484 0.061536473 -1.5812311 0.92966531
23000 0.45 -2.063928 0.055870989 -1.558432 1.0935065
24000 0.45329768 -2.0734293 0.060520515 -1.5599888 1.0461956
25000 0.45681319 -2.0872139 0.067350615 -1.5634308 0.85836474
26000 0.44583013 -2.0743622 0.059876855 -1.5690267 0.97050732
27000 0.44808108 -2.0876059 0.070652406 -1.5692458 0.86892607
28000 0.44385833 -2.0962374 0.060999392 -1.5917496 0.72973926
29000 0.44956166 -2.0991557 0.063446674 -1.586522 0.69730962
30000 0.45705136 -2.1080785 0.063316064 -1.588092 0.67479754
31000 0.46482099 -2.0970514 0.05740009 -1.5752176 0.81521862
32000 0.45364967 -2.0971667 0.052600611 -1.5912945 0.78898109
33000 0.45385702 -2.0887209 0.054779495 -1.5804626 0.91662113
34000 0.43708562 -2.0882541 0.065272457 -1.5862602 0.74846999
35000 0.46011213 -2.105422 0.06543394 -1.5802594 0.79254265
36000 0.43836246 -2.1030463 0.055383361 -1.6096658 0.81971531
37000 0.44491302 -2.1165092 0.061213159 -1.6107538 0.72827756
38000 0.44411182 -2.0967838 0.07024247 -1.5827996 0.62405192
39000 0.4652381 -2.1072257 0.060295721 -1.5820796 0.72242433
40000 0.4330116 -2.0975339 0.052804789 -1.6120784 0.88172486
41000 0.46563679 -2.1136635 0.056632893 -1.5917818 0.76149098
42000 0.43103564 -2.0993028 0.065196562 -1.6034298 0.61042397
43000 0.44462993 -2.1079126 0.05608375 -1.6075695 0.73672778
44000 0.45425384 -2.1223201 0.060482945 -1.6079619 0.71258088
45000 0.44110675 -2.1200786 0.061448277 -1.6178912 0.74411683
46000 0.4378992 -2.1108872 0.059602813 -1.6137501 0.72798368
47000 0.44583384 -2.1069635 0.0600688 -1.6014324 0.72077491
48000 0.44302348 -2.1081347 0.057510566 -1.6079698 0.8069197
49000 0.44419128 -2.1181433 0.063504044 -1.6108181 0.67517074
50000 0.45390413 -2.1092822 0.059857025 -1.5958993 0.62284507
51000 0.44109908 -2.0904088 0.069414676 -1.5802627 0.90667788
52000 0.44966512 -2.1139717 0.054713676 -1.6099676 0.57131384
53000 0.45254608 -2.1325691 0.065566583 -1.6148336 0.65040311
54000 0.45399241 -2.1211047 0.064668702 -1.6028219 0.6967839
55000 0.45065271 -2.1197256 0.059831839 -1.6096166 0.72432124
56000 0.44944902 -2.1127808 0.066363238 -1.5973431 0.74175523
57000 0.46434143 -2.1326736 0.058493135 -1.6102259 0.63248335
58000 0.45747759 -2.1262076 0.063397292 -1.605714 0.50174168
59000 0.46484128 -2.1322565 0.059584755 -1.6082178 0.56928364
60000 0.46462811 -2.1338631 0.062672867 -1.6069493 0.66404612
Loop time of 13.6587 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 9.19082 (67.2892)
Bond time (%) = 0.559916 (4.09934)
Neigh time (%) = 1.90328 (13.9346)
Comm time (%) = 0.3128 (2.29012)
Outpt time (%) = 0.111663 (0.817525)
Other time (%) = 1.58021 (11.5692)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 385 ave 385 max 385 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9701 ave 9701 max 9701 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9701
Ave neighs/atom = 8.08417
Ave special neighs/atom = 0.5
Neighbor list builds = 4896
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.79445 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0567175 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0264016 (46.5494)
Bond time (%) = 0.00241357 (4.25543)
Neigh time (%) = 0.0048123 (8.48469)
Comm time (%) = 0.0124914 (22.0239)
Outpt time (%) = 0.000479639 (0.845663)
Other time (%) = 0.0101189 (17.8409)
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 500 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 2.79445 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727852 0.0586182 -1.464542 1.9980664
2000 0.46082446 -1.977605 0.057039794 -1.4601247 1.726013
3000 0.45 -2.0006402 0.05562923 -1.495386 1.511225
4000 0.4623338 -2.0091993 0.059138048 -1.4881127 1.3542907
5000 0.45 -2.0395585 0.061066034 -1.5288674 1.1830193
6000 0.45905159 -2.0634848 0.058991931 -1.5458239 1.1082099
7000 0.45 -2.0508705 0.061559594 -1.5396859 1.2020831
8000 0.44666556 -2.0397402 0.066632486 -1.5268144 1.2612013
9000 0.45034184 -2.03446 0.064174681 -1.5203188 1.1644088
10000 0.44920732 -2.0856804 0.059525789 -1.5773216 0.93583471
11000 0.45896474 -2.063989 0.064678373 -1.5407284 1.0732096
12000 0.45848122 -2.0752398 0.061533665 -1.555607 1.0281395
13000 0.46738009 -2.0629007 0.067132245 -1.5287778 0.96711354
14000 0.44988856 -2.062354 0.062693783 -1.5501466 1.0123189
15000 0.45098377 -2.072531 0.051120563 -1.5708025 0.97044948
16000 0.45 -2.1017479 0.064909547 -1.5872134 0.90299146
17000 0.4552102 -2.0765865 0.056648474 -1.5651072 0.91280438
18000 0.44824933 -2.0828037 0.058978706 -1.5759492 0.92795752
19000 0.44079166 -2.0556475 0.059088524 -1.5561347 1.1454216
20000 0.44463382 -2.0859907 0.057486911 -1.5842405 0.92599126
21000 0.44406551 -2.0826296 0.056776522 -1.5821577 0.99925665
22000 0.44911834 -2.0711967 0.059641892 -1.5628107 0.95834342
23000 0.43655144 -2.0909928 0.062696368 -1.5921088 0.91119509
24000 0.44867934 -2.1018259 0.055592487 -1.597928 0.76348634
25000 0.45260844 -2.0937068 0.059149636 -1.5823259 0.89135412
26000 0.44898273 -2.1016995 0.066566046 -1.5865249 0.74284381
27000 0.43221936 -2.084773 0.062900549 -1.5900132 0.87821534
28000 0.46292457 -2.0965745 0.055816359 -1.5782193 0.74158202
29000 0.45 -2.1306418 0.063790424 -1.6172264 0.53967764
30000 0.44871717 -2.0907319 0.055486729 -1.586902 0.99873528
31000 0.46125755 -2.0755203 0.056517719 -1.5581294 0.9347469
32000 0.45941056 -2.0914092 0.057505763 -1.5748757 0.89468013
33000 0.46026614 -2.0984679 0.056646234 -1.5819391 0.80740251
34000 0.46916633 -2.1193229 0.054211886 -1.5963356 0.61039936
35000 0.43884901 -2.0922975 0.061924634 -1.5918896 0.79377862
36000 0.43947177 -2.0909805 0.053228588 -1.5986464 0.90484301
37000 0.45414812 -2.1030789 0.055686423 -1.5936228 0.87060399
38000 0.44280127 -2.0908535 0.058003408 -1.5904178 0.8046892
39000 0.45516585 -2.1008067 0.058183565 -1.5878366 0.6089312
40000 0.43067796 -2.0848319 0.062869447 -1.5916434 0.74412702
41000 0.44165418 -2.1259603 0.064019775 -1.6206544 0.6221064
42000 0.43982239 -2.1055547 0.064067567 -1.6020312 0.62130789
43000 0.46586098 -2.1382757 0.05819116 -1.6146118 0.54791918
44000 0.45469796 -2.1328327 0.066699087 -1.6118146 0.52752596
45000 0.45358824 -2.1251041 0.063138554 -1.6087553 0.64714368
46000 0.44191865 -2.1041137 0.059520035 -1.6030433 0.62417966
47000 0.45804456 -2.1075048 0.066124313 -1.5837176 0.82334648
48000 0.45700413 -2.1298865 0.065741607 -1.6075216 0.58174639
49000 0.45842123 -2.1362735 0.056849019 -1.6213852 0.51934277
50000 0.44239274 -2.1182037 0.053635135 -1.6225444 0.59636555
51000 0.45869721 -2.1176213 0.059785615 -1.5995207 0.62467419
52000 0.45 -2.1136347 0.062713868 -1.6012959 0.71773796
53000 0.44480469 -2.1070829 0.061995737 -1.6006531 0.72790523
54000 0.45834924 -2.1352139 0.056517736 -1.6207289 0.64257865
55000 0.44776128 -2.1167768 0.051321782 -1.6180669 0.52184371
56000 0.46087785 -2.1186123 0.059414538 -1.598704 0.72628855
57000 0.44514743 -2.1107461 0.062138072 -1.6038315 0.68847034
58000 0.44897344 -2.1218568 0.056966905 -1.6162906 0.66787759
59000 0.43532599 -2.1262526 0.062848971 -1.6284404 0.61398862
60000 0.44623012 -2.105934 0.05919675 -1.600879 0.73556885
Loop time of 4.54773 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 2.35982 (51.89)
Bond time (%) = 0.144139 (3.16948)
Neigh time (%) = 0.498476 (10.961)
Comm time (%) = 0.923059 (20.2971)
Outpt time (%) = 0.0965258 (2.1225)
Other time (%) = 0.525711 (11.5599)
Nlocal: 300 ave 320 max 287 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 218.75 ave 232 max 205 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 2461 ave 2617 max 2321 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 9844
Ave neighs/atom = 8.20333
Ave special neighs/atom = 0.5
Neighbor list builds = 4879
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.202955 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.127084 (62.6168)
Neigh time (%) = 0.0454805 (22.4091)
Comm time (%) = 0.00529456 (2.60874)
Outpt time (%) = 0.00619006 (3.04997)
Other time (%) = 0.0189059 (9.31531)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74947 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
1050 3.3134849 -2.808351 0 0.50099208 1.7334413
1100 3.3134849 -2.8586611 0 0.45068195 1.6058414
1150 3.3134849 -2.8712625 0 0.43808058 1.6049732
1200 3.3134849 -2.8785429 0 0.43080018 1.5883814
1250 3.3134849 -2.8832131 0 0.42612994 1.6155122
1300 3.3134849 -2.8882533 0 0.42108976 1.6323994
1350 3.3134849 -2.8953262 0 0.41401689 1.5991374
1365 3.3134849 -2.895477 0 0.41386606 1.5988878
Loop time of 0.287008 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.23213 (80.8794)
Neigh time (%) = 0.0182872 (6.37167)
Comm time (%) = 0.00441384 (1.53788)
Outpt time (%) = 0.00858235 (2.99029)
Other time (%) = 0.0235941 (8.22073)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 2.06114 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.0822566 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.032889 (39.9834)
Neigh time (%) = 0.0120565 (14.6572)
Comm time (%) = 0.0212089 (25.7839)
Outpt time (%) = 0.00666136 (8.09826)
Other time (%) = 0.00944078 (11.4772)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74779 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
1050 3.2803075 -2.8198371 0 0.45636995 1.6553949
1100 3.2803075 -2.8554989 0 0.42070813 1.6571551
1150 3.2803075 -2.8646695 0 0.41153758 1.7045388
1200 3.2803075 -2.8688213 0 0.40738582 1.6922085
1250 3.2803075 -2.8764988 0 0.39970826 1.6948532
1300 3.2803075 -2.8776606 0 0.39854651 1.6821387
1350 3.2803075 -2.8789379 0 0.39726915 1.6715024
1365 3.2803075 -2.879076 0 0.3971311 1.66923
Loop time of 0.117383 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.0659144 (56.1533)
Neigh time (%) = 0.00463283 (3.94676)
Comm time (%) = 0.0184944 (15.7556)
Outpt time (%) = 0.00752294 (6.40888)
Other time (%) = 0.0208185 (17.7355)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.202823 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.12714 (62.6852)
Neigh time (%) = 0.0455041 (22.4354)
Comm time (%) = 0.0052371 (2.58211)
Outpt time (%) = 0.00616384 (3.03902)
Other time (%) = 0.0187778 (9.25825)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74947 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.7783474 0 -0.7783474 12.864955
1050 0 -2.808351 0 -2.808351 -1.0603061
1100 0 -2.8586611 0 -2.8586611 -1.1879061
1150 0 -2.8712625 0 -2.8712625 -1.1887742
1200 0 -2.8785429 0 -2.8785429 -1.205366
1250 0 -2.8832131 0 -2.8832131 -1.1782352
1300 0 -2.8882533 0 -2.8882533 -1.1613481
1350 0 -2.8953262 0 -2.8953262 -1.19461
1365 0 -2.895477 0 -2.895477 -1.1948596
Loop time of 0.286365 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.231558 (80.861)
Neigh time (%) = 0.018275 (6.38172)
Comm time (%) = 0.00431538 (1.50695)
Outpt time (%) = 0.00861835 (3.00957)
Other time (%) = 0.0235987 (8.24077)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.74947 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.895477 -1.2253391 -1.16438 0.0029844696
1400 0 -2.9030976 -1.037803 -0.93005749 0.0031404612
1450 0 -2.9111551 -0.7499331 -0.56417894 0.0034000612
1500 0 -2.9156371 -0.43928981 -0.16010757 0.0035245948
1550 0 -2.9163428 -0.10594305 0.28509585 0.0032633165
1600 0 -2.9130905 0.24756873 0.77173179 0.0031641803
1650 0 -2.9057825 0.61404479 1.3012733 0.0027648207
1700 0 -2.89482 0.95908927 1.8613816 0.0019393979
1750 0 -2.8933049 0.99529993 1.9941577 0.0021678943
1800 0 -2.8939511 1.0012795 2.0015661 0.0031356568
1850 0 -2.8950515 0.9885657 1.9848225 0.0042714138
1900 0 -2.8955548 1.0043227 2.0056317 0.0057590594
1950 0 -2.8962734 1.0022958 2.003091 0.0067349808
2000 0 -2.8971275 0.9931408 1.9913265 0.0073647859
2050 0 -2.8974953 0.99305637 1.98895 0.0076449594
2100 0 -2.897625 0.99141237 1.9951979 0.0076099706
2150 0 -2.8978589 0.99614462 1.9926458 0.0077325835
2200 0 -2.8981266 0.99176161 1.9904497 0.0077484915
2250 0 -2.8982497 0.99558977 1.9926392 0.0077121837
2300 0 -2.8985369 0.99066798 1.9882943 0.0076202125
2350 0 -2.8986352 0.9942664 1.9906635 0.0072762859
2400 0 -2.8988022 0.99146069 1.9908564 0.0070241888
2450 0 -2.8989158 0.99516649 1.9915587 0.0068829039
2500 0 -2.8990911 0.9915646 1.9907668 0.0066581668
2550 0 -2.8991871 0.99532047 1.9918817 0.006382668
2600 0 -2.8993486 0.99183872 1.9914592 0.0060681416
2650 0 -2.899448 0.99547541 1.9920191 0.0058402105
2700 0 -2.8996068 0.99193191 1.9912528 0.0055426972
2750 0 -2.8996874 0.99546923 1.9921572 0.0050653671
2800 0 -2.8998406 0.99197237 1.9913804 0.0046697215
2850 0 -2.8999222 0.99559066 1.992314 0.0042365844
2900 0 -2.9000779 0.99222254 1.9916219 0.0038259745
2950 0 -2.9001638 0.99571698 1.9924536 0.003472226
3000 0 -2.9003157 0.99232832 1.9918649 0.003058491
3050 0 -2.9004128 0.99559345 1.9924259 0.0028157008
3100 0 -2.9005359 0.99256602 1.9929372 0.0025313906
3150 0 -2.900648 0.99621425 1.9929077 0.0022715594
3200 0 -2.900821 0.99255795 1.9919287 0.0019588961
3250 0 -2.9009336 0.99564849 1.9925536 0.0017431269
3300 0 -2.9010948 0.99272999 1.9924543 0.0015162674
3350 0 -2.9012292 0.9956649 1.9926704 0.0015289566
3400 0 -2.9014175 0.99281944 1.9922749 0.0014151321
3450 0 -2.9015604 0.99612848 1.9930717 0.0014874993
3500 0 -2.9017768 0.99283735 1.9924579 0.001562883
3550 0 -2.9019617 0.99567844 1.9926026 0.0017342061
3600 0 -2.902198 0.99282006 1.9921791 0.0019547622
3650 0 -2.9023908 0.99608265 1.9931926 0.002215163
3700 0 -2.9026678 0.99286877 1.9923654 0.0024753338
3750 0 -2.9028992 0.99600861 1.9930144 0.0028529718
3800 0 -2.9032155 0.99257097 1.9910651 0.0032303558
3850 0 -2.9034183 0.99620478 1.9935804 0.0036325923
3900 0 -2.9037443 0.99287324 1.9924736 0.0040585391
3950 0 -2.904025 0.9958276 1.9929886 0.0045308105
4000 0 -2.9043638 0.99280556 1.9924234 0.0049859237
4050 0 -2.9046617 0.99582527 1.9929274 0.0055129234
4100 0 -2.9050302 0.9926886 1.9920078 0.0059846996
4150 0 -2.9053294 0.9961847 1.9933666 0.0066656521
4200 0 -2.9057229 0.99281574 1.9923661 0.0073779251
4250 0 -2.9060488 0.99589526 1.9932547 0.0081443757
4300 0 -2.9064542 0.99285449 1.9923723 0.0089062547
4350 0 -2.9068054 0.9960413 1.9933722 0.010078361
4400 0 -2.9072435 0.99291584 1.9923151 0.011483392
4450 0 -2.9076347 0.99613857 1.9936336 0.013242664
4500 0 -2.9081171 0.99298997 1.9930253 0.01529874
4550 0 -2.9085768 0.99623069 1.9935791 0.018049067
4600 0 -2.9091216 0.99323445 1.9926588 0.021167236
4650 0 -2.9096005 0.99592923 1.9929534 0.024673039
4700 0 -2.9100899 0.99317072 1.9926721 0.027966732
4750 0 -2.9105316 0.99566334 1.9927923 0.031385416
4800 0 -2.9109846 0.9931913 1.9929214 0.034620897
4850 0 -2.9114035 0.99565744 1.9930947 0.03790758
4900 0 -2.9118616 0.993285 1.9931759 0.041031177
4950 0 -2.9123267 0.99606745 1.9935959 0.044729933
5000 0 -2.9127996 0.9990062 1.9957078 0.049138935
5050 0 -2.9132115 0.99978484 1.9924929 0.052329472
5100 0 -2.9133625 1.0024495 2.0024917 0.055574393
5150 0 -2.9138916 0.99874483 1.9956823 0.058956101
5200 0 -2.9142948 0.99375881 1.9911174 0.061331164
5250 0 -2.9148611 0.99363549 1.996526 0.065995974
5300 0 -2.9149835 1.0020569 2.0021942 0.067663045
5350 0 -2.9156095 0.998859 1.9959547 0.069858837
5400 0 -2.9160052 1.005639 2.0021373 0.071715223
5450 0 -2.9164495 0.99706096 1.9922081 0.071941888
5500 0 -2.9163204 1.0090495 2.0080766 0.072399968
5550 0 -2.9168919 0.99651099 1.9996067 0.072534064
5600 0 -2.9175462 0.99659763 1.9966921 0.072957779
5650 0 -2.9179285 0.99738806 1.998678 0.073220148
5700 0 -2.918451 0.99461628 1.995391 0.073118338
5750 0 -2.9189092 0.99499165 1.9980806 0.073042328
5800 0 -2.9194799 0.99624278 1.9937132 0.07304114
5850 0 -2.9198635 0.99577891 1.9980989 0.072620138
5900 0 -2.9203934 0.99891965 1.9928659 0.072366
5950 0 -2.9209722 0.99340181 1.9923689 0.071641881
6000 0 -2.9214463 0.99457938 1.9912102 0.071016324
6050 0 -2.9220308 1.0008602 1.9970241 0.070278563
6100 0 -2.9226893 0.99792151 1.9932307 0.06943713
6150 0 -2.9235098 0.99227063 1.9897419 0.068465698
6200 0 -2.9237506 1.0038087 2.0025404 0.068249883
6250 0 -2.9244281 1.0005718 2.0021021 0.067990601
6300 0 -2.9249697 1.0062933 2.0090234 0.068250892
6350 0 -2.9257154 1.0030034 2.0036477 0.068940394
6400 0 -2.9262715 1.0050738 2.0055581 0.070006764
6450 0 -2.9269133 1.0047577 2.0044087 0.071788673
6500 0 -2.9273289 1.0033446 2.0072672 0.073499832
6550 0 -2.9283266 1.0076677 2.0030225 0.077667056
6600 0 -2.9287195 1.0030896 1.9975323 0.078905039
6650 0 -2.9290562 0.99432984 1.9996725 0.080216144
6700 0 -2.9290598 1.0104194 2.008212 0.081793986
6750 0 -2.9294974 0.99403196 2.00267 0.082537245
6800 0 -2.9300151 1.005569 2.0036333 0.085755451
6850 0 -2.9306019 0.99370379 1.9890889 0.086730188
6900 0 -2.9308139 0.99041002 1.9921336 0.08778407
6950 0 -2.9309773 0.99599112 1.9922988 0.08894069
7000 0 -2.9311928 0.99338451 1.9951543 0.090125744
7050 0 -2.9313893 0.9958889 1.9993482 0.091686979
7100 0 -2.9313303 1.00816 2.0100033 0.093067025
7150 0 -2.9317699 1.0047236 1.997872 0.09423765
7200 0 -2.9321227 0.9975045 1.9946848 0.095521143
7250 0 -2.9323823 0.98848428 1.9928746 0.096368983
7300 0 -2.9322751 1.0015163 2.004104 0.097830982
7350 0 -2.9326179 0.99601059 1.9965114 0.098806079
7400 0 -2.9326943 1.0052615 2.0013723 0.10039937
7450 0 -2.9329323 1.0012091 2.001249 0.10169285
7500 0 -2.933212 1.0036193 1.9987958 0.10340044
7550 0 -2.9336561 0.99284287 1.9967039 0.10526363
7600 0 -2.9339919 1.0037499 2.0078067 0.10921457
7650 0 -2.9348858 0.99864397 1.9937474 0.11311047
7700 0 -2.9351291 1.0004878 2.0038588 0.11587001
7750 0 -2.9354359 1.0037756 2.0057263 0.1182476
7800 0 -2.9357784 1.0044561 2.0038243 0.12009711
7850 0 -2.9360208 1.0065102 2.0058248 0.12185984
7900 0 -2.9363878 1.0030446 2.0047489 0.12359256
7950 0 -2.936912 1.0011868 2.0015998 0.12594296
8000 0 -2.9374852 0.99365742 1.9935081 0.12745547
8050 0 -2.9378124 0.99341101 1.9923754 0.12864518
8100 0 -2.9381419 0.99415804 1.9938563 0.1300876
8150 0 -2.938484 0.99660796 1.9931718 0.13139602
8200 0 -2.9387718 0.99901598 1.9954096 0.13237231
8250 0 -2.9390715 0.99505194 1.996006 0.13307938
8300 0 -2.939423 0.99385933 1.9956476 0.13395986
8350 0 -2.9397799 0.99480714 1.9917444 0.13496967
8400 0 -2.9401728 0.99282971 1.9926565 0.13599307
8450 0 -2.9404807 0.99773074 1.9927352 0.13715329
8500 0 -2.9408624 0.99302383 1.9923586 0.13797646
8550 0 -2.9412431 0.99552116 1.9926935 0.13916828
8600 0 -2.9415984 0.99318371 1.99432 0.13996321
8650 0 -2.9420325 0.99392787 1.9914978 0.14111571
8700 0 -2.9423194 0.99346973 1.9931288 0.14199262
8750 0 -2.9426423 0.99354643 1.9934267 0.14292686
8800 0 -2.9429109 0.99340612 1.9946868 0.14374725
8850 0 -2.943365 0.99056338 1.9888312 0.14479857
8900 0 -2.9436688 0.99589617 1.9932265 0.14623597
8950 0 -2.9442012 0.99350323 1.9930137 0.14787782
9000 0 -2.9448056 0.99605027 1.9935613 0.15036262
9050 0 -2.9457 0.9937002 1.9933526 0.15430149
9100 0 -2.9461435 0.99743873 1.9955187 0.15685614
9150 0 -2.9466789 0.99777376 1.9920466 0.1591211
9200 0 -2.9469111 0.99313958 1.9943908 0.16003968
9250 0 -2.9469552 1.0056783 2.0016512 0.16137227
9300 0 -2.9472939 1.0017975 1.9989921 0.16215333
9350 0 -2.9475134 0.99805495 2.0059438 0.16298775
9400 0 -2.9477067 1.0051775 2.0062197 0.16391539
9450 0 -2.9479111 0.99831145 2.0047546 0.16407774
9500 0 -2.9482447 0.99930603 1.9963738 0.16447053
9550 0 -2.948327 1.0101585 2.0000122 0.16506399
9600 0 -2.9488093 0.99066285 1.9949896 0.1644946
9650 0 -2.9495068 1.0060732 1.998603 0.16487638
9700 0 -2.9498927 0.99416934 1.993023 0.16431692
9750 0 -2.9501915 0.99794357 1.9977593 0.16409568
9800 0 -2.9503301 1.0013601 2.0015327 0.16394552
9850 0 -2.9509928 0.99540881 1.9906278 0.16340106
9900 0 -2.9510973 1.0028842 1.9950601 0.16326575
9950 0 -2.9513759 0.98845981 1.996388 0.16215709
10000 0 -2.9520177 0.99596367 1.9897363 0.16157811
10050 0 -2.9522468 0.99679581 2.0001656 0.16070069
10100 0 -2.9524726 1.0022967 2.0041742 0.16051775
10150 0 -2.9533965 1.0066965 2.0041661 0.15987033
10200 0 -2.95372 1.0064187 2.0080976 0.15944129
10250 0 -2.9542481 1.00212 2.003804 0.15894079
10300 0 -2.9547387 1.0002364 2.0030264 0.15845404
10350 0 -2.9550625 1.0023699 2.0048795 0.15811212
10400 0 -2.9555375 1.0057419 2.0057972 0.15758359
10450 0 -2.9558283 1.0068905 2.0070409 0.15712094
10500 0 -2.9564079 1.0054007 2.006672 0.1561737
10550 0 -2.9570593 1.0026508 2.0042346 0.1552457
10600 0 -2.9574214 1.0059383 2.0058107 0.15489731
10650 0 -2.9577546 1.005882 2.0057875 0.15467861
10700 0 -2.9581171 1.0052836 2.0050208 0.15448129
10750 0 -2.9584536 1.0060913 2.0077875 0.1542476
10800 0 -2.9588969 1.0015916 2.0047995 0.15397106
10850 0 -2.9593001 1.0001643 2.0022744 0.15384155
10900 0 -2.9596522 1.0060791 2.0077143 0.15364284
10950 0 -2.9601255 1.0049537 2.0052504 0.15341378
11000 0 -2.9604759 1.0054856 2.0067028 0.15320131
11050 0 -2.9610382 1.0052597 2.0063512 0.15273334
11100 0 -2.9618788 1.0029076 2.0053227 0.15159317
11150 0 -2.9623432 1.0053897 2.0059129 0.1505748
11200 0 -2.9628034 1.0059443 2.0077882 0.14932624
11250 0 -2.9633145 1.0049694 2.0084286 0.14765038
11300 0 -2.9639729 0.99732434 1.9995257 0.145922
11350 0 -2.964303 1.0049486 2.000248 0.14460607
11365 0 -2.9643087 1.0049729 2.0053533 0.14403899
Loop time of 2.83502 on 1 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.89547702741 -2.96460328213 -2.96430868154
Force two-norm initial, final = 3665.97 9.17614
Force max component initial, final = 2998.7 4.66725
Final line search alpha, max atom move = 3.63787e-05 0.000169788
Iterations, force evaluations = 10000 10013
Pair time (%) = 1.92875 (68.033)
Neigh time (%) = 0.00763345 (0.269255)
Comm time (%) = 0.0281737 (0.993773)
Outpt time (%) = 0.247626 (8.73452)
Other time (%) = 0.622838 (21.9694)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 329 ave 329 max 329 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7348 ave 7348 max 7348 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7348
Ave neighs/atom = 9.185
Neighbor list builds = 34
Dangerous builds = 0

352
examples/min/log.min.box.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 2.06114 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.0715443 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0323449 (45.2097)
Neigh time (%) = 0.0118631 (16.5815)
Comm time (%) = 0.0133407 (18.6468)
Outpt time (%) = 0.00649107 (9.07279)
Other time (%) = 0.00750446 (10.4893)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74779 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.74465936 0 -0.74465936 13.069823
1050 0 -2.8198371 0 -2.8198371 -1.1103791
1100 0 -2.8554989 0 -2.8554989 -1.1086189
1150 0 -2.8646695 0 -2.8646695 -1.0612352
1200 0 -2.8688213 0 -2.8688213 -1.0735655
1250 0 -2.8764988 0 -2.8764988 -1.0709208
1300 0 -2.8776606 0 -2.8776606 -1.0836353
1350 0 -2.8789379 0 -2.8789379 -1.0942716
1365 0 -2.879076 0 -2.879076 -1.096544
Loop time of 0.11008 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.0649455 (58.9985)
Neigh time (%) = 0.00446945 (4.06019)
Comm time (%) = 0.0151595 (13.7714)
Outpt time (%) = 0.00723684 (6.57416)
Other time (%) = 0.0182686 (16.5958)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.74779 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
1400 0 -2.8859021 -0.86433583 -0.91383427 0.038857701
1450 0 -2.8929425 -0.58254768 -0.55566103 0.040538566
1500 0 -2.8965978 -0.28286668 -0.1626189 0.042018049
1550 0 -2.8967407 0.032456402 0.26748547 0.043240071
1600 0 -2.8932955 0.35812302 0.7335883 0.044447837
1650 0 -2.8863237 0.682558 1.2350215 0.044882248
1700 0 -2.8764383 0.96551454 1.7560104 0.044121022
1750 0 -2.8722126 1.0007211 2.001659 0.040886669
1800 0 -2.8731947 0.99598883 1.9944489 0.039649372
1850 0 -2.8735769 1.0019679 2.0025324 0.038214836
1900 0 -2.8740924 1.0039028 2.0049661 0.0364131
1950 0 -2.8744449 1.0036154 2.0046688 0.035279925
2000 0 -2.8749546 1.0003317 2.0003019 0.033624392
2050 0 -2.8752113 1.0024154 2.003108 0.032529652
2100 0 -2.8755863 1.0006463 2.0008216 0.031332915
2150 0 -2.8758611 1.002097 2.0027278 0.030028028
2200 0 -2.8763456 0.99313594 1.9909038 0.029170399
2250 0 -2.8763611 1.001124 2.0014434 0.028055774
2300 0 -2.8768055 0.99268167 1.9903215 0.027423255
2350 0 -2.876596 1.0044503 2.0063366 0.026630517
2400 0 -2.8768156 1.0048052 2.006267 0.025754063
2450 0 -2.877 1.0029729 2.0042275 0.025312769
2500 0 -2.8771948 1.0009424 2.0018459 0.024849257
2550 0 -2.8773052 1.0021762 2.0015675 0.0245549
2600 0 -2.877329 1.0032552 2.0053419 0.024285495
2650 0 -2.8774169 1.0045103 2.0055678 0.023951101
2700 0 -2.8775487 1.0026961 2.0043051 0.023528378
2750 0 -2.8776381 1.0038373 2.0043152 0.023284152
2800 0 -2.8777438 1.0025852 2.0042121 0.023038202
2850 0 -2.8778409 1.0036658 2.0040164 0.022781788
2900 0 -2.8779418 1.0024241 2.0040794 0.022526058
2950 0 -2.8780469 1.0033018 2.003366 0.022367971
3000 0 -2.8781459 1.0021012 2.0037093 0.02218872
3050 0 -2.8782281 1.0037187 2.0040777 0.021947328
3100 0 -2.8783303 1.0026555 2.0043585 0.021767142
3150 0 -2.8784265 1.0040469 2.0045436 0.021689896
3200 0 -2.8785393 1.002822 2.0046627 0.02147584
3250 0 -2.8786445 1.0039501 2.0045554 0.021385033
3300 0 -2.8787673 1.0027297 2.0045142 0.021210518
3350 0 -2.8788761 1.0039942 2.0044454 0.021184019
3400 0 -2.8789983 1.0027675 2.0046286 0.021031369
3450 0 -2.8791331 1.0036619 2.0039691 0.021012703
3500 0 -2.8792551 1.0028017 2.004602 0.020966397
3550 0 -2.8793894 1.003909 2.0042982 0.021192971
3600 0 -2.8795326 1.0027503 2.0044902 0.021201934
3650 0 -2.8796806 1.0038568 2.0042569 0.021417386
3700 0 -2.8798273 1.0029323 2.0047788 0.021514403
3750 0 -2.8799858 1.0038788 2.0042954 0.0218479
3800 0 -2.8801358 1.0030669 2.0049202 0.022078412
3850 0 -2.88031 1.0038017 2.0042978 0.022506483
3900 0 -2.8804829 1.0027534 2.0044844 0.022850647
3950 0 -2.8806581 1.0038138 2.0042384 0.023292834
4000 0 -2.8808407 1.0028503 2.0046401 0.02376443
4050 0 -2.8810335 1.0038535 2.0042663 0.024339409
4100 0 -2.8812238 1.002887 2.0047023 0.024860826
4150 0 -2.8814293 1.0037623 2.0041634 0.025508754
4200 0 -2.8816388 1.0024715 2.0041878 0.02612545
4250 0 -2.8818341 1.0040196 2.0045261 0.02670395
4300 0 -2.8820541 1.0027644 2.004513 0.027345325
4350 0 -2.8822741 1.003823 2.0042576 0.027932695
4400 0 -2.8824966 1.0029548 2.0048004 0.028481166
4450 0 -2.8827271 1.0038939 2.0043389 0.028965346
4500 0 -2.8829624 1.0027782 2.0045337 0.029379154
4550 0 -2.8831963 1.003917 2.0043942 0.029883101
4600 0 -2.8834415 1.0027006 2.0044529 0.030194687
4650 0 -2.8836707 1.004204 2.0047435 0.03058987
4700 0 -2.8839385 1.0025337 2.0041677 0.030956131
4750 0 -2.8841696 1.0040513 2.0045812 0.031267718
4800 0 -2.8844289 1.0028263 2.0046087 0.031459971
4850 0 -2.8846789 1.0039962 2.0045076 0.031559649
4900 0 -2.8849423 1.0027103 2.0044871 0.031541119
4950 0 -2.8851984 1.0038987 2.0043501 0.031504737
5000 0 -2.8854623 1.0028106 2.0045239 0.03131034
5050 0 -2.8857234 1.0039197 2.004387 0.031135545
5100 0 -2.8859937 1.0027585 2.0044828 0.030697605
5150 0 -2.8862597 1.0038645 2.0043089 0.030293541
5200 0 -2.8865381 1.0027994 2.0045186 0.029623524
5250 0 -2.88681 1.0038811 2.0042537 0.028917165
5300 0 -2.8870885 1.002855 2.0045603 0.028128479
5350 0 -2.8873684 1.0038929 2.0043454 0.027396573
5400 0 -2.8876533 1.0028036 2.0045349 0.026515815
5450 0 -2.8879295 1.0039241 2.0044708 0.025605993
5500 0 -2.8882196 1.0028328 2.0045839 0.024608793
5550 0 -2.8884951 1.0042254 2.0048137 0.023592363
5600 0 -2.8888019 1.0026824 2.0043615 0.022365696
5650 0 -2.8890695 1.0042573 2.004858 0.021119983
5700 0 -2.8893683 1.0029897 2.0048243 0.019655885
5750 0 -2.8896608 1.0040217 2.004519 0.018148474
5800 0 -2.889929 1.003452 2.0055345 0.016414507
5850 0 -2.8902232 1.0043388 2.0049496 0.014558996
5900 0 -2.8905138 1.003015 2.0051027 0.012718438
5950 0 -2.8908027 1.0044593 2.0050273 0.010731375
6000 0 -2.8910994 1.0033418 2.0054062 0.0084243617
6050 0 -2.8913886 1.0048448 2.005437 0.0061645349
6100 0 -2.8917017 1.0032273 2.0053302 0.0035239708
6150 0 -2.892013 1.0046181 2.005243 0.0010297208
6200 0 -2.8922986 1.0052427 2.0036436 -0.00085451809
6250 0 -2.8925105 1.0045386 2.0043105 -0.0025359113
6300 0 -2.8927378 1.0048511 2.0054923 -0.0043813223
6350 0 -2.8930645 1.0042348 2.0065259 -0.007028015
6400 0 -2.8934703 1.0050593 2.0053088 -0.0097510973
6450 0 -2.8938803 1.0033855 2.0056149 -0.012358676
6500 0 -2.8943093 1.0053618 2.005737 -0.015043321
6550 0 -2.8947601 1.003862 2.0061985 -0.017476288
6600 0 -2.8952234 1.0054734 2.0061331 -0.01911825
6650 0 -2.8957243 1.0031743 2.0056224 -0.020515558
6700 0 -2.896183 1.0053521 2.0059515 -0.021398167
6750 0 -2.8966895 1.0030525 2.0053788 -0.021802355
6800 0 -2.897176 1.0056564 2.0063377 -0.021873988
6850 0 -2.8977738 1.0039066 2.0069573 -0.02211484
6900 0 -2.8984952 1.0059427 2.0063163 -0.022900331
6950 0 -2.8989903 1.0054436 2.0053754 -0.023744754
7000 0 -2.8994101 1.0041684 2.0027747 -0.024042754
7050 0 -2.8995952 1.003052 2.007007 -0.024317104
7100 0 -2.8999857 1.0059315 2.0033946 -0.024390198
7150 0 -2.9003558 1.0049199 2.0042743 -0.024516916
7200 0 -2.9007205 1.0039168 2.0056056 -0.024415801
7250 0 -2.9009886 1.0064434 2.0088317 -0.024333418
7300 0 -2.9015123 1.0032604 2.0056309 -0.024156095
7350 0 -2.9019505 1.0052277 2.00585 -0.02371615
7400 0 -2.9023932 1.0034613 2.0055996 -0.02336249
7450 0 -2.9027998 1.0049075 2.0055153 -0.02276292
7500 0 -2.9032147 1.0027226 2.0048171 -0.022349666
7550 0 -2.9035717 1.0048114 2.0053416 -0.021639322
7600 0 -2.9039627 1.0033139 2.0053568 -0.021010643
7650 0 -2.9043227 1.0049116 2.0055618 -0.020157464
7700 0 -2.9047039 1.0035393 2.0056222 -0.019429487
7750 0 -2.9050783 1.0047122 2.0052737 -0.018516554
7800 0 -2.9054697 1.0032076 2.0050219 -0.017915121
7850 0 -2.9058331 1.0049294 2.0055711 -0.017217886
7900 0 -2.9062384 1.0030931 2.0051791 -0.016803466
7950 0 -2.9066111 1.004879 2.0054492 -0.016446429
8000 0 -2.9070015 1.0037406 2.0059179 -0.016190429
8050 0 -2.9073907 1.0051121 2.0058715 -0.015959072
8100 0 -2.9078101 1.0027672 2.0048264 -0.015781535
8150 0 -2.9082048 1.0040906 2.0043566 -0.015660761
8200 0 -2.9085905 1.0027881 2.0047646 -0.015522749
8250 0 -2.9089503 1.0048712 2.0054963 -0.015327484
8300 0 -2.9093266 1.0039977 2.0061915 -0.015223258
8350 0 -2.9097087 1.0052083 2.0060824 -0.015242163
8400 0 -2.9101292 1.0032469 2.0052187 -0.015187053
8450 0 -2.910503 1.0050404 2.0057517 -0.014991867
8500 0 -2.9109187 1.0035111 2.0055974 -0.014904615
8550 0 -2.9113211 1.0049816 2.0057457 -0.01460732
8600 0 -2.9117378 1.002511 2.0044632 -0.014524792
8650 0 -2.9121228 1.0051961 2.0058515 -0.014176362
8700 0 -2.9125913 1.0034798 2.0055631 -0.013984156
8750 0 -2.913083 1.0050889 2.0054245 -0.013555799
8800 0 -2.9136265 1.0036018 2.0059662 -0.013073369
8850 0 -2.914259 1.0052194 2.0053716 -0.012320294
8900 0 -2.9149375 1.0034679 2.0057923 -0.011296714
8950 0 -2.9156352 1.00521 2.0054938 -0.010164259
9000 0 -2.9162926 1.0039334 2.0062977 -0.0097560664
9050 0 -2.9170336 0.99949421 2.0032139 -0.010037986
9100 0 -2.9174081 1.0054956 2.0075396 -0.010458294
9150 0 -2.9177587 1.0054855 2.0076688 -0.011020089
9200 0 -2.9181874 1.0045191 2.0083857 -0.012042582
9250 0 -2.9190522 0.99503626 1.9897169 -0.012752965
9300 0 -2.9191691 1.0005501 2.0010133 -0.013720313
9350 0 -2.9193578 1.0022621 2.0063209 -0.014421856
9400 0 -2.9197682 1.0050286 1.9991984 -0.014436476
9450 0 -2.9198328 1.0050846 2.0092974 -0.015229781
9500 0 -2.9202672 1.0042767 2.0024193 -0.015659591
9550 0 -2.9206876 0.99326798 1.9998234 -0.016390989
9600 0 -2.9207514 1.0011542 2.006155 -0.016584682
9650 0 -2.9211179 0.99713277 1.9959592 -0.016544806
9700 0 -2.921385 0.99349094 1.9916373 -0.016497285
9750 0 -2.9213164 1.0068609 2.0014286 -0.016156031
9800 0 -2.9219889 0.99723396 1.989454 -0.015264383
9850 0 -2.9218239 1.0017119 2.0037569 -0.014952239
9900 0 -2.9223294 1.0002507 1.9946351 -0.012804563
9950 0 -2.9223583 0.99412043 2.0011985 -0.012053285
10000 0 -2.9227193 0.99631795 1.9913372 -0.010017438
10050 0 -2.9227183 1.0019551 1.9979539 -0.0083216351
10100 0 -2.9228518 0.99803723 1.9958844 -0.0074905453
10150 0 -2.9226182 0.99786623 2.0129249 -0.006833704
10200 0 -2.9228329 0.99962232 2.0077079 -0.0049436783
10250 0 -2.9230958 1.0033134 2.0009986 -0.0023993558
10300 0 -2.9230785 1.0080784 2.0070812 -0.00051734835
10350 0 -2.9233427 1.0018114 2.0004348 0.0011874278
10400 0 -2.9234583 1.0006407 2.0004739 0.0030329504
10450 0 -2.9237261 0.99842738 1.9982674 0.006833001
10500 0 -2.9235931 1.0037677 2.0087914 0.0084276101
10550 0 -2.924115 1.0010028 1.9948024 0.013005956
10600 0 -2.9241951 0.99553091 1.9995839 0.015682423
10650 0 -2.9244907 0.99285012 1.9946234 0.019162956
10700 0 -2.9244299 1.006106 2.0030262 0.022319215
10750 0 -2.924846 0.99853313 1.9962008 0.026667777
10800 0 -2.9251948 0.99061339 1.9921659 0.030216187
10850 0 -2.9256677 0.99267741 1.99072 0.037019074
10900 0 -2.925891 0.99070701 1.9947866 0.040699308
10950 0 -2.9260822 0.99861686 1.9949331 0.043805098
11000 0 -2.9263829 0.9958498 1.9960836 0.047265756
11050 0 -2.926857 0.99510422 1.9918631 0.051663736
11100 0 -2.9272027 1.0012537 1.9979068 0.056939839
11150 0 -2.9275484 0.99693761 1.9999955 0.060601765
11200 0 -2.9280849 0.99569292 1.9942811 0.064732592
11250 0 -2.9286135 0.99170686 1.9913206 0.068852289
11300 0 -2.9288315 0.99652109 1.993871 0.071466174
11350 0 -2.9291322 0.99683019 2.0011103 0.075036039
11365 0 -2.9293296 0.99866306 1.9934484 0.075716815
Loop time of 1.26641 on 4 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.8790759758 -2.9296800688 -2.92932964187
Force two-norm initial, final = 3556.23 8.72586
Force max component initial, final = 2979.1 5.72551
Final line search alpha, max atom move = 4.8931e-05 0.000280155
Iterations, force evaluations = 10000 10049
Pair time (%) = 0.498641 (39.3744)
Neigh time (%) = 0.00170106 (0.134321)
Comm time (%) = 0.104978 (8.28939)
Outpt time (%) = 0.206677 (16.3199)
Other time (%) = 0.454413 (35.882)
Nlocal: 200 ave 205 max 194 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 178 ave 181 max 173 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 1857.5 ave 1884 max 1825 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 7430
Ave neighs/atom = 9.2875
Neighbor list builds = 29
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 17.1392 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.44651 -1917.3971 0 -149.11346 1306.17
20 539.94305 -1778.786 0 -150.72199 2492.7873
30 449.49509 -1506.4706 0 -151.12989 4667.6248
40 331.86049 -1151.7344 0 -151.09164 7379.764
50 258.27083 -929.8024 0 -151.05092 9103.558
60 256.1869 -923.58742 0 -151.1195 9252.9158
70 281.76061 -1000.7367 0 -151.1576 8739.2518
80 300.28534 -1056.589 0 -151.15321 8324.8812
90 305.83368 -1073.3097 0 -151.14426 8175.2478
100 304.06857 -1067.9843 0 -151.14112 8191.234
Loop time of 3.42775 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.28266 (95.7673)
Neigh time (%) = 0.0646169 (1.88511)
Comm time (%) = 0.0221677 (0.646713)
Outpt time (%) = 0.000880957 (0.0257008)
Other time (%) = 0.05742 (1.67515)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22235 ave 22235 max 22235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183715
Ave neighs/atom = 93.6092
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.10679e+03
Fix MSST e0 = to be -1.51141e+02
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 17.1456 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
Loop time of 4.37407 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.29205 (75.2628)
Neigh time (%) = 0.130561 (2.98489)
Comm time (%) = 0.0217173 (0.496501)
Outpt time (%) = 0.0132883 (0.303796)
Other time (%) = 0.916456 (20.952)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22205 ave 22205 max 22205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183494
Ave neighs/atom = 93.5997
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 5.52775 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.47212 -1917.4465 0 -149.08565 1305.7368
20 540.13678 -1779.3375 0 -150.68935 2488.8545
30 450.11466 -1508.2891 0 -151.08028 4655.1306
40 332.99843 -1155.1208 0 -151.04685 7357.5162
50 259.2571 -932.72753 0 -151.0022 9086.2087
60 256.22581 -923.67654 0 -151.0913 9257.1571
70 281.12085 -998.79866 0 -151.14863 8759.7887
80 299.37658 -1053.8476 0 -151.1519 8352.9467
90 304.24026 -1068.4941 0 -151.13319 8218.1594
100 301.9683 -1061.6332 0 -151.12284 8244.1277
Loop time of 0.927677 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.843839 (90.9625)
Neigh time (%) = 0.0167245 (1.80284)
Comm time (%) = 0.0490033 (5.28237)
Outpt time (%) = 0.000532866 (0.0574408)
Other time (%) = 0.0175777 (1.89481)
Nlocal: 5832 ave 5850 max 5813 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 10571 ave 10590 max 10553 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 545762 ave 548069 max 543643 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 2183047
Ave neighs/atom = 93.5805
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.18624e+03
Fix MSST e0 = to be -1.51123e+02
Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 5.52775 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
Loop time of 1.20185 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.855886 (71.214)
Neigh time (%) = 0.0341639 (2.84261)
Comm time (%) = 0.0578396 (4.81254)
Outpt time (%) = 0.00427949 (0.356076)
Other time (%) = 0.249681 (20.7747)
Nlocal: 5832 ave 5874 max 5803 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 10563.8 ave 10588 max 10526 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 545708 ave 550787 max 542668 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 2182834
Ave neighs/atom = 93.5714
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4394.41 2794.68 0.412792 4.89878 4588.5 0.435986 0.429935 1.89114 0 -3.05358 0.333333 -2.61759 0.666667 -2.74485 1 -3.04753
100 0.164918 0.117043 0.0732537 0.15376 0.168525 0.00709739 0.00227166 2.29242 0 -3.05359 0.320281 -3.04734 0.632798 -3.04649 1 -3.04876
167 0.0994897 0.0756458 0.0581442 0.0748326 0.209589 0.00708285 0.00226221 2.30722 0 -3.05359 0.31926 -3.04735 0.643078 -3.04651 1 -3.04877
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
167 0.209589 0.180304 0.0581442 0.0748326 0.209589 0.00708285 0.00226221 2.30722 0 -3.05359 0.31926 -3.04735 0.643078 -3.04651 1 -3.04877
267 0.15398 0.138423 0.0531882 0.0645605 0.15398 0.00709334 0.00227324 2.30913 0 -3.05359 0.319343 -3.04735 0.633026 -3.0465 1 -3.04877
339 0.0993121 0.0884507 0.0425229 0.0483306 0.0993121 0.00710366 0.00228423 2.31323 0 -3.05359 0.316066 -3.04739 0.617532 -3.04649 1 -3.04877

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LAMMPS (10 Jan 2012)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.4706 10.6542 0.404678 5.00393 14.6544 0.00184975 0.000683899 0.983929 0 -3.05148 0.333333 -3.04963 0.666667 -3.04964 1 -3.05032
100 0.306936 0.142146 0.0645404 0.189924 0.558396 0.00153707 0.00153179 1.15591 0 -3.05149 0.287862 -3.05036 0.589376 -3.04995 1 -3.05148
200 0.108674 0.0574548 0.0438421 0.05149 0.848466 0.00145851 0.00145766 1.16921 0 -3.05149 0.296608 -3.05032 0.622995 -3.05003 1 -3.05149
300 0.116622 0.0305167 0.0306663 0.034651 1.01168 0.00140647 0.00140608 1.17007 0 -3.05149 0.309843 -3.05026 0.641883 -3.05009 1 -3.05149
400 0.0571062 0.0165129 0.0209893 0.0233489 1.10722 0.0013733 0.00137311 1.17045 0 -3.05149 0.319454 -3.05022 0.652519 -3.05012 1 -3.05149
500 0.0936843 0.0214814 0.0148238 0.0166974 1.15805 0.0013547 0.00135461 1.17063 0 -3.05149 0.324916 -3.0502 0.658164 -3.05014 1 -3.05149
600 0.0256037 0.00569449 0.00957937 0.010672 1.19522 0.00134096 0.00134092 1.17082 0 -3.05149 0.328921 -3.05019 0.662223 -3.05015 1 -3.05149
700 0.0537028 0.0124766 0.00682065 0.00772411 1.24647 0.00133485 0.00133482 1.17089 0 -3.05149 0.330657 -3.05018 0.663973 -3.05016 1 -3.05149
720 0.00938685 0.0029987 0.00659695 0.00738331 1.24685 0.0013344 0.00133437 1.17091 0 -3.05149 0.330771 -3.05018 0.664084 -3.05016 1 -3.05149
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
720 1.24685 1.21665 0.00659695 0.00738331 1.24685 0.0013344 0.00133437 1.17091 0 -3.05149 0.330771 -3.05018 0.664084 -3.05016 1 -3.05149
820 0.141266 0.078847 0.00449505 0.0051238 0.141266 0.00160235 0.00160233 1.17165 0 -3.05149 0.285752 -3.05036 0.501494 -3.04989 1 -3.05149
920 0.0431108 0.0386382 0.00357902 0.00407779 0.0120304 0.00160204 0.00160203 1.17255 0 -3.05149 0.269474 -3.05045 0.503342 -3.04989 1 -3.05149
1020 0.0302964 0.0117196 0.0024504 0.00286103 0.0302964 0.00160193 0.00160192 1.17392 0 -3.05149 0.257973 -3.05051 0.504507 -3.04989 1 -3.05149
1102 0.00929979 0.00561668 0.00189518 0.00224715 0.00789551 0.00160187 0.00160187 1.17439 0 -3.05149 0.255249 -3.05053 0.504922 -3.04989 1 -3.05149

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LAMMPS (10 Jan 2012)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd id type x y z
thermo 1000
run 50000
Memory usage per processor = 2.06269 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1132807 0.27905278 0 1.3853755 6.5147704 189.52855
2000 1.0443617 0.2588631 0 1.2966975 5.8123077 189.52855
3000 0.99740048 0.30663122 0 1.2977979 6.7893948 189.52855
4000 1.0452154 0.2549558 0 1.2936386 5.9682721 189.52855
5000 1.0446171 0.24804329 0 1.2861316 6.0510081 189.52855
6000 0.99414736 0.27672942 0 1.2646634 6.1314117 189.52855
7000 0.98222339 0.25264497 0 1.2287295 5.835047 189.52855
8000 1.0949044 0.21576814 0 1.3038294 5.491461 189.52855
9000 1.0926686 0.24221385 0 1.3280532 6.3130763 189.52855
10000 1.076097 0.2855754 0 1.3549468 5.8734258 189.52855
11000 0.99180114 0.32327904 0 1.3088814 6.7664177 189.52855
12000 0.92157563 0.3649801 0 1.2807959 7.1346057 189.52855
13000 1.0357975 0.24757954 0 1.2769033 5.1431799 189.52855
14000 1.0007104 0.23333402 0 1.22779 5.7856096 189.52855
15000 0.99137134 0.24780673 0 1.232982 6.1361025 189.52855
16000 0.94735806 0.285215 0 1.2266521 6.5489235 189.52855
17000 0.92947519 0.35111458 0 1.2747806 6.8906691 189.52855
18000 0.93468492 0.30314528 0 1.2319884 6.7846869 189.52855
19000 0.97664561 0.22133285 0 1.1918744 5.1668518 189.52855
20000 0.92288444 0.24361535 0 1.1607318 5.8575076 189.52855
21000 0.95982212 0.23711835 0 1.1909416 6.1133698 189.52855
22000 0.94710657 0.30873344 0 1.2499206 6.7011709 189.52855
23000 0.95315902 0.25917016 0 1.2063719 6.436954 189.52855
24000 0.92248708 0.25883982 0 1.1755614 6.7367986 189.52855
25000 0.90317019 0.26834925 0 1.1658746 5.8271823 189.52855
26000 0.91432206 0.29952864 0 1.2081362 7.2639988 189.52855
27000 1.0070883 0.25437551 0 1.2551695 5.9319042 189.52855
28000 0.90757676 0.33894646 0 1.2408509 6.5341369 189.52855
29000 0.93635654 0.27447038 0 1.2049747 5.7410459 189.52855
30000 1.0260914 0.26547724 0 1.2851555 6.7175944 189.52855
31000 1.0885528 0.22068838 0 1.3024377 5.9614548 189.52855
32000 0.99983894 0.26432646 0 1.2579164 5.6537115 189.52855
33000 0.98254278 0.25012552 0 1.2265274 6.00352 189.52855
34000 1.0461448 0.239846 0 1.2794524 5.8594944 189.52855
35000 1.0600085 0.32706153 0 1.3804449 7.1757696 189.52855
36000 1.0293724 0.37370741 0 1.3966463 7.1818303 189.52855
37000 0.99724062 0.35645069 0 1.3474586 7.3712517 189.52855
38000 1.1355196 0.23285267 0 1.3612752 5.9101916 189.52855
39000 1.0750755 0.31068535 0 1.3790417 6.7523098 189.52855
40000 1.0269017 0.38361397 0 1.4040975 7.532356 189.52855
41000 0.98265149 0.34340216 0 1.3199121 6.9652101 189.52855
42000 0.95262128 0.36420847 0 1.3108759 7.5380723 189.52855
43000 1.0124646 0.25137287 0 1.2575095 6.6275506 189.52855
44000 0.95142407 0.29804153 0 1.2435192 5.9780096 189.52855
45000 0.99724723 0.19281581 0 1.1838302 5.4332418 189.52855
46000 0.90112949 0.29935892 0 1.1948564 7.0600659 189.52855
47000 0.8786086 0.34312007 0 1.2162374 6.4678979 189.52855
48000 1.0516991 0.17931414 0 1.2244401 5.5158284 189.52855
49000 0.98386816 0.26044721 0 1.2381662 5.8913908 189.52855
50000 1.0316312 0.19654107 0 1.2217246 5.2461518 189.52855
Loop time of 1.11272 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.191342 (17.1959)
Neigh time (%) = 0.138042 (12.4059)
Comm time (%) = 0.0544281 (4.89147)
Outpt time (%) = 0.0165617 (1.48841)
Other time (%) = 0.712341 (64.0183)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 351 ave 351 max 351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 351
Ave neighs/atom = 2.19375
Neighbor list builds = 5281
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd id type x y z
thermo 1000
run 50000
Memory usage per processor = 2.06107 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.124295 0.28924371 0 1.4065119 7.0530596 189.52855
2000 0.95544082 0.41610026 0 1.3655696 8.2906389 189.52855
3000 1.0379332 0.3006166 0 1.3320627 6.6571959 189.52855
4000 1.0384606 0.21868978 0 1.25066 5.5810527 189.52855
5000 0.94117133 0.28986466 0 1.2251537 6.7004134 189.52855
6000 0.8855088 0.29250925 0 1.1724836 6.0234641 189.52855
7000 0.89371735 0.22907448 0 1.1172061 6.0996491 189.52855
8000 0.91424769 0.21379978 0 1.1223334 5.3165508 189.52855
9000 0.90042293 0.21884136 0 1.1136366 5.488714 189.52855
10000 0.85048519 0.25030732 0 1.095477 5.6995459 189.52855
11000 0.84698813 0.26740545 0 1.1090999 6.0227022 189.52855
12000 0.84154976 0.27476871 0 1.1110588 6.1957407 189.52855
13000 0.95858623 0.24922085 0 1.2018159 6.1788034 189.52855
14000 1.0157016 0.23244337 0 1.2417968 5.2814755 189.52855
15000 0.97926185 0.25586043 0 1.2290019 5.7214261 189.52855
16000 0.97227188 0.31314055 0 1.2793357 6.8241506 189.52855
17000 0.96852981 0.35100395 0 1.3134804 7.0649028 189.52855
18000 1.1085654 0.27395528 0 1.3755921 6.7712736 189.52855
19000 0.96398963 0.37791005 0 1.3358747 7.2803968 189.52855
20000 1.1052139 0.22151699 0 1.3198233 6.1052352 189.52855
21000 1.0247925 0.27137274 0 1.2897603 6.5849207 189.52855
22000 0.93938839 0.30314207 0 1.2366593 6.595332 189.52855
23000 0.99334679 0.23591222 0 1.2230506 6.1878225 189.52855
24000 0.9073739 0.27521816 0 1.176921 5.9267087 189.52855
25000 0.94494463 0.22935535 0 1.1683941 5.9152216 189.52855
26000 0.86853642 0.29409501 0 1.1572031 5.954043 189.52855
27000 0.91743759 0.22878785 0 1.1404915 5.1643423 189.52855
28000 0.95477588 0.23984744 0 1.188656 5.7184042 189.52855
29000 0.9728079 0.302162 0 1.2688898 6.1654993 189.52855
30000 1.0845432 0.25760404 0 1.3353688 6.6720682 189.52855
31000 1.0888846 0.30003878 0 1.3821178 6.8362396 189.52855
32000 1.2042881 0.23686646 0 1.4336278 6.0455518 189.52855
33000 1.0808179 0.39386743 0 1.4679303 7.7909089 189.52855
34000 1.1867656 0.28673543 0 1.4660837 6.5948047 189.52855
35000 0.97028185 0.41374453 0 1.3779621 7.7807884 189.52855
36000 1.0002227 0.27651055 0 1.2704819 7.3760836 189.52855
37000 0.94660455 0.24652778 0 1.187216 6.332323 189.52855
38000 0.83178765 0.28892942 0 1.1155184 6.4123419 189.52855
39000 0.86265113 0.22371815 0 1.0809777 5.2045565 189.52855
40000 0.80881572 0.28461642 0 1.088377 6.5566203 189.52855
41000 0.94600979 0.1896898 0 1.129787 4.6552838 189.52855
42000 0.92929867 0.21915148 0 1.142642 5.2363189 189.52855
43000 0.90225107 0.25879289 0 1.1554049 5.4810849 189.52855
44000 0.93214308 0.25236925 0 1.1786864 5.90167 189.52855
45000 0.94582471 0.25130262 0 1.1912159 5.8566866 189.52855
46000 0.981087 0.23592648 0 1.2108817 5.5938166 189.52855
47000 0.92897315 0.28026887 0 1.2034359 6.4933631 189.52855
48000 0.94342409 0.25722392 0 1.1947516 5.9003272 189.52855
49000 0.95473713 0.24804712 0 1.1968171 5.451928 189.52855
50000 0.93532095 0.24225736 0 1.1717326 5.9796847 189.52855
Loop time of 1.00497 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.050068 (4.98203)
Neigh time (%) = 0.0387559 (3.85642)
Comm time (%) = 0.420196 (41.8117)
Outpt time (%) = 0.0153387 (1.52628)
Other time (%) = 0.480613 (47.8236)
Nlocal: 40 ave 41 max 38 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 35.75 ave 41 max 33 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 86.75 ave 90 max 82 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 347
Ave neighs/atom = 2.16875
Neighbor list builds = 5286
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom id type x y z vx vy
run 25000
Memory usage per processor = 2.06342 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.463265 1142.8674
1000 1 -0.33689286 0 0.34971312 1.2907615 1286.5545
2000 1 -0.36746164 0 0.31914434 1.1670767 1313.2217
3000 1 -0.52004751 0 0.16655848 1.4180076 1324.2707
4000 1 -0.50683859 0 0.17976739 1.4853867 1370.6777
5000 1 -0.49212307 0 0.19448291 1.2865932 1411.3324
6000 1 -0.45795739 0 0.22864859 1.242781 1441.6839
7000 1 -0.443252 0 0.24335398 1.2417302 1445.4704
8000 1 -0.37679433 0 0.30981165 1.1957462 1448.9419
9000 1 -0.41492237 0 0.27168361 1.0747045 1450.089
10000 1 -0.40197739 0 0.28462859 1.0279259 1456.1397
11000 1 -0.43056157 0 0.25604441 1.0722172 1449.4829
12000 1 -0.41156343 0 0.27504255 1.1499381 1452.9273
13000 1 -0.41466957 0 0.27193641 1.0548151 1455.565
14000 1 -0.41349951 0 0.27310647 1.0064325 1459.8774
15000 1 -0.4058151 0 0.28079088 0.96339054 1459.8033
16000 1 -0.37996671 0 0.30663928 1.0352366 1455.9433
17000 1 -0.35238448 0 0.3342215 0.94045311 1467.1239
18000 1 -0.39054272 0 0.29606326 1.0575731 1462.7124
19000 1 -0.36310964 0 0.32349634 0.97451832 1467.3645
20000 1 -0.37725444 0 0.30935154 0.98660138 1461.9506
21000 1 -0.37974771 0 0.30685827 0.94488958 1460.4569
22000 1 -0.35523952 0 0.33136646 1.0169815 1461.2727
23000 1 -0.36389429 0 0.32271169 1.0120096 1467.6367
24000 1 -0.40916195 0 0.27744403 0.95800623 1463.0811
25000 1 -0.39382698 0 0.292779 0.95226646 1460.6167
Loop time of 1.79053 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.497143 (27.7651)
Neigh time (%) = 0.13512 (7.54639)
Comm time (%) = 0.0265169 (1.48095)
Outpt time (%) = 0.147151 (8.21829)
Other time (%) = 0.984599 (54.9892)
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1647 ave 1647 max 1647 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1647
Ave neighs/atom = 2.14174
Neighbor list builds = 1647
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom id type x y z vx vy
run 25000
Memory usage per processor = 2.0558 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46218884 1142.8674
1000 1 -0.32494012 0 0.36166587 1.2242587 1282.3056
2000 1 -0.37815616 0 0.30844982 1.0644647 1312.3508
3000 1 -0.49062349 0 0.1959825 1.524186 1322.0444
4000 1 -0.50104961 0 0.18555637 1.4608096 1367.4322
5000 1 -0.46523216 0 0.22137383 1.3335657 1406.7051
6000 1 -0.47059773 0 0.21600825 1.2548634 1423.0902
7000 1 -0.44657953 0 0.24002645 1.106616 1436.7658
8000 1 -0.43539162 0 0.25121437 1.0742654 1442.8753
9000 1 -0.38186467 0 0.30474131 1.0117035 1447.3876
10000 1 -0.39896866 0 0.28763732 1.0524893 1446.5995
11000 1 -0.37849424 0 0.30811174 1.0893542 1442.4734
12000 1 -0.39472467 0 0.29188132 1.0838529 1443.7807
13000 1 -0.37490702 0 0.31169896 1.1173928 1457.8891
14000 1 -0.36757971 0 0.31902627 1.027341 1463.8882
15000 1 -0.40485222 0 0.28175376 1.0862575 1461.3309
16000 1 -0.38136304 0 0.30524295 1.0094705 1460.0656
17000 1 -0.37412919 0 0.3124768 0.99444621 1458.5668
18000 1 -0.36780296 0 0.31880302 0.99102309 1454.7293
19000 1 -0.36676642 0 0.31983956 0.98342341 1456.8015
20000 1 -0.39037633 0 0.29622965 1.0065285 1458.0052
21000 1 -0.37528404 0 0.31132195 0.93202146 1457.1218
22000 1 -0.40600625 0 0.28059973 1.0458453 1457.5121
23000 1 -0.37632791 0 0.31027808 0.91482419 1461.225
24000 1 -0.37066269 0 0.31594329 0.97118976 1456.6596
25000 1 -0.39711429 0 0.28949169 0.99340063 1456.4638
Loop time of 0.985739 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.12752 (12.9365)
Neigh time (%) = 0.0371044 (3.76412)
Comm time (%) = 0.235177 (23.858)
Outpt time (%) = 0.113567 (11.521)
Other time (%) = 0.47237 (47.9204)
Nlocal: 192.25 ave 234 max 156 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 42 ave 50 max 38 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 405 ave 561 max 281 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 1620
Ave neighs/atom = 2.10663
Neighbor list builds = 1629
Dangerous builds = 1

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LAMMPS (10 Jan 2012)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
compute bnd all property/local btype batom1 batom2
dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector = 0.268721
grid = 15 15 15
stencil order = 5
RMS precision = 4.86052e-05
using double precision FFTs
brick FFT buffer size/proc = 10648 3375 5808
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 23.1624 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4762
---------------- Step 50 ----- CPU = 0.9789 (sec) ----------------
TotEng = -5247.5491 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9502 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1770
E_coul = 26803.9897 E_long = -33907.2410 Press = -1331.7985
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23444e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38017e-06
31 104.52 0.000502314
---------------- Step 100 ----- CPU = 1.9692 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0555 Temp = 267.9664
PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.2248 E_long = -33906.1028 Press = -648.6626
---------------- Step 150 ----- CPU = 2.9897 (sec) ----------------
TotEng = -5287.2844 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26716.7991 E_long = -33906.8220 Press = -333.1910
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50835e-07
8 1.08 6.58286e-08
10 1.111 5.55388e-07
12 1.08 1.99221e-07
14 0.96 0
18 0.957201 3.59665e-06
31 104.52 0.000388185
---------------- Step 200 ----- CPU = 3.9658 (sec) ----------------
TotEng = -5308.4533 KinEng = 1100.5081 Temp = 273.5473
PotEng = -6408.9613 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253
E_coul = 26735.6522 E_long = -33901.9341 Press = -1470.4128
---------------- Step 250 ----- CPU = 4.9940 (sec) ----------------
TotEng = -5294.1792 KinEng = 1071.1638 Temp = 266.2533
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1951
E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442
E_coul = 26713.3850 E_long = -33908.2636 Press = -188.7517
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78179e-06
6 0.997001 3.49518e-06
8 1.08 2.09282e-06
10 1.111 5.64213e-06
12 1.08 2.10337e-06
14 0.96 0
18 0.957202 7.67601e-06
31 104.52 0.000806296
---------------- Step 300 ----- CPU = 6.0238 (sec) ----------------
TotEng = -5251.4367 KinEng = 1123.6268 Temp = 279.2938
PotEng = -6375.0634 E_bond = 14.2250 E_angle = 38.4733
E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4579
E_coul = 26744.9481 E_long = -33908.6682 Press = -469.4706
Loop time of 6.02383 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 4.59309 (76.2487)
Bond time (%) = 0.0151336 (0.251229)
Kspce time (%) = 0.68294 (11.3373)
Neigh time (%) = 0.624885 (10.3735)
Comm time (%) = 0.0330999 (0.549482)
Outpt time (%) = 0.00389695 (0.0646922)
Other time (%) = 0.0707846 (1.17508)
FFT time (% of Kspce) = 0.0814104 (11.9206)
FFT Gflps 3d (1d only) = 2.0208 3.32284
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708037 ave 708037 max 708037 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708037
Ave neighs/atom = 353.312
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
compute bnd all property/local btype batom1 batom2
dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector = 0.268721
grid = 15 15 15
stencil order = 5
RMS precision = 4.86052e-05
using double precision FFTs
brick FFT buffer size/proc = 4312 960 3696
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 10.6052 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4762
---------------- Step 50 ----- CPU = 0.2787 (sec) ----------------
TotEng = -5247.5491 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9502 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1770
E_coul = 26803.9897 E_long = -33907.2410 Press = -1331.7985
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23444e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38017e-06
31 104.52 0.000502314
---------------- Step 100 ----- CPU = 0.5594 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0555 Temp = 267.9664
PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.2248 E_long = -33906.1028 Press = -648.6626
---------------- Step 150 ----- CPU = 0.8540 (sec) ----------------
TotEng = -5287.2844 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26716.7991 E_long = -33906.8220 Press = -333.1910
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50835e-07
8 1.08 6.58286e-08
10 1.111 5.55388e-07
12 1.08 1.99221e-07
14 0.96 0
18 0.957201 3.59665e-06
31 104.52 0.000388185
---------------- Step 200 ----- CPU = 1.1363 (sec) ----------------
TotEng = -5308.4533 KinEng = 1100.5081 Temp = 273.5473
PotEng = -6408.9613 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253
E_coul = 26735.6522 E_long = -33901.9341 Press = -1470.4128
---------------- Step 250 ----- CPU = 1.4334 (sec) ----------------
TotEng = -5294.1792 KinEng = 1071.1638 Temp = 266.2533
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1951
E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442
E_coul = 26713.3850 E_long = -33908.2636 Press = -188.7517
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78179e-06
6 0.997001 3.49518e-06
8 1.08 2.09282e-06
10 1.111 5.64213e-06
12 1.08 2.10337e-06
14 0.96 0
18 0.957202 7.67601e-06
31 104.52 0.000806296
---------------- Step 300 ----- CPU = 1.7303 (sec) ----------------
TotEng = -5251.4368 KinEng = 1123.6268 Temp = 279.2938
PotEng = -6375.0636 E_bond = 14.2250 E_angle = 38.4733
E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4579
E_coul = 26744.9480 E_long = -33908.6682 Press = -469.4709
Loop time of 1.73038 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 1.19151 (68.8584)
Bond time (%) = 0.00421888 (0.243812)
Kspce time (%) = 0.250195 (14.459)
Neigh time (%) = 0.15806 (9.13441)
Comm time (%) = 0.0630846 (3.64571)
Outpt time (%) = 0.00369966 (0.213807)
Other time (%) = 0.0596095 (3.44488)
FFT time (% of Kspce) = 0.0367641 (14.6942)
FFT Gflps 3d (1d only) = 4.47485 11.6077
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177009 ave 180567 max 170213 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708037
Ave neighs/atom = 353.312
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
dump 1 all custom 100 dump.peri id type x y z c_1
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 24.3063 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.41008e-07
100 1.7890585e+24 552721.8 0 681881.47 1.5915936e+11 5.41008e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.0978012e+14 5.9404973e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.8437951e+14 8.6166616e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.7151711e+14 1.0705801e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.5382376e+14 1.3323008e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.6440558e+14 1.6138199e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.8055357e+14 2.0255833e-06
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.269543e+14 2.6348959e-06
900 1.2358398e+28 4532420.8 0 8.9673716e+08 1.8249063e+14 3.2593627e-06
1000 1.2341036e+28 3219674.5 0 8.9417099e+08 1.5276012e+14 3.8882369e-06
Loop time of 20.4975 on 1 procs for 1000 steps with 3487 atoms
Pair time (%) = 19.7817 (96.5078)
Neigh time (%) = 0.544173 (2.65483)
Comm time (%) = 0.00148797 (0.00725928)
Outpt time (%) = 0.0562642 (0.274493)
Other time (%) = 0.113892 (0.55564)
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 567135 ave 567135 max 567135 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
dump 1 all custom 100 dump.peri id type x y z c_1
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 18.8075 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.41008e-07
100 1.7890585e+24 552721.8 0 681881.47 1.5915936e+11 5.41008e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.0978012e+14 5.9404973e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.8437951e+14 8.6166616e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.7151711e+14 1.0705801e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.5382376e+14 1.3323008e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.6440558e+14 1.6138199e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.8055357e+14 2.0255833e-06
800 1.2424839e+28 2407365.3 0 8.994088e+08 2.269543e+14 2.6348959e-06
900 1.2358398e+28 4532420.4 0 8.9673716e+08 1.8249063e+14 3.2593627e-06
1000 1.2341035e+28 3219665.5 0 8.9417095e+08 1.5276012e+14 3.8882369e-06
Loop time of 5.88161 on 4 procs for 1000 steps with 3487 atoms
Pair time (%) = 5.07499 (86.2858)
Neigh time (%) = 0.140587 (2.39029)
Comm time (%) = 0.571109 (9.71008)
Outpt time (%) = 0.0524437 (0.891656)
Other time (%) = 0.0424765 (0.722191)
Nlocal: 871.75 ave 907 max 837 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1343.25 ave 1378 max 1308 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 141784 ave 169570 max 116650 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 9.58 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 185.87695 0 5000
2000 224 348.08417 0 5000
3000 224 565.2162 0 5000
4000 448 1042.9716 0 5000
5000 448 1542.0614 0 5000
6000 448 1766.5136 41.192729 5000
7000 672 1846.4596 67.352592 5000
8000 672 1814.3429 92.898167 5000
9000 672 1662.3648 111.88805 5000
10000 896 1654.7992 91.210682 5000
11000 896 1539.2643 72.174442 5000
12000 896 1479.3613 60.304466 5000
13000 1000 1464.6099 54.360683 5000
14000 1000 1357.776 50.981395 5000
15000 1000 1129.2816 50.644045 5000
16000 1000 795.55925 47.94934 5000
17000 1000 448.80612 42.4465 5000
18000 1000 320.15236 34.231318 5000
19000 1000 150.74762 35.789901 5000
20000 1000 49.636313 19.317565 5000
21000 1000 24.980341 13.517257 5000
22000 1000 17.164368 9.7652983 5000
23000 1000 15.131329 7.6229469 5000
24000 1000 13.291283 5.8822567 5000
25000 1000 12.481182 3.8348041 5000
Loop time of 2.97817 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.23279 (41.3941)
Neigh time (%) = 0.302755 (10.1658)
Comm time (%) = 0.0113213 (0.380143)
Outpt time (%) = 0.0628569 (2.11059)
Other time (%) = 1.36845 (45.9494)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2377 ave 2377 max 2377 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2377
Ave neighs/atom = 2.377
Neighbor list builds = 2001
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 9.54553 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 185.87695 0 5000
2000 224 348.08417 0 5000
3000 224 565.2162 0 5000
4000 448 1042.9716 0 5000
5000 448 1542.0614 0 5000
6000 448 1766.5136 41.192729 5000
7000 672 1846.4596 67.352592 5000
8000 672 1814.3429 92.898167 5000
9000 672 1662.3648 111.88805 5000
10000 896 1652.9645 91.148046 5000
11000 896 1544.0839 72.455734 5000
12000 896 1482.8514 61.292588 5000
13000 1000 1475.79 53.415861 5000
14000 1000 1352.8641 48.564355 5000
15000 1000 1139.726 49.60352 5000
16000 1000 764.34421 48.189757 5000
17000 1000 455.09361 40.071967 5000
18000 1000 327.13469 31.827836 5000
19000 1000 148.91195 27.999011 5000
20000 1000 38.454385 18.618798 5000
21000 1000 22.643678 12.282344 5000
22000 1000 15.147799 9.0623019 5000
23000 1000 14.799777 6.3928279 5000
24000 1000 13.08654 4.3024153 5000
25000 1000 9.9394032 2.8165017 5000
Loop time of 1.00262 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 0.317535 (31.6705)
Neigh time (%) = 0.0773075 (7.71053)
Comm time (%) = 0.0878609 (8.76312)
Outpt time (%) = 0.0486338 (4.85067)
Other time (%) = 0.471284 (47.0052)
Nlocal: 250 ave 256 max 242 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 17.75 ave 27 max 10 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 593.25 ave 615 max 562 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 2373
Ave neighs/atom = 2.373
Neighbor list builds = 1970
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 9.46169 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1425.0863 12.9927 6600
4000 804 1724.8532 47.325647 6600
5000 804 1598.6681 64.779741 6600
6000 804 1364.8231 61.75911 6600
7000 1206 1519.7287 69.028648 6600
8000 1206 1409.6162 62.604938 6600
9000 1206 1243.5344 53.025705 6600
10000 1608 1400.9581 57.452979 6600
11000 1608 1225.6036 52.631505 6600
12000 1608 1184.2735 45.623535 6600
13000 2010 1298.3639 50.266254 6600
14000 2010 1177.6607 41.899866 6600
15000 2010 986.18539 45.283438 6600
16000 2412 1032.5845 41.218715 6600
17000 2412 1024.6469 39.790283 6600
18000 2412 913.80876 40.351496 6600
19000 2814 1010.144 39.468447 6600
20000 2814 953.92496 40.689106 6600
21000 2814 762.62053 42.228087 6600
22000 2814 517.63012 38.535819 6600
23000 3000 424.8833 34.836058 6600
24000 3000 363.8636 21.972506 6600
25000 3000 210.08035 24.819644 6600
Loop time of 9.40419 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 5.45799 (58.0379)
Neigh time (%) = 1.0322 (10.9759)
Comm time (%) = 0.250612 (2.66489)
Outpt time (%) = 0.0380349 (0.404446)
Other time (%) = 2.62535 (27.9168)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 670 ave 670 max 670 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13595 ave 13595 max 13595 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13595
Ave neighs/atom = 4.53167
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.2619 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 210.08035 24.819644 6600
26000 3000 114.38566 17.150932 6600
27000 3000 104.67608 12.322911 6600
28000 3000 183.35846 11.491313 6600
29000 3000 304.77431 13.371079 6600
30000 3000 483.13283 15.775148 6600
31000 3000 698.65983 22.583167 6600
32000 3000 997.91493 29.132887 6600
33000 3000 1381.6582 36.071846 6600
34000 3000 1807.7933 39.766028 6600
35000 3000 2308.8013 49.301118 6600
36000 3000 2872.3529 55.638219 6600
37000 3000 3528.2521 68.672321 6600
38000 3000 4243.7668 78.210271 6600
39000 3000 5050.5727 86.453776 6600
40000 3000 5777.2063 90.664206 6600
41000 3000 6697.0059 105.74557 6600
42000 3000 7649.5485 121.09489 6600
43000 3000 8695.8277 129.0904 6600
44000 3000 9843.446 146.82081 6600
45000 3000 10998.776 143.2563 6600
46000 3000 12138.363 170.04079 6600
47000 3000 13412.445 174.29258 6600
48000 3000 14479.945 179.49372 6600
49000 3000 15616.206 182.18045 6600
50000 3000 16633.42 195.0737 6600
Loop time of 18.5002 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 12.0726 (65.2567)
Neigh time (%) = 1.54973 (8.37683)
Comm time (%) = 0.540591 (2.92209)
Outpt time (%) = 0.0597088 (0.322747)
Other time (%) = 4.27755 (23.1217)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 747 ave 747 max 747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13861 ave 13861 max 13861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13861
Ave neighs/atom = 4.62033
Neighbor list builds = 807
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
dump id all atom 1000 dump.pour
run 25000
Memory usage per processor = 9.33681 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1425.0863 12.9927 6600
4000 804 1724.8627 47.36161 6600
5000 804 1599.9516 63.808734 6600
6000 804 1359.1774 63.495338 6600
7000 1206 1532.7896 68.602762 6600
8000 1206 1403.0157 62.695773 6600
9000 1206 1247.1628 52.19506 6600
10000 1608 1387.5362 50.008374 6600
11000 1608 1228.9965 56.530496 6600
12000 1608 1182.7545 41.38682 6600
13000 2010 1319.2313 50.362256 6600
14000 2010 1190.8341 41.724733 6600
15000 2010 988.00931 42.639716 6600
16000 2412 1031.9305 42.375533 6600
17000 2412 1023.2524 38.401997 6600
18000 2412 888.81798 40.234895 6600
19000 2814 1013.2166 37.977584 6600
20000 2814 961.0454 42.964962 6600
21000 2814 756.00399 43.054932 6600
22000 2814 503.12293 39.636291 6600
23000 3000 412.84921 37.815016 6600
24000 3000 353.49951 20.864487 6600
25000 3000 222.50381 24.26074 6600
Loop time of 2.95472 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 1.40256 (47.4686)
Neigh time (%) = 0.270042 (9.13935)
Comm time (%) = 0.360771 (12.21)
Outpt time (%) = 0.0365846 (1.23818)
Other time (%) = 0.88476 (29.9439)
Nlocal: 750 ave 767 max 734 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 380.5 ave 388 max 372 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 3552 ave 3598 max 3519 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 14208
Ave neighs/atom = 4.736
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.1161 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 222.50381 24.26074 6600
26000 3000 103.84389 17.673297 6600
27000 3000 117.46883 12.700769 6600
28000 3000 202.8228 11.854593 6600
29000 3000 338.12554 14.379583 6600
30000 3000 530.86986 19.321511 6600
31000 3000 824.66397 26.939631 6600
32000 3000 1155.8653 30.710187 6600
33000 3000 1546.6549 39.339113 6600
34000 3000 1977.8218 45.981666 6600
35000 3000 2493.4385 56.240346 6600
36000 3000 3128.6938 61.747587 6600
37000 3000 3751.9442 68.433001 6600
38000 3000 4449.2141 80.107271 6600
39000 3000 5236.7855 88.674736 6600
40000 3000 6065.0048 98.949373 6600
41000 3000 6988.557 108.17154 6600
42000 3000 7978.2872 122.87119 6600
43000 3000 9163.9553 140.17673 6600
44000 3000 10400.417 145.57715 6600
45000 3000 11691.456 177.59735 6600
46000 3000 13208.301 188.38293 6600
47000 3000 14621.935 175.09272 6600
48000 3000 15911.432 200.24219 6600
49000 3000 17240.493 211.19416 6600
50000 3000 18716.039 229.23732 6600
Loop time of 5.63779 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 3.14085 (55.7107)
Neigh time (%) = 0.425642 (7.5498)
Comm time (%) = 0.570795 (10.1244)
Outpt time (%) = 0.0593259 (1.05229)
Other time (%) = 1.44118 (25.5628)
Nlocal: 750 ave 767 max 738 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 403.75 ave 414 max 396 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 3687.25 ave 3795 max 3643 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 14749
Ave neighs/atom = 4.91633
Neighbor list builds = 832
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
Processor partition = 0
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.02216 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.193194 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.189124 (97.8932)
Neigh time (%) = 0.00134206 (0.694669)
Comm time (%) = 0.000858307 (0.444272)
Outpt time (%) = 8.13007e-05 (0.0420825)
Other time (%) = 0.00178862 (0.925814)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.835
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:199)
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.054163 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1453.2509 -2126.4979 -2126.4979 16449.583 -16449.583
120 1640.3958 -2113.5727 -2113.5727 18469.616 -18469.616
130 1765.8167 -2109.1554 -2109.1554 19438.152 -19438.152
140 1727.5983 -2102.4557 -2102.4557 18703.763 -18703.763
150 1873.8652 -2105.5049 -2105.5049 18700.015 -18700.015
160 1740.1521 -2099.9445 -2099.9445 17850.695 -17850.695
170 1854.5372 -2101.9702 -2101.9702 17723.367 -17723.367
180 1788.5252 -2099.7644 -2099.7644 17796.757 -17796.757
190 1782.0313 -2097.2111 -2097.2111 17085.932 -17085.932
200 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
Loop time of 0.218796 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
100 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
110 1739.6511 -2090.6077 -2090.6077 15948.63 -15948.63
120 1712.9864 -2087.5346 -2087.5346 16028.758 -16028.758
130 1632.023 -2080.8455 -2080.8455 16292.761 -16292.761
140 1733.3057 -2086.0742 -2086.0742 15090.31 -15090.31
150 1739.3938 -2084.9124 -2084.9124 15081.918 -15081.918
160 1656.2093 -2077.9071 -2077.9071 16611.003 -16611.003
170 1734.9792 -2081.5311 -2081.5311 16511.598 -16511.598
180 1867.0258 -2088.5786 -2088.5786 16517.663 -16517.663
190 1859.2979 -2086.5014 -2086.5014 15835.134 -15835.134
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
Loop time of 0.225404 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
216 1868.7353 -2213.2677 -2213.2677 9444.9178 -9444.9178
Loop time of 0.0421531 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
200 1868.7353 -2083.245 -2083.245 15572.348 -15572.348
210 1881.8867 -2082.857 -2082.857 15333.566 -15333.566
220 1935.757 -2085.3056 -2085.3056 15507.872 -15507.872
230 1912.3683 -2082.841 -2082.841 14338.661 -14338.661
240 1753.2588 -2071.6079 -2071.6079 13605.421 -13605.421
250 1728.2117 -2069.2341 -2069.2341 12820.588 -12820.588
260 1835.1212 -2075.4787 -2075.4787 11970.037 -11970.037
270 1760.8425 -2069.7609 -2069.7609 13431.399 -13431.399
280 1819.1145 -2072.7978 -2072.7978 13843.416 -13843.416
290 1931.6502 -2079.3975 -2079.3975 14257.316 -14257.316
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
Loop time of 0.229863 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
318 1991.315 -2213.2946 -2213.2946 10290.671 -10290.671
Loop time of 0.0474689 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
310 1912.141 -2083.3513 -2083.3513 14100.457 -14100.457
320 1767.1362 -2080.7508 -2080.7508 13738.15 -13738.15
330 1893.2627 -2086.4709 -2086.4709 13308.437 -13308.437
340 1779.3615 -2084.7222 -2084.7222 11290.367 -11290.367
350 1840.5794 -2087.0052 -2087.0052 12245.306 -12245.306
360 1712.927 -2080.8869 -2080.8869 11630.287 -11630.287
370 1795.1829 -2080.1542 -2080.1542 11903.52 -11903.52
380 1828.9719 -2081.6588 -2081.6588 12611.779 -12611.779
390 1860.397 -2085.2626 -2085.2626 11645.979 -11645.979
400 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
Loop time of 0.227062 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
300 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
310 1717.6388 -2079.0268 -2079.0268 10581.957 -10581.957
320 1789.9235 -2083.2531 -2083.2531 11258.441 -11258.441
330 1764.9794 -2081.0181 -2081.0181 11462.171 -11462.171
340 1726.7798 -2077.8759 -2077.8759 11685.977 -11685.977
350 1794.5158 -2081.6454 -2081.6454 11583.204 -11583.204
360 1808.19 -2081.8003 -2081.8003 12387.732 -12387.732
370 1858.3457 -2084.3825 -2084.3825 13197.68 -13197.68
380 1906.8872 -2086.92 -2086.92 13054.839 -13054.839
390 1848.16 -2082.5114 -2082.5114 13515.286 -13515.286
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
Loop time of 0.227389 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
417 1820.8925 -2213.2897 -2213.2897 9117.3067 -9117.3067
Loop time of 0.042871 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
410 1847.8771 -2081.6391 -2081.6391 12838.569 -12838.569
420 1782.8346 -2076.9831 -2076.9831 12294.226 -12294.226
430 1758.055 -2074.9742 -2074.9742 11409.107 -11409.107
440 1849.7159 -2080.6063 -2080.6063 11615.729 -11615.729
450 1869.1231 -2081.506 -2081.506 12455.826 -12455.826
460 1790.313 -2075.9994 -2075.9994 13049.633 -13049.633
470 1815.1995 -2077.3516 -2077.3516 13045.061 -13045.061
480 1880.6611 -2081.396 -2081.396 11970.764 -11970.764
490 1815.7853 -2076.9102 -2076.9102 12251.974 -12251.974
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
Loop time of 0.229265 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
517 1864.8064 -2213.2124 -2213.2124 9411.2128 -9411.2128
Loop time of 0.0424261 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
510 1834.5308 -2077.9186 -2077.9186 12623.531 -12623.531
520 1821.9414 -2077.0496 -2077.0496 13905.708 -13905.708
530 1926.5524 -2083.9748 -2083.9748 14022.223 -14022.223
540 1900.0475 -2082.3932 -2082.3932 13519.516 -13519.516
550 1844.7474 -2079.0522 -2079.0522 13017.172 -13017.172
560 1851.9925 -2079.9135 -2079.9135 12830.136 -12830.136
570 1817.9413 -2078.1133 -2078.1133 12446.332 -12446.332
580 1765.4615 -2075.1011 -2075.1011 11172.734 -11172.734
590 1841.9645 -2080.5964 -2080.5964 11252.344 -11252.344
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
Loop time of 0.227968 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
619 1832.5281 -2213.2705 -2213.2705 9195.2704 -9195.2704
Loop time of 0.0435331 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
610 1787.5429 -2078.0256 -2078.0256 13240.463 -13240.463
620 1823.7995 -2080.9486 -2080.9486 12375.051 -12375.051
630 1853.2062 -2083.4589 -2083.4589 12983.625 -12983.625
640 1834.2035 -2082.851 -2082.851 13067.13 -13067.13
650 1789.0195 -2080.5378 -2080.5378 12947.796 -12947.796
660 1805.2876 -2082.2756 -2082.2756 12528.317 -12528.317
670 1839.5253 -2085.2087 -2085.2087 12508.998 -12508.998
680 1819.135 -2084.6004 -2084.6004 12615.631 -12615.631
690 1742.0477 -2080.2199 -2080.2199 12867.541 -12867.541
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
Loop time of 0.226393 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
716 1771.846 -2213.2414 -2213.2414 8780.9495 -8780.9495
Loop time of 0.0363538 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
700 1771.846 -2088.3939 -2088.3939 12152.346 -12152.346
710 1762.7562 -2088.4048 -2088.4048 11588.828 -11588.828
720 1677.307 -2083.3065 -2083.3065 10323.038 -10323.038
730 1638.8947 -2081.1322 -2081.1322 10662.708 -10662.708
740 1733.4188 -2087.5736 -2087.5736 11190.078 -11190.078
750 1745.235 -2088.4473 -2088.4473 12275.541 -12275.541
760 1799.948 -2092.108 -2092.108 13287.26 -13287.26
770 1805.9054 -2092.5319 -2092.5319 14221.436 -14221.436
780 1802.4038 -2092.3583 -2092.3583 13453.411 -13453.411
790 1728.5017 -2087.5173 -2087.5173 12749.412 -12749.412
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
Loop time of 0.226539 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
817 1695.7727 -2213.2643 -2213.2643 8256.0666 -8256.0666
Loop time of 0.045238 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
810 1723.8878 -2077.4775 -2077.4775 14056.576 -14056.576
820 1819.4569 -2078.5591 -2078.5591 14126.224 -14126.224
830 1857.684 -2082.1666 -2082.1666 13988.119 -13988.119
840 1817.2451 -2083.1231 -2083.1231 13507.31 -13507.31
850 1801.7367 -2083.0485 -2083.0485 13398.987 -13398.987
860 1800.2129 -2082.8677 -2082.8677 13538.068 -13538.068
870 1829.4598 -2084.6232 -2084.6232 13353.506 -13353.506
880 1713.8058 -2078.7287 -2078.7287 12668.351 -12668.351
890 1801.1051 -2078.5303 -2078.5303 12620.955 -12620.955
900 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
Loop time of 0.227415 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
800 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
810 1875.9494 -2083.067 -2083.067 12404.086 -12404.086
820 1765.2324 -2075.6435 -2075.6435 12708.749 -12708.749
830 1805.1712 -2078.1447 -2078.1447 12187.198 -12187.198
840 1899.9714 -2084.2726 -2084.2726 12555.644 -12555.644
850 1823.6926 -2079.2062 -2079.2062 12933.086 -12933.086
860 1809.2646 -2078.2623 -2078.2623 11742.131 -11742.131
870 1909.7967 -2084.9627 -2084.9627 11229.754 -11229.754
880 1764.4244 -2075.5143 -2075.5143 11457.095 -11457.095
890 1771.6808 -2076.1399 -2076.1399 11453.854 -11453.854
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
Loop time of 0.227548 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
919 1865.5698 -2213.3124 -2213.3124 9426.4803 -9426.4803
Loop time of 0.048948 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
900 1865.5698 -2081.8053 -2081.8053 13628.128 -13628.128
910 1841.8133 -2080.4515 -2080.4515 13654.3 -13654.3
920 1749.7144 -2074.6188 -2074.6188 12839.204 -12839.204
930 1821.6017 -2079.6013 -2079.6013 12167.782 -12167.782
940 1780.9248 -2077.1578 -2077.1578 12235.554 -12235.554
950 1762.8345 -2076.2012 -2076.2012 11833.919 -11833.919
960 1806.203 -2079.2727 -2079.2727 12022.387 -12022.387
970 1804.2459 -2079.3716 -2079.3716 12365.406 -12365.406
980 1761.8387 -2076.7964 -2076.7964 12458.703 -12458.703
990 1836.2958 -2081.9304 -2081.9304 12598.164 -12598.164
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
Loop time of 0.227442 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
1017 1865.0257 -2213.2668 -2213.2668 9416.317 -9416.317
Loop time of 0.042254 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
1010 1761.782 -2083.3408 -2083.3408 12613.089 -12613.089
1020 1770.1696 -2081.6751 -2081.6751 12434.518 -12434.518
1030 1768.5769 -2079.8994 -2079.8994 12854.085 -12854.085
1040 1792.1357 -2079.6761 -2079.6761 12773.174 -12773.174
1050 1806.4749 -2080.3993 -2080.3993 13958.637 -13958.637
1060 1845.1324 -2083.7096 -2083.7096 13427.182 -13427.182
1070 1876.1853 -2089.1565 -2089.1565 12775.944 -12775.944
1080 1765.8044 -2087.3727 -2087.3727 12387.705 -12387.705
1090 1838.2298 -2090.426 -2090.426 12939.571 -12939.571
1100 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
Loop time of 0.225438 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1000 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
1010 1772.8609 -2089.6666 -2089.6666 12540.188 -12540.188
1020 1770.1379 -2089.9786 -2089.9786 12184.488 -12184.488
1030 1656.6786 -2082.9255 -2082.9255 12022.316 -12022.316
1040 1702.4827 -2086.2684 -2086.2684 10641.654 -10641.654
1050 1674.8977 -2084.6421 -2084.6421 11257.979 -11257.979
1060 1676.1205 -2084.7766 -2084.7766 12111.764 -12111.764
1070 1778.8497 -2091.4724 -2091.4724 12971.534 -12971.534
1080 1779.3081 -2091.3613 -2091.3613 12566.776 -12566.776
1090 1668.192 -2083.8243 -2083.8243 12813.326 -12813.326
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
Loop time of 0.226201 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
1116 1754.5887 -2213.2659 -2213.2659 8660.0106 -8660.0106
Loop time of 0.0410688 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
1110 1848.3952 -2094.8662 -2094.8662 12871.151 -12871.151
1120 1738.0586 -2087.0603 -2087.0603 13998.616 -13998.616
1130 1728.3695 -2085.8036 -2085.8036 14319.362 -14319.362
1140 1841.826 -2092.4967 -2092.4967 13691.837 -13691.837
1150 1797.9782 -2088.7251 -2088.7251 13942.683 -13942.683
1160 1783.6033 -2086.8622 -2086.8622 13738.416 -13738.416
1170 1807.3027 -2087.4147 -2087.4147 13420.976 -13420.976
1180 1815.9792 -2086.9303 -2086.9303 12722.057 -12722.057
1190 1739.4179 -2080.8105 -2080.8105 12854.023 -12854.023
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
Loop time of 0.226756 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
1218 1761.8697 -2213.3017 -2213.3017 8713.6317 -8713.6317
Loop time of 0.047081 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
1210 1760.7244 -2079.9528 -2079.9528 12012.593 -12012.593
1220 1752.9287 -2078.2871 -2078.2871 11916.806 -11916.806
1230 1838.3629 -2082.7918 -2082.7918 12841.149 -12841.149
1240 1870.3467 -2083.881 -2083.881 13974.686 -13974.686
1250 1781.4455 -2077.1866 -2077.1866 13743.967 -13743.967
1260 1829.5891 -2079.6638 -2079.6638 12847.61 -12847.61
1270 1859.3421 -2081.0235 -2081.0235 12227.579 -12227.579
1280 1778.2976 -2075.2099 -2075.2099 12092.041 -12092.041
1290 1802.5006 -2076.4007 -2076.4007 12166.805 -12166.805
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
Loop time of 0.228955 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
1319 1858.5552 -2213.2905 -2213.2905 9377.5263 -9377.5263
Loop time of 0.0523891 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
1310 1883.892 -2081.1414 -2081.1414 13154.969 -13154.969
1320 1918.1413 -2083.2747 -2083.2747 14133.403 -14133.403
1330 1939.2365 -2084.7147 -2084.7147 14302.027 -14302.027
1340 1866.4525 -2080.1222 -2080.1222 14374.257 -14374.257
1350 1810.4562 -2076.7079 -2076.7079 12997.156 -12997.156
1360 1814.6292 -2077.2746 -2077.2746 11910.098 -11910.098
1370 1755.1167 -2073.6137 -2073.6137 11855.888 -11855.888
1380 1782.5531 -2075.6399 -2075.6399 12156.35 -12156.35
1390 1816.7724 -2078.0849 -2078.0849 12765.305 -12765.305
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
Loop time of 0.226615 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
1418 1837.2515 -2213.2909 -2213.2909 9231.4256 -9231.4256
Loop time of 0.045079 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1400 1837.2515 -2083.1407 -2083.1407 12986.943 -12986.943
1410 1822.713 -2082.4248 -2082.4248 14004.789 -14004.789
1420 1832.5229 -2083.3398 -2083.3398 15470.52 -15470.52
1430 1914.5807 -2089.0996 -2089.0996 15354.125 -15354.125
1440 1857.9286 -2085.8454 -2085.8454 13988.104 -13988.104
1450 1754.4226 -2079.5406 -2079.5406 13819.892 -13819.892
1460 1818.444 -2084.2673 -2084.2673 12996.924 -12996.924
1470 1825.4699 -2085.2741 -2085.2741 12289.466 -12289.466
1480 1723.4843 -2079.0743 -2079.0743 12726.17 -12726.17
1490 1818.4232 -2085.8377 -2085.8377 12243.424 -12243.424
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
Loop time of 0.228456 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
1519 1808.3404 -2213.302 -2213.302 9037.7704 -9037.7704
Loop time of 0.051872 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1500 1808.3404 -2088.1491 -2088.1491 13315.668 -13315.668
1510 1935.1323 -2097.1896 -2097.1896 13464.858 -13464.858
1520 1678.3356 -2081.0029 -2081.0029 13813.289 -13813.289
1530 1740.6495 -2085.7701 -2085.7701 12852.328 -12852.328
1540 1858.7458 -2094.2425 -2094.2425 11105.92 -11105.92
1550 1599.0288 -2077.7804 -2077.7804 10438.389 -10438.389
1560 1555.965 -2075.3756 -2075.3756 11066.476 -11066.476
1570 1782.1645 -2090.5618 -2090.5618 11513.89 -11513.89
1580 1639.6945 -2081.3242 -2081.3242 13028.031 -13028.031
1590 1706.6709 -2085.7625 -2085.7625 13989.78 -13989.78
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
Loop time of 0.226932 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
1617 2022.0741 -2213.2036 -2213.2036 10476.808 -10476.808
Loop time of 0.0423861 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
1610 1709.9018 -2082.1738 -2082.1738 11779.399 -11779.399
1620 1843.2806 -2085.0227 -2085.0227 12079.368 -12079.368
1630 1781.7944 -2083.8272 -2083.8272 11339.308 -11339.308
1640 1858.9199 -2087.7445 -2087.7445 11680.172 -11680.172
1650 1676.4808 -2079.6354 -2079.6354 10807.862 -10807.862
1660 1784.4381 -2078.5909 -2078.5909 10825.528 -10825.528
1670 1797.7974 -2078.4044 -2078.4044 11402.613 -11402.613
1680 1832.5315 -2080.5079 -2080.5079 12031.263 -12031.263
1690 1859.9425 -2084.4511 -2084.4511 12027.239 -12027.239
1700 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
Loop time of 0.226488 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1600 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
1610 1719.0554 -2079.054 -2079.054 11178.847 -11178.847
1620 1785.874 -2083.3136 -2083.3136 11151.584 -11151.584
1630 1709.212 -2078.0262 -2078.0262 11909.487 -11909.487
1640 1724.909 -2078.7337 -2078.7337 12338.207 -12338.207
1650 1851.0445 -2086.6016 -2086.6016 13182.101 -13182.101
1660 1877.9938 -2087.9289 -2087.9289 13545.96 -13545.96
1670 1859.7098 -2086.3587 -2086.3587 13586.735 -13586.735
1680 1856.0077 -2085.8266 -2085.8266 13326.439 -13326.439
1690 1852.5537 -2085.3781 -2085.3781 12829.132 -12829.132
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
Loop time of 0.22924 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
1719 1781.9012 -2213.2828 -2213.2828 8850.0906 -8850.0906
Loop time of 0.04285 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
1710 1744.9008 -2077.9268 -2077.9268 11732.091 -11732.091
1720 1752.0816 -2078.1361 -2078.1361 11741.531 -11741.531
1730 1828.2888 -2082.842 -2082.842 11720.773 -11720.773
1740 1786.3351 -2079.7361 -2079.7361 12450.459 -12450.459
1750 1778.8339 -2078.8936 -2078.8936 13103.956 -13103.956
1760 1869.5607 -2084.4952 -2084.4952 13328.105 -13328.105
1770 1901.6696 -2086.2777 -2086.2777 13723.6 -13723.6
1780 1863.4556 -2083.5556 -2083.5556 14468.139 -14468.139
1790 1783.3884 -2078.1381 -2078.1381 14221.764 -14221.764
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
Loop time of 0.227876 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
1819 1808.5452 -2213.309 -2213.309 9036.9782 -9036.9782
Loop time of 0.0527811 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1800 1808.5452 -2076.1141 -2076.1141 12641.91 -12641.91
1810 1782.0254 -2074.2029 -2074.2029 11987.656 -11987.656
1820 1834.1279 -2077.4569 -2077.4569 11478.352 -11478.352
1830 1791.6785 -2074.4904 -2074.4904 11268.276 -11268.276
1840 1710.0109 -2068.909 -2068.909 10673.193 -10673.193
1850 1793.8245 -2074.1497 -2074.1497 11497.954 -11497.954
1860 1876.3222 -2079.2504 -2079.2504 12338.777 -12338.777
1870 1854.3831 -2077.5204 -2077.5204 13414.981 -13414.981
1880 1873.4141 -2078.5705 -2078.5705 13586.534 -13586.534
1890 1905.1875 -2080.5343 -2080.5343 13730.745 -13730.745
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
Loop time of 0.228732 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
1920 1928.0686 -2213.2849 -2213.2849 9852.9888 -9852.9888
Loop time of 0.0546579 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
1910 1792.83 -2084.9923 -2084.9923 14194.264 -14194.264
1920 1848.1085 -2088.3062 -2088.3062 14021.427 -14021.427
1930 1801.6152 -2088.6097 -2088.6097 12402.211 -12402.211
1940 1728.0714 -2084.0635 -2084.0635 12172.687 -12172.687
1950 1873.5978 -2089.1424 -2089.1424 12450.15 -12450.15
1960 1750.3387 -2086.13 -2086.13 11887.665 -11887.665
1970 1810.8301 -2087.1529 -2087.1529 12874.661 -12874.661
1980 1698.2365 -2080.73 -2080.73 12126.298 -12126.298
1990 1825.6087 -2082.7204 -2082.7204 12862.535 -12862.535
2000 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
Loop time of 0.225392 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1900 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
1910 1792.7661 -2082.8528 -2082.8528 12367.878 -12367.878
1920 1800.2311 -2083.6545 -2083.6545 11883.087 -11883.087
1930 1804.2647 -2084.2645 -2084.2645 12020.625 -12020.625
1940 1854.7421 -2088.0162 -2088.0162 12265.553 -12265.553
1950 1748.1756 -2081.4807 -2081.4807 12398.959 -12398.959
1960 1715.3022 -2079.7847 -2079.7847 11986.482 -11986.482
1970 1809.2371 -2086.4247 -2086.4247 11679.461 -11679.461
1980 1800.4344 -2086.3399 -2086.3399 12025.457 -12025.457
1990 1697.0311 -2080.0216 -2080.0216 12687.338 -12687.338
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
Loop time of 0.225257 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
2019 1742.3339 -2213.2888 -2213.2888 8577.2768 -8577.2768
Loop time of 0.05128 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
2010 1819.1825 -2088.9481 -2088.9481 10969.804 -10969.804
2020 1688.1794 -2080.7333 -2080.7333 12075.819 -12075.819
2030 1742.9277 -2084.7042 -2084.7042 12353.472 -12353.472
2040 1852.3585 -2092.2678 -2092.2678 12215.689 -12215.689
2050 1752.6535 -2086.0967 -2086.0967 12274.557 -12274.557
2060 1678.177 -2081.5424 -2081.5424 12559.192 -12559.192
2070 1796.9922 -2089.6689 -2089.6689 12144.946 -12144.946
2080 1801.5169 -2090.2547 -2090.2547 12446.852 -12446.852
2090 1759.1092 -2087.7653 -2087.7653 12345.933 -12345.933
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
Loop time of 0.228941 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
2117 1761.5053 -2213.3069 -2213.3069 8711.9275 -8711.9275
Loop time of 0.0467501 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2100 1761.5053 -2081.5748 -2081.5748 11355.026 -11355.026
Loop time of 7.15226 on 1 procs for 17 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.35059 (18.8834)
Dynamics time (%) = 4.55177 (63.6411)
Quench time (%) = 0.919441 (12.8553)
Other time (%) = 0.0736308 (1.02948)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 96
Dangerous builds = 0

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examples/prd/log.prd.1.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
Processor partition = 1
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.02216 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.199531 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.195381 (97.92)
Neigh time (%) = 0.00138903 (0.696146)
Comm time (%) = 0.000852823 (0.427414)
Outpt time (%) = 6.96182e-05 (0.034891)
Other time (%) = 0.00183868 (0.921504)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.835
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:199)
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.05426 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1407.6264 -2123.5255 -2123.5255 16796.664 -16796.664
120 1740.5244 -2117.1258 -2117.1258 18709.166 -18709.166
130 1713.1995 -2109.2989 -2109.2989 18919.818 -18919.818
140 1779.4809 -2106.0183 -2106.0183 18935.633 -18935.633
150 1774.6703 -2102.5814 -2102.5814 18566.259 -18566.259
160 1764.4555 -2098.5966 -2098.5966 18247.113 -18247.113
170 1807.273 -2097.5073 -2097.5073 19262.305 -19262.305
180 1802.9051 -2096.2207 -2096.2207 18967.398 -18967.398
190 1818.8653 -2096.042 -2096.042 18419.673 -18419.673
200 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
Loop time of 0.219425 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
110 1745.3032 -2089.8161 -2089.8161 17154.684 -17154.684
120 1759.657 -2089.5011 -2089.5011 15296.251 -15296.251
130 1716.433 -2085.3645 -2085.3645 14320.132 -14320.132
140 1665.0731 -2080.6773 -2080.6773 13663.224 -13663.224
150 1673.2986 -2079.8264 -2079.8264 13049.78 -13049.78
160 1748.3061 -2083.2698 -2083.2698 13797.007 -13797.007
170 1765.6267 -2082.8476 -2082.8476 15017.251 -15017.251
180 1819.2949 -2084.8604 -2084.8604 15341.074 -15341.074
190 1856.6017 -2085.841 -2085.841 15232.338 -15232.338
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
Loop time of 0.227457 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
222 1837.7362 -2213.2958 -2213.2958 9231.1053 -9231.1053
Loop time of 0.051192 on 1 procs for 22 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
210 1840.6293 -2082.2033 -2082.2033 14844.948 -14844.948
220 1876.4513 -2083.4211 -2083.4211 14044.573 -14044.573
230 1830.1329 -2079.331 -2079.331 13271.066 -13271.066
240 1796.9539 -2076.207 -2076.207 13181.701 -13181.701
250 1815.7837 -2076.5264 -2076.5264 13920.64 -13920.64
260 1864.2627 -2078.8288 -2078.8288 14446.65 -14446.65
270 1823.3876 -2075.3079 -2075.3079 14537.612 -14537.612
280 1819.1185 -2074.2612 -2074.2612 14161.795 -14161.795
290 1917.7731 -2080.0422 -2080.0422 14106.458 -14106.458
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
Loop time of 0.227711 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
320 1873.3899 -2213.3069 -2213.3069 9479.7746 -9479.7746
Loop time of 0.0571289 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
310 1774.8865 -2074.3353 -2074.3353 15109.591 -15109.591
320 1909.8713 -2081.0651 -2081.0651 14297.983 -14297.983
330 1831.1736 -2082.648 -2082.648 13911.946 -13911.946
340 1782.9014 -2081.0633 -2081.0633 12948.277 -12948.277
350 1824.5061 -2082.2008 -2082.2008 12862.649 -12862.649
360 1872.7321 -2086.5367 -2086.5367 12420.995 -12420.995
370 1688.5932 -2078.7564 -2078.7564 11683.93 -11683.93
380 1864.9804 -2082.5641 -2082.5641 11669.845 -11669.845
390 1781.3406 -2080.8891 -2080.8891 11392.404 -11392.404
400 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
Loop time of 0.227479 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
310 1849.1709 -2083.1493 -2083.1493 11171.322 -11171.322
320 1830.1419 -2081.4047 -2081.4047 11369.031 -11369.031
330 1763.0288 -2076.5299 -2076.5299 12094.669 -12094.669
340 1878.1833 -2083.6662 -2083.6662 13264.506 -13264.506
350 1917.2697 -2085.8435 -2085.8435 13291.842 -13291.842
360 1795.9824 -2077.5749 -2077.5749 13016.539 -13016.539
370 1837.3619 -2080.0809 -2080.0809 11654.708 -11654.708
380 1885.8321 -2083.0993 -2083.0993 10923.765 -10923.765
390 1745.3951 -2073.7224 -2073.7224 11432.075 -11432.075
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
Loop time of 0.227269 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
420 1739.6563 -2213.2706 -2213.2706 8556.9364 -8556.9364
Loop time of 0.0570951 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
410 1865.528 -2081.2965 -2081.2965 11369.72 -11369.72
420 1817.039 -2077.9231 -2077.9231 12284.358 -12284.358
430 1841.0037 -2079.3779 -2079.3779 12199.662 -12199.662
440 1933.3949 -2085.4168 -2085.4168 12571.997 -12571.997
450 1824.2691 -2078.3022 -2078.3022 12475.107 -12475.107
460 1742.7526 -2073.0352 -2073.0352 13123.36 -13123.36
470 1904.6385 -2083.8117 -2083.8117 12367.287 -12367.287
480 1900.8084 -2083.7693 -2083.7693 11586.764 -11586.764
490 1765.8738 -2075.1817 -2075.1817 11148.626 -11148.626
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
Loop time of 0.226688 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
520 1818.1562 -2213.3028 -2213.3028 9100.7638 -9100.7638
Loop time of 0.0549002 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
510 1855.4317 -2081.7363 -2081.7363 10646.37 -10646.37
520 1767.2976 -2076.3 -2076.3 11298.884 -11298.884
530 1800.7868 -2078.8762 -2078.8762 10799.285 -10799.285
540 1817.9627 -2080.3797 -2080.3797 10703.952 -10703.952
550 1790.4703 -2078.9532 -2078.9532 11128.572 -11128.572
560 1808.189 -2080.5096 -2080.5096 10652.116 -10652.116
570 1830.4747 -2082.3843 -2082.3843 10627.271 -10627.271
580 1816.8801 -2081.9375 -2081.9375 10664.365 -10664.365
590 1746.6186 -2077.7546 -2077.7546 11742.416 -11742.416
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
Loop time of 0.227686 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
620 1761.9264 -2213.3164 -2213.3164 8715.1081 -8715.1081
Loop time of 0.050616 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
610 1830.7639 -2084.073 -2084.073 11771.278 -11771.278
620 1769.7037 -2080.4252 -2080.4252 11979.886 -11979.886
630 1822.9172 -2084.3132 -2084.3132 11300.932 -11300.932
640 1824.3493 -2084.8166 -2084.8166 10829.863 -10829.863
650 1733.4412 -2079.2284 -2079.2284 11599.031 -11599.031
660 1789.5315 -2083.281 -2083.281 12317.055 -12317.055
670 1854.9044 -2087.957 -2087.957 12396.242 -12396.242
680 1770.0585 -2082.762 -2082.762 12312.359 -12312.359
690 1791.3498 -2084.5474 -2084.5474 11710.405 -11710.405
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
Loop time of 0.227343 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
718 1879.1336 -2213.3003 -2213.3003 9517.1887 -9517.1887
Loop time of 0.046087 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
700 1879.1336 -2088.3939 -2088.3939 12889.204 -12889.204
710 1814.1237 -2084.5974 -2084.5974 12285.032 -12285.032
720 1755.5486 -2081.2365 -2081.2365 12206.775 -12206.775
730 1775.9721 -2083.0461 -2083.0461 12733.094 -12733.094
740 1774.9985 -2083.4078 -2083.4078 12653.923 -12653.923
750 1775.7013 -2083.8599 -2083.8599 12379.764 -12379.764
760 1776.7454 -2084.2994 -2084.2994 12627.379 -12627.379
770 1819.9834 -2087.5129 -2087.5129 11631.061 -11631.061
780 1809.3834 -2087.2039 -2087.2039 11047.665 -11047.665
790 1714.0167 -2081.2937 -2081.2937 11340.179 -11340.179
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
Loop time of 0.227306 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
818 1712.7589 -2213.2955 -2213.2955 8376.1803 -8376.1803
Loop time of 0.0474691 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
810 1792.7684 -2082.4358 -2082.4358 13429.873 -13429.873
820 1739.1918 -2078.6129 -2078.6129 13178.104 -13178.104
830 1864.638 -2083.0747 -2083.0747 12836.897 -12836.897
840 1765.781 -2081.0309 -2081.0309 13384.756 -13384.756
850 1752.7636 -2078.0967 -2078.0967 14021.396 -14021.396
860 1855.6782 -2081.935 -2081.935 13079.266 -13079.266
870 1819.6679 -2083.4249 -2083.4249 12377.61 -12377.61
880 1847.0607 -2086.7402 -2086.7402 13476.796 -13476.796
890 1788.2771 -2086.2175 -2086.2175 12947.672 -12947.672
900 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
Loop time of 0.225055 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
810 1817.715 -2087.8364 -2087.8364 11341.557 -11341.557
820 1719.0788 -2081.5392 -2081.5392 10897.597 -10897.597
830 1676.1893 -2078.8268 -2078.8268 11397.802 -11397.802
840 1780.9587 -2085.7277 -2085.7277 10862.292 -10862.292
850 1819.7436 -2088.2381 -2088.2381 11156.469 -11156.469
860 1718.1718 -2081.4821 -2081.4821 12556.104 -12556.104
870 1759.3307 -2084.0658 -2084.0658 13115.925 -13115.925
880 1878.3559 -2091.7336 -2091.7336 12178.258 -12178.258
890 1807.6117 -2086.9376 -2086.9376 11895.674 -11895.674
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
Loop time of 0.226523 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
920 1746.8208 -2213.2983 -2213.2983 8611.3134 -8611.3134
Loop time of 0.0547321 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
900 1746.8208 -2081.8053 -2081.8053 12812.552 -12812.552
910 1792.6751 -2084.6689 -2084.6689 12725.248 -12725.248
920 1789.7336 -2084.2674 -2084.2674 11813.766 -11813.766
930 1783.4345 -2083.6379 -2083.6379 11831.318 -11831.318
940 1713.795 -2078.7772 -2078.7772 11723.525 -11723.525
950 1711.3789 -2078.256 -2078.256 11640.181 -11640.181
960 1711.9374 -2077.7861 -2077.7861 12079.854 -12079.854
970 1759.9375 -2080.3175 -2080.3175 12605.261 -12605.261
980 1794.9009 -2081.8774 -2081.8774 13293.854 -13293.854
990 1839.5283 -2084.0415 -2084.0415 14232.329 -14232.329
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
Loop time of 0.228535 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
1018 1891.8985 -2213.3115 -2213.3115 9611.9555 -9611.9555
Loop time of 0.0493231 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
1010 1807.931 -2085.4113 -2085.4113 13673.347 -13673.347
1020 1848.8179 -2087.9387 -2087.9387 12159.14 -12159.14
1030 1783.9124 -2086.2028 -2086.2028 12085.317 -12085.317
1040 1802.125 -2085.6618 -2085.6618 13060.527 -13060.527
1050 1866.9247 -2089.4183 -2089.4183 12550.017 -12550.017
1060 1727.9726 -2084.048 -2084.048 12894.09 -12894.09
1070 1797.1898 -2083.1976 -2083.1976 13473.224 -13473.224
1080 1798.1026 -2082.3986 -2082.3986 13076.343 -13076.343
1090 1902.6166 -2088.501 -2088.501 13792.144 -13792.144
1100 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
Loop time of 0.224829 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
1010 1750.2024 -2083.9278 -2083.9278 12435.817 -12435.817
1020 1790.2529 -2085.7919 -2085.7919 12295.779 -12295.779
1030 1770.1234 -2083.6823 -2083.6823 12925.751 -12925.751
1040 1766.3321 -2082.6385 -2082.6385 13147.877 -13147.877
1050 1791.6431 -2083.5004 -2083.5004 13631.61 -13631.61
1060 1829.9027 -2085.2288 -2085.2288 14240.689 -14240.689
1070 1859.399 -2086.4419 -2086.4419 14082.458 -14082.458
1080 1885.6176 -2087.5558 -2087.5558 14640.987 -14640.987
1090 1886.2609 -2087.1345 -2087.1345 15532.317 -15532.317
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
Loop time of 0.226567 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
1118 1790.9433 -2213.2987 -2213.2987 8913.1864 -8913.1864
Loop time of 0.047663 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
1110 1814.3939 -2081.769 -2081.769 13689.839 -13689.839
1120 1833.7192 -2082.7815 -2082.7815 13519.243 -13519.243
1130 1796.837 -2080.1348 -2080.1348 14072.965 -14072.965
1140 1818.7494 -2081.3921 -2081.3921 13916.101 -13916.101
1150 1818.9994 -2081.2488 -2081.2488 13140.548 -13140.548
1160 1761.0556 -2077.2848 -2077.2848 13308.506 -13308.506
1170 1805.8494 -2080.0847 -2080.0847 13471.127 -13471.127
1180 1865.5836 -2083.8741 -2083.8741 14278.524 -14278.524
1190 1890.5694 -2085.4621 -2085.4621 15255.857 -15255.857
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
Loop time of 0.228073 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
1219 1871.5608 -2213.3158 -2213.3158 9468.276 -9468.276
Loop time of 0.0486791 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
1210 1868.7203 -2084.2286 -2084.2286 14757.029 -14757.029
1220 1845.9795 -2082.9747 -2082.9747 13416.768 -13416.768
1230 1721.0072 -2074.9829 -2074.9829 12653.426 -12653.426
1240 1728.2984 -2075.6335 -2075.6335 11904.94 -11904.94
1250 1760.6468 -2077.838 -2077.838 12363.743 -12363.743
1260 1790.6407 -2079.8354 -2079.8354 13772.489 -13772.489
1270 1855.4774 -2084.1181 -2084.1181 14259.348 -14259.348
1280 1909.5179 -2087.7772 -2087.7772 14969.305 -14969.305
1290 1843.272 -2083.6147 -2083.6147 15655.108 -15655.108
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
Loop time of 0.227671 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
1320 1850.0586 -2213.3195 -2213.3195 9322.6568 -9322.6568
Loop time of 0.052906 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
1310 1901.2957 -2088.0828 -2088.0828 14348.338 -14348.338
1320 1845.8424 -2084.9061 -2084.9061 13222.237 -13222.237
1330 1703.2439 -2075.9846 -2075.9846 13160.468 -13160.468
1340 1759.3432 -2080.0715 -2080.0715 12678.444 -12678.444
1350 1848.0856 -2086.283 -2086.283 12513.213 -12513.213
1360 1766.9936 -2081.3221 -2081.3221 13413.575 -13413.575
1370 1759.0589 -2081.1569 -2081.1569 14027.4 -14027.4
1380 1854.7078 -2087.8131 -2087.8131 13488.284 -13488.284
1390 1861.4274 -2088.694 -2088.694 13755.794 -13755.794
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
Loop time of 0.227602 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
1418 1786.8881 -2213.2846 -2213.2846 8886.069 -8886.069
Loop time of 0.0461481 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1786.8881 -2083.1407 -2083.1407 12641.043 -12641.043
1410 1812.2443 -2085.4259 -2085.4259 13130.596 -13130.596
1420 1781.5601 -2084.1148 -2084.1148 13794.095 -13794.095
1430 1816.6843 -2087.3261 -2087.3261 14262.13 -14262.13
1440 1776.0284 -2085.8037 -2085.8037 13506.678 -13506.678
1450 1747.7998 -2085.4471 -2085.4471 13056.821 -13056.821
1460 1778.5134 -2089.39 -2089.39 13266.78 -13266.78
1470 1840.1712 -2095.8688 -2095.8688 13524.008 -13524.008
1480 1746.1558 -2092.2341 -2092.2341 12369.096 -12369.096
1490 1661.5852 -2088.7904 -2088.7904 11360.287 -11360.287
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
Loop time of 0.227244 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
1519 1655.5694 -2213.2819 -2213.2819 7982.3333 -7982.3333
Loop time of 0.0530219 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1655.5694 -2088.1491 -2088.1491 12266.426 -12266.426
1510 1858.3169 -2102.6683 -2102.6683 11486.74 -11486.74
1520 1589.6231 -2085.7524 -2085.7524 12341.834 -12341.834
1530 1569.3501 -2084.7933 -2084.7933 11907.599 -11907.599
1540 1796.1688 -2099.8918 -2099.8918 10462.273 -10462.273
1550 1603.8116 -2087.2233 -2087.2233 11406.623 -11406.623
1560 1542.9429 -2083.0325 -2083.0325 12076.743 -12076.743
1570 1817.7406 -2100.7606 -2100.7606 11813.995 -11813.995
1580 1646.4361 -2088.9642 -2088.9642 13492.322 -13492.322
1590 1632.6599 -2087.4811 -2087.4811 14603.481 -14603.481
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
Loop time of 0.225425 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
1619 2009.4138 -2213.2965 -2213.2965 10413.156 -10413.156
Loop time of 0.0541222 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
1610 1697.1733 -2080.6515 -2080.6515 12137.525 -12137.525
1620 1884.5359 -2085.4978 -2085.4978 12301.761 -12301.761
1630 1799.0114 -2084.7875 -2084.7875 13001.402 -13001.402
1640 1822.4374 -2085.6471 -2085.6471 12188.808 -12188.808
1650 1813.8575 -2085.9718 -2085.9718 11877.305 -11877.305
1660 1784.9861 -2084.4001 -2084.4001 12331.077 -12331.077
1670 1847.3065 -2086.9388 -2086.9388 13451.768 -13451.768
1680 1758.4974 -2083.6409 -2083.6409 12744.573 -12744.573
1690 1865.6773 -2087.3989 -2087.3989 13885.825 -13885.825
1700 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
Loop time of 0.224672 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
1610 1781.1589 -2085.0991 -2085.0991 11779.473 -11779.473
1620 1751.0492 -2082.5729 -2082.5729 12098.338 -12098.338
1630 1750.1596 -2081.9145 -2081.9145 11669.766 -11669.766
1640 1799.536 -2084.5103 -2084.5103 12073.924 -12073.924
1650 1788.3038 -2083.0848 -2083.0848 12401.815 -12401.815
1660 1706.9461 -2077.0226 -2077.0226 11867.225 -11867.225
1670 1769.7603 -2080.398 -2080.398 11782.054 -11782.054
1680 1855.9414 -2085.2452 -2085.2452 11953.771 -11953.771
1690 1794.599 -2080.4156 -2080.4156 12986.207 -12986.207
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
Loop time of 0.226852 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
1717 1796.6882 -2213.286 -2213.286 8952.1586 -8952.1586
Loop time of 0.041991 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
1710 1908.9407 -2086.4998 -2086.4998 13426.557 -13426.557
1720 1895.1818 -2084.9898 -2084.9898 14259.836 -14259.836
1730 1821.3737 -2079.6705 -2079.6705 14430.721 -14430.721
1740 1891.4293 -2083.9221 -2083.9221 12809.819 -12809.819
1750 1839.7569 -2080.2332 -2080.2332 12449.372 -12449.372
1760 1742.4817 -2073.6038 -2073.6038 12438.333 -12438.333
1770 1747.721 -2073.6808 -2073.6808 12684.968 -12684.968
1780 1840.5898 -2079.4792 -2079.4792 12821.365 -12821.365
1790 1835.8529 -2078.8524 -2078.8524 12445.058 -12445.058
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
Loop time of 0.229047 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
1820 1839.1137 -2213.3043 -2213.3043 9252.8762 -9252.8762
Loop time of 0.053695 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1839.1137 -2076.1141 -2076.1141 12851.856 -12851.856
1810 1847.1948 -2076.4193 -2076.4193 12095.243 -12095.243
1820 1852.6203 -2076.6095 -2076.6095 12588.549 -12588.549
1830 1834.9309 -2075.3368 -2075.3368 12532.297 -12532.297
1840 1781.6431 -2071.7471 -2071.7471 11609.17 -11609.17
1850 1762.9842 -2070.4212 -2070.4212 11879.69 -11879.69
1860 1835.9552 -2075.0851 -2075.0851 12540.983 -12540.983
1870 1921.2641 -2080.5952 -2080.5952 13447.361 -13447.361
1880 1908.7351 -2079.7868 -2079.7868 13484.028 -13484.028
1890 1893.6986 -2078.9917 -2078.9917 13954.252 -13954.252
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
Loop time of 0.229312 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
1921 1883.1217 -2213.3197 -2213.3197 9553.4902 -9553.4902
Loop time of 0.05761 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
1910 1784.5237 -2084.6905 -2084.6905 13389.919 -13389.919
1920 1731.1905 -2080.6963 -2080.6963 12970.939 -12970.939
1930 1850.3131 -2084.6718 -2084.6718 13719.542 -13719.542
1940 1831.2993 -2087.5516 -2087.5516 13434.958 -13434.958
1950 1743.2339 -2084.7246 -2084.7246 14362.929 -14362.929
1960 1853.8244 -2089.3655 -2089.3655 13929.842 -13929.842
1970 1699.1334 -2083.859 -2083.859 13684.756 -13684.756
1980 1812.1618 -2085.8552 -2085.8552 14478.969 -14478.969
1990 1802.7775 -2087.2555 -2087.2555 14695.415 -14695.415
2000 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
Loop time of 0.226889 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
1910 1758.6133 -2087.016 -2087.016 13616.046 -13616.046
1920 1700.711 -2084.2588 -2084.2588 12824.655 -12824.655
1930 1751.7857 -2088.5085 -2088.5085 12349.562 -12349.562
1940 1754.9537 -2089.478 -2089.478 12280.371 -12280.371
1950 1685.603 -2085.509 -2085.509 13197.034 -13197.034
1960 1713.2304 -2087.7626 -2087.7626 13267.547 -13267.547
1970 1760.9078 -2091.2137 -2091.2137 13458.047 -13458.047
1980 1752.4605 -2090.8824 -2090.8824 14025.525 -14025.525
1990 1783.2844 -2093.0833 -2093.0833 13878.972 -13878.972
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
Loop time of 0.226081 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
2017 1795.4952 -2213.2891 -2213.2891 8939.1137 -8939.1137
Loop time of 0.0416958 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
2010 1716.471 -2088.9279 -2088.9279 13720.493 -13720.493
2020 1648.4001 -2084.439 -2084.439 13359.443 -13359.443
2030 1677.6114 -2086.2033 -2086.2033 13113.177 -13113.177
2040 1698.0201 -2087.2241 -2087.2241 13276.862 -13276.862
2050 1732.5808 -2089.0495 -2089.0495 13460.966 -13460.966
2060 1779.8938 -2091.6181 -2091.6181 13393.474 -13393.474
2070 1764.0047 -2089.9669 -2089.9669 14040.691 -14040.691
2080 1777.9135 -2090.2448 -2090.2448 14162.157 -14162.157
2090 1772.5816 -2089.2159 -2089.2159 13499.045 -13499.045
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
Loop time of 0.228604 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
2118 1714.5393 -2213.2509 -2213.2509 8384.1471 -8384.1471
Loop time of 0.0485499 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1714.5393 -2081.5748 -2081.5748 11032.46 -11032.46
Loop time of 7.15227 on 1 procs for 18 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.34835 (18.852)
Dynamics time (%) = 4.549 (63.6021)
Quench time (%) = 1.01463 (14.1861)
Other time (%) = 0.0759022 (1.06123)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 95
Dangerous builds = 0

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examples/prd/log.prd.2.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
Processor partition = 2
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.02216 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.194531 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.190471 (97.9129)
Neigh time (%) = 0.00134182 (0.689772)
Comm time (%) = 0.000848055 (0.435949)
Outpt time (%) = 7.72476e-05 (0.0397097)
Other time (%) = 0.00179291 (0.921657)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.835
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:199)
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.0546598 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1453.0014 -2126.4815 -2126.4815 17039.938 -17039.938
120 1712.5747 -2118.2811 -2118.2811 19245.699 -19245.699
130 1816.1055 -2117.2078 -2117.2078 19172.109 -19172.109
140 1741.5479 -2111.5113 -2111.5113 18643.317 -18643.317
150 1779.1262 -2108.4242 -2108.4242 18055.809 -18055.809
160 1708.5416 -2100.8014 -2100.8014 18706.608 -18706.608
170 1810.3199 -2099.9306 -2099.9306 18691.592 -18691.592
180 1805.675 -2098.8187 -2098.8187 17517.611 -17517.611
190 1827.5401 -2099.2194 -2099.2194 17130.547 -17130.547
200 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
Loop time of 0.218632 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
110 1740.3774 -2092.6139 -2092.6139 15523.606 -15523.606
120 1781.5972 -2093.9535 -2093.9535 14428.677 -14428.677
130 1684.5193 -2086.1781 -2086.1781 14825.487 -14825.487
140 1613.5723 -2080.1384 -2080.1384 14868.993 -14868.993
150 1755.5164 -2087.9807 -2087.9807 13748.119 -13748.119
160 1738.7712 -2085.2666 -2085.2666 14802.112 -14802.112
170 1674.8255 -2079.507 -2079.507 15674.35 -15674.35
180 1760.9622 -2083.599 -2083.599 15769.066 -15769.066
190 1899.9806 -2091.1229 -2091.1229 16231.019 -16231.019
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
Loop time of 0.22704 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
217 1814.7529 -2213.2613 -2213.2613 9069.1206 -9069.1206
Loop time of 0.037106 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
200 1814.7529 -2083.245 -2083.245 15201.593 -15201.593
210 1801.6419 -2081.0472 -2081.0472 15342.659 -15342.659
220 1881.8236 -2085.0669 -2085.0669 14755.087 -14755.087
230 1866.0873 -2082.8539 -2082.8539 13894.752 -13894.752
240 1792.3297 -2076.96 -2076.96 13354.538 -13354.538
250 1787.3004 -2075.652 -2075.652 13316.541 -13316.541
260 1830.871 -2077.5427 -2077.5427 12617.353 -12617.353
270 1791.7089 -2074.006 -2074.006 13195.786 -13195.786
280 1849.0237 -2076.8667 -2076.8667 13418.75 -13418.75
290 1929.6949 -2081.3067 -2081.3067 14728.325 -14728.325
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
Loop time of 0.226948 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
317 1879.9418 -2213.2283 -2213.2283 9516.969 -9516.969
Loop time of 0.044131 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
310 1838.8029 -2078.0409 -2078.0409 14753.009 -14753.009
320 1789.8725 -2076.7713 -2076.7713 15560.98 -15560.98
330 1950.1614 -2086.0999 -2086.0999 13361.512 -13361.512
340 1759.3354 -2082.9137 -2082.9137 12750.26 -12750.26
350 1857.8525 -2086.2264 -2086.2264 13541.869 -13541.869
360 1873.6249 -2090.6161 -2090.6161 12790.402 -12790.402
370 1704.2028 -2083.8532 -2083.8532 12022.063 -12022.063
380 1824.0288 -2084.9296 -2084.9296 13078.149 -13078.149
390 1823.8695 -2086.0185 -2086.0185 12394.039 -12394.039
400 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
Loop time of 0.226467 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
310 1790.3054 -2084.4713 -2084.4713 11190.448 -11190.448
320 1732.854 -2080.2375 -2080.2375 11020.269 -11020.269
330 1679.9775 -2076.2292 -2076.2292 10476.6 -10476.6
340 1706.236 -2077.3108 -2077.3108 10973.286 -10973.286
350 1798.7321 -2082.6213 -2082.6213 12099.734 -12099.734
360 1827.8354 -2083.7164 -2083.7164 12269.553 -12269.553
370 1803.5781 -2081.3205 -2081.3205 11882.622 -11882.622
380 1831.5584 -2082.4022 -2082.4022 11868.591 -11868.591
390 1865.1115 -2083.8776 -2083.8776 12451.163 -12451.163
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
Loop time of 0.226438 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
421 1885.8707 -2213.3072 -2213.3072 9565.3643 -9565.3643
Loop time of 0.0584321 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
410 1840.8997 -2081.0851 -2081.0851 13049.359 -13049.359
420 1860.5306 -2081.9195 -2081.9195 12866.668 -12866.668
430 1842.0725 -2080.3072 -2080.3072 11967.296 -11967.296
440 1778.5284 -2075.7716 -2075.7716 11672.911 -11672.911
450 1792.767 -2076.3662 -2076.3662 11362.562 -11362.562
460 1812.368 -2077.2861 -2077.2861 11982.449 -11982.449
470 1805.4534 -2076.4744 -2076.4744 11355.668 -11355.668
480 1771.7109 -2073.8789 -2073.8789 11574.724 -11574.724
490 1895.5684 -2081.6811 -2081.6811 10875.512 -10875.512
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
Loop time of 0.226524 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
519 1863.4356 -2213.2964 -2213.2964 9413.3063 -9413.3063
Loop time of 0.0513601 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
510 1811.0452 -2075.5953 -2075.5953 12654.915 -12654.915
520 1939.3016 -2083.9091 -2083.9091 12699.136 -12699.136
530 1865.6263 -2079.0274 -2079.0274 13205.704 -13205.704
540 1840.8195 -2077.4842 -2077.4842 13607.888 -13607.888
550 1910.185 -2082.2276 -2082.2276 13164.337 -13164.337
560 1897.5018 -2081.7046 -2081.7046 12541.871 -12541.871
570 1805.2364 -2076.0408 -2076.0408 12518.288 -12518.288
580 1820.8895 -2077.5197 -2077.5197 12510.55 -12510.55
590 1880.7209 -2081.9748 -2081.9748 11279.988 -11279.988
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
Loop time of 0.227256 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
621 1774.2632 -2213.3211 -2213.3211 8802.4378 -8802.4378
Loop time of 0.058917 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
610 1776.4519 -2076.2072 -2076.2072 11432.057 -11432.057
620 1866.4889 -2082.7151 -2082.7151 11939.587 -11939.587
630 1757.9348 -2076.135 -2076.135 12794.432 -12794.432
640 1821.0434 -2080.8738 -2080.8738 12398.818 -12398.818
650 1878.4228 -2085.2725 -2085.2725 13017.551 -13017.551
660 1874.4782 -2085.7432 -2085.7432 13297.304 -13297.304
670 1796.8744 -2081.4171 -2081.4171 12112.746 -12112.746
680 1789.2824 -2081.7003 -2081.7003 11627.391 -11627.391
690 1769.7646 -2081.1645 -2081.1645 12468.2 -12468.2
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
Loop time of 0.22626 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
720 1781.4831 -2213.249 -2213.249 8849.8358 -8849.8358
Loop time of 0.0443921 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
700 1781.4831 -2088.3939 -2088.3939 12218.534 -12218.534
710 1724.4898 -2085.2684 -2085.2684 11903.569 -11903.569
720 1764.7152 -2088.4829 -2088.4829 11526.3 -11526.3
730 1724.9813 -2086.3524 -2086.3524 12129.067 -12129.067
740 1711.2186 -2085.8354 -2085.8354 12875.329 -12875.329
750 1774.7765 -2090.326 -2090.326 12385.579 -12385.579
760 1787.964 -2091.4692 -2091.4692 11889.535 -11889.535
770 1711.6992 -2086.6713 -2086.6713 12283.555 -12283.555
780 1717.7443 -2087.2139 -2087.2139 11537.044 -11537.044
790 1683.3367 -2084.9743 -2084.9743 10800.126 -10800.126
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
Loop time of 0.226974 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
819 1631.6415 -2213.3087 -2213.3087 7818.8075 -7818.8075
Loop time of 0.0485699 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
810 1790.007 -2081.8313 -2081.8313 13202.119 -13202.119
820 1849.219 -2084.8387 -2084.8387 12576.218 -12576.218
830 1792.8687 -2084.1604 -2084.1604 11392.768 -11392.768
840 1731.9467 -2079.4445 -2079.4445 12892.679 -12892.679
850 1785.6213 -2078.2286 -2078.2286 13776.917 -13776.917
860 1831.1149 -2080.0094 -2080.0094 12904.24 -12904.24
870 1819.41 -2081.0253 -2081.0253 12547.946 -12547.946
880 1758.8325 -2078.0286 -2078.0286 12618.106 -12618.106
890 1763.5444 -2075.2871 -2075.2871 13398.793 -13398.793
900 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
Loop time of 0.226231 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
810 1851.8312 -2077.9782 -2077.9782 12015.32 -12015.32
820 1808.4808 -2074.7871 -2074.7871 11857.883 -11857.883
830 1828.2295 -2075.7871 -2075.7871 11715.86 -11715.86
840 1836.1989 -2076.03 -2076.03 12095.951 -12095.951
850 1806.7992 -2073.8356 -2073.8356 12485.462 -12485.462
860 1889.8731 -2079.0926 -2079.0926 12485.696 -12485.696
870 1879.6457 -2078.2828 -2078.2828 13039.623 -13039.623
880 1832.0939 -2075.1105 -2075.1105 12938.4 -12938.4
890 1875.4331 -2078.0004 -2078.0004 12216.702 -12216.702
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
Loop time of 0.228267 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
919 1914.4276 -2213.3188 -2213.3188 9764.087 -9764.087
Loop time of 0.049171 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
900 1914.4276 -2081.8053 -2081.8053 13963.686 -13963.686
910 1810.633 -2075.2099 -2075.2099 14043.827 -14043.827
920 1839.0572 -2077.3907 -2077.3907 13195.428 -13195.428
930 1875.3856 -2080.1678 -2080.1678 12550.917 -12550.917
940 1774.6978 -2073.9954 -2073.9954 12878.164 -12878.164
950 1739.4586 -2072.1025 -2072.1025 12381.741 -12381.741
960 1860.7393 -2080.5553 -2080.5553 11340.855 -11340.855
970 1675.5209 -2068.7733 -2068.7733 12264.795 -12264.795
980 1794.0159 -2076.9546 -2076.9546 12079.272 -12079.272
990 1965.1199 -2088.653 -2088.653 12866.959 -12866.959
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
Loop time of 0.228576 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
1016 1860.4796 -2213.2478 -2213.2478 9385.9786 -9385.9786
Loop time of 0.04145 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
1010 1725.5676 -2081.2141 -2081.2141 12659.195 -12659.195
1020 1776.6517 -2080.2782 -2080.2782 14283.292 -14283.292
1030 1892.8575 -2087.068 -2087.068 14207.132 -14207.132
1040 1779.8487 -2086.4423 -2086.4423 13177.279 -13177.279
1050 1827.1799 -2088.9648 -2088.9648 12860.512 -12860.512
1060 1788.3529 -2088.9653 -2088.9653 12121.719 -12121.719
1070 1710.9667 -2083.8206 -2083.8206 12445.746 -12445.746
1080 1828.553 -2086.433 -2086.433 12715.209 -12715.209
1090 1823.9802 -2088.7607 -2088.7607 12059.344 -12059.344
1100 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
Loop time of 0.223155 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
1010 1699.0134 -2083.5757 -2083.5757 11300.601 -11300.601
1020 1628.0232 -2079.447 -2079.447 11165.976 -11165.976
1030 1649.3552 -2081.1852 -2081.1852 11327.923 -11327.923
1040 1780.5559 -2090.032 -2090.032 11432.453 -11432.453
1050 1757.6796 -2088.6549 -2088.6549 11052.281 -11052.281
1060 1707.3484 -2085.4178 -2085.4178 11557.124 -11557.124
1070 1740.6914 -2087.5927 -2087.5927 12294.274 -12294.274
1080 1770.6598 -2089.4669 -2089.4669 12907.34 -12907.34
1090 1742.39 -2087.4355 -2087.4355 13144.749 -13144.749
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
Loop time of 0.22732 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
1116 1806.4889 -2213.2741 -2213.2741 9022.1362 -9022.1362
Loop time of 0.0412889 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
1110 1759.3742 -2088.0631 -2088.0631 12373.16 -12373.16
1120 1741.0508 -2086.5288 -2086.5288 11902.565 -11902.565
1130 1752.2435 -2086.8177 -2086.8177 11844.496 -11844.496
1140 1786.7182 -2088.5202 -2088.5202 11401.503 -11401.503
1150 1760.1379 -2086.0667 -2086.0667 11634.293 -11634.293
1160 1737.621 -2083.7432 -2083.7432 12261.472 -12261.472
1170 1706.1721 -2080.6152 -2080.6152 11900.384 -11900.384
1180 1692.9524 -2078.4392 -2078.4392 11857.894 -11857.894
1190 1845.4734 -2086.9009 -2086.9009 12368.868 -12368.868
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
Loop time of 0.226668 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
1217 1931.9798 -2213.2743 -2213.2743 9876.9115 -9876.9115
Loop time of 0.0441182 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
1210 1844.6662 -2083.5459 -2083.5459 13676.012 -13676.012
1220 1823.5246 -2080.8506 -2080.8506 13754.811 -13754.811
1230 1855.1817 -2081.8069 -2081.8069 13072.56 -13072.56
1240 1817.3161 -2078.3873 -2078.3873 13440.344 -13440.344
1250 1846.7917 -2079.601 -2079.601 13176.331 -13176.331
1260 1879.5517 -2081.1956 -2081.1956 12521.935 -12521.935
1270 1856.8093 -2079.3203 -2079.3203 12606.391 -12606.391
1280 1802.8957 -2075.5089 -2075.5089 13433.639 -13433.639
1290 1858.5815 -2079.0007 -2079.0007 11938.06 -11938.06
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
Loop time of 0.229218 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
1320 1855.8203 -2213.31 -2213.31 9361.0005 -9361.0005
Loop time of 0.0519319 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
1310 1874.9965 -2079.9692 -2079.9692 11644.669 -11644.669
1320 1769.8025 -2073.0867 -2073.0867 11913.24 -11913.24
1330 1767.7322 -2072.9816 -2072.9816 11519.778 -11519.778
1340 1877.3892 -2080.2309 -2080.2309 11401.149 -11401.149
1350 1832.5468 -2077.3496 -2077.3496 11388.096 -11388.096
1360 1824.2863 -2076.9333 -2076.9333 13175.108 -13175.108
1370 1878.976 -2080.7152 -2080.7152 13742.012 -13742.012
1380 1853.0704 -2079.2587 -2079.2587 13419.479 -13419.479
1390 1879.4579 -2081.3358 -2081.3358 13342.696 -13342.696
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
Loop time of 0.227635 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
1418 1900.1245 -2213.3012 -2213.3012 9665.7068 -9665.7068
Loop time of 0.044939 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
1410 1901.6666 -2083.8299 -2083.8299 13518.235 -13518.235
1420 1818.6697 -2079.0462 -2079.0462 13733.805 -13733.805
1430 1760.3629 -2075.8907 -2075.8907 13140.244 -13140.244
1440 1797.4632 -2078.982 -2078.982 11102.802 -11102.802
1450 1787.354 -2078.9476 -2078.9476 11338.448 -11338.448
1460 1762.8326 -2077.925 -2077.925 11770.958 -11770.958
1470 1798.49 -2080.8371 -2080.8371 11559.353 -11559.353
1480 1811.1557 -2082.2118 -2082.2118 13113.303 -13113.303
1490 1874.659 -2086.985 -2086.985 13079.855 -13079.855
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
Loop time of 0.228696 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
1519 1882.075 -2213.3023 -2213.3023 9541.1899 -9541.1899
Loop time of 0.0427539 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
1510 1847.5745 -2086.6473 -2086.6473 13865.395 -13865.395
1520 1776.4045 -2082.7466 -2082.7466 12604.819 -12604.819
1530 1744.8455 -2081.3864 -2081.3864 11823.185 -11823.185
1540 1769.32 -2083.6389 -2083.6389 10753.254 -10753.254
1550 1767.1256 -2084.0617 -2084.0617 10187.637 -10187.637
1560 1736.4738 -2082.5362 -2082.5362 11049.891 -11049.891
1570 1700.4926 -2080.5399 -2080.5399 12042.247 -12042.247
1580 1696.0678 -2080.4908 -2080.4908 11552.055 -11552.055
1590 1720.0071 -2082.1654 -2082.1654 11110.307 -11110.307
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
Loop time of 0.228001 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
1617 1810.361 -2213.2909 -2213.2909 9047.1326 -9047.1326
Loop time of 0.0451331 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
1610 1738.2296 -2084.0656 -2084.0656 11367.025 -11367.025
1620 1732.2548 -2079.551 -2079.551 11352.482 -11352.482
1630 1823.6067 -2081.0447 -2081.0447 11759.019 -11759.019
1640 1747.0418 -2077.4773 -2077.4773 11967.929 -11967.929
1650 1811.7099 -2078.1627 -2078.1627 11353.138 -11353.138
1660 1706.9977 -2071.9188 -2071.9188 10638.169 -10638.169
1670 1829.7223 -2073.7338 -2073.7338 11869.478 -11869.478
1680 1811.4357 -2074.3495 -2074.3495 12307.737 -12307.737
1690 1714.1408 -2068.5122 -2068.5122 13422.716 -13422.716
1700 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
Loop time of 0.225181 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
1610 1960.8575 -2078.866 -2078.866 12934.864 -12934.864
1620 1923.6166 -2076.54 -2076.54 14112.707 -14112.707
1630 1944.7555 -2078.2457 -2078.2457 13865.325 -13865.325
1640 1902.2989 -2075.9002 -2075.9002 13297.512 -13297.512
1650 1849.5907 -2072.9273 -2072.9273 13933.385 -13933.385
1660 1926.326 -2078.5135 -2078.5135 13981.854 -13981.854
1670 1920.9614 -2078.7358 -2078.7358 13767.146 -13767.146
1680 1850.6527 -2074.6766 -2074.6766 13812.372 -13812.372
1690 1863.9535 -2076.0517 -2076.0517 12782.004 -12782.004
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
Loop time of 0.227535 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
1716 1893.9231 -2213.2837 -2213.2837 9620.0072 -9620.0072
Loop time of 0.038758 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
1710 1875.7299 -2077.7377 -2077.7377 13345.116 -13345.116
1720 1898.0515 -2079.6613 -2079.6613 14132.452 -14132.452
1730 1882.8777 -2079.146 -2079.146 13699.059 -13699.059
1740 1816.9287 -2075.2717 -2075.2717 13073.965 -13073.965
1750 1862.4091 -2078.7296 -2078.7296 12789.163 -12789.163
1760 1893.0397 -2081.2522 -2081.2522 13312.699 -13312.699
1770 1834.7444 -2077.9575 -2077.9575 14033.233 -14033.233
1780 1864.6391 -2080.5104 -2080.5104 13228.094 -13228.094
1790 1854.6185 -2080.4852 -2080.4852 12156.34 -12156.34
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
Loop time of 0.228311 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
1817 1783.2906 -2213.2924 -2213.2924 8858.239 -8858.239
Loop time of 0.042892 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1783.2906 -2076.1141 -2076.1141 12468.46 -12468.46
1810 1845.4581 -2080.8627 -2080.8627 12506.58 -12506.58
1820 1801.3296 -2078.6098 -2078.6098 13055.572 -13055.572
1830 1777.9523 -2077.7188 -2077.7188 12729.867 -12729.867
1840 1758.541 -2077.0154 -2077.0154 12518.443 -12518.443
1850 1828.6136 -2082.1861 -2082.1861 11837.329 -11837.329
1860 1826.6839 -2082.6205 -2082.6205 12848.747 -12848.747
1870 1848.9771 -2084.6985 -2084.6985 14273.245 -14273.245
1880 1859.0854 -2086.037 -2086.037 13956.23 -13956.23
1890 1826.3509 -2084.6002 -2084.6002 13737.356 -13737.356
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
Loop time of 0.226686 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
1921 1856.0966 -2213.3256 -2213.3256 9364.6843 -9364.6843
Loop time of 0.0561171 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
1910 1732.1651 -2081.2025 -2081.2025 13648.771 -13648.771
1920 1791.3554 -2081.3056 -2081.3056 13652.014 -13652.014
1930 1824.4855 -2083.5698 -2083.5698 13761.469 -13761.469
1940 1789.0389 -2083.4838 -2083.4838 12938.14 -12938.14
1950 1754.5722 -2081.062 -2081.062 13678.133 -13678.133
1960 1790.0373 -2080.9357 -2080.9357 13972.404 -13972.404
1970 1815.9084 -2082.4892 -2082.4892 13423.516 -13423.516
1980 1741.0456 -2079.056 -2079.056 13024.446 -13024.446
1990 1845.2042 -2082.4853 -2082.4853 12369.149 -12369.149
2000 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
Loop time of 0.226301 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
1910 1859.235 -2087.1634 -2087.1634 12382.624 -12382.624
1920 1859.3456 -2087.6091 -2087.6091 12482.545 -12482.545
1930 1748.0548 -2080.7392 -2080.7392 13217.457 -13217.457
1940 1876.5822 -2089.6972 -2089.6972 12827.369 -12827.369
1950 1858.9549 -2089.1237 -2089.1237 12267.563 -12267.563
1960 1661.6597 -2076.6976 -2076.6976 13069.247 -13069.247
1970 1739.6756 -2082.3166 -2082.3166 13000.655 -13000.655
1980 1831.8527 -2088.8393 -2088.8393 11823.386 -11823.386
1990 1661.818 -2078.0492 -2078.0492 12159.308 -12159.308
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
Loop time of 0.228493 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
2019 1700.7919 -2213.3012 -2213.3012 8294.8879 -8294.8879
Loop time of 0.0509 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
2010 1861.3608 -2091.7401 -2091.7401 11627.567 -11627.567
2020 1723.5921 -2082.9109 -2082.9109 11679.426 -11679.426
2030 1715.155 -2082.5582 -2082.5582 12295.003 -12295.003
2040 1850.4844 -2091.6449 -2091.6449 12563.959 -12563.959
2050 1761.29 -2085.9529 -2085.9529 13011.92 -13011.92
2060 1706.9101 -2082.541 -2082.541 13421.673 -13421.673
2070 1819.5707 -2090.0959 -2090.0959 12744.935 -12744.935
2080 1798.901 -2088.8739 -2088.8739 12477.746 -12477.746
2090 1722.8968 -2084.0198 -2084.0198 12266.395 -12266.395
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
Loop time of 0.226199 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
2118 1780.5329 -2213.3048 -2213.3048 8843.7542 -8843.7542
Loop time of 0.048214 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1780.5329 -2081.5748 -2081.5748 11485.708 -11485.708
Loop time of 7.15228 on 1 procs for 18 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.34597 (18.8187)
Dynamics time (%) = 4.54905 (63.6027)
Quench time (%) = 0.940575 (13.1507)
Other time (%) = 0.0726786 (1.01616)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 98
Dangerous builds = 0

630
examples/prd/log.prd.3.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
Processor partition = 3
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.02216 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.200245 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.196106 (97.9332)
Neigh time (%) = 0.00138807 (0.693188)
Comm time (%) = 0.000854492 (0.426724)
Outpt time (%) = 7.39098e-05 (0.0369097)
Other time (%) = 0.00182223 (0.910002)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.835
dump events all custom 1 dump.prd id type x y z
dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:199)
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.0545528 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1495.0763 -2129.2427 -2129.2427 17292.034 -17292.034
120 1695.6936 -2119.9568 -2119.9568 19395.276 -19395.276
130 1720.2165 -2112.5918 -2112.5918 19379.647 -19379.647
140 1792.9012 -2110.2027 -2110.2027 20162.681 -20162.681
150 1826.4633 -2110.1906 -2110.1906 19821.473 -19821.473
160 1707.1346 -2102.4592 -2102.4592 19283.638 -19283.638
170 1889.7308 -2106.7875 -2106.7875 19121.04 -19121.04
180 1726.1399 -2100.5051 -2100.5051 17912.961 -17912.961
190 1725.2909 -2094.183 -2094.183 17836.706 -17836.706
200 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
Loop time of 0.220981 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
100 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
110 1749.1865 -2088.09 -2088.09 17886.987 -17886.987
120 1730.091 -2085.5138 -2085.5138 16298.238 -16298.238
130 1725.5695 -2083.8602 -2083.8602 14810.515 -14810.515
140 1742.8337 -2083.604 -2083.604 14304.4 -14304.4
150 1755.1691 -2082.9974 -2082.9974 14289.749 -14289.749
160 1730.1652 -2079.9294 -2079.9294 14796.483 -14796.483
170 1746.47 -2079.5667 -2079.5667 14891.286 -14891.286
180 1867.6791 -2086.0994 -2086.0994 15143.089 -15143.089
190 1826.3577 -2081.9693 -2081.9693 14842.324 -14842.324
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
Loop time of 0.227842 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
218 1890.4086 -2213.3051 -2213.3051 9595.2117 -9595.2117
Loop time of 0.0460188 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
200 1890.4086 -2083.245 -2083.245 15721.201 -15721.201
210 1895.0321 -2082.3794 -2082.3794 16182.652 -16182.652
220 1967.6529 -2086.173 -2086.173 15532.872 -15532.872
230 1820.3126 -2075.6591 -2075.6591 15093.435 -15093.435
240 1713.4056 -2067.9324 -2067.9324 14623.702 -14623.702
250 1806.5325 -2073.3192 -2073.3192 13241.861 -13241.861
260 1838.2185 -2074.62 -2074.62 12793.039 -12793.039
270 1796.1907 -2071.1002 -2071.1002 13382.202 -13382.202
280 1855.3253 -2074.2821 -2074.2821 14014.125 -14014.125
290 1915.1832 -2077.5543 -2077.5543 15817.805 -15817.805
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
Loop time of 0.231957 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
320 1943.8007 -2213.3262 -2213.3262 9968.2615 -9968.2615
Loop time of 0.054142 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
310 1830.358 -2077.8168 -2077.8168 14980.856 -14980.856
320 1816.8748 -2078.525 -2078.525 14548.875 -14548.875
330 1812.5384 -2078.949 -2078.949 13614.012 -13614.012
340 1854.3003 -2082.1223 -2082.1223 13185.902 -13185.902
350 1853.1764 -2085.2567 -2085.2567 12110.408 -12110.408
360 1853.1119 -2088.4344 -2088.4344 12224.055 -12224.055
370 1837.6042 -2090.6376 -2090.6376 11312.576 -11312.576
380 1790.0042 -2089.7364 -2089.7364 11726.39 -11726.39
390 1704.071 -2083.1405 -2083.1405 11697.254 -11697.254
400 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
Loop time of 0.225539 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
300 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
310 1818.7058 -2083.7777 -2083.7777 13364.201 -13364.201
320 1784.6932 -2081.2738 -2081.2738 13319.356 -13319.356
330 1781.3136 -2080.7661 -2080.7661 12726.586 -12726.586
340 1850.504 -2085.0411 -2085.0411 12804.72 -12804.72
350 1806.9896 -2081.9086 -2081.9086 12799.418 -12799.418
360 1797.0754 -2081.008 -2081.008 12932.182 -12932.182
370 1939.3485 -2090.1815 -2090.1815 12022.081 -12022.081
380 1833.459 -2083.0989 -2083.0989 12722.114 -12722.114
390 1767.2468 -2078.7079 -2078.7079 12994.83 -12994.83
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
Loop time of 0.226355 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
418 1840.9497 -2213.3059 -2213.3059 9257.8757 -9257.8757
Loop time of 0.0465908 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
410 1825.8375 -2082.5217 -2082.5217 12012.844 -12012.844
420 1723.3215 -2075.7602 -2075.7602 11394.557 -11394.557
430 1764.1446 -2078.4055 -2078.4055 9429.6621 -9429.6621
440 1722.8256 -2075.5423 -2075.5423 10622.932 -10622.932
450 1746.9424 -2076.92 -2076.92 11529.679 -11529.679
460 1837.7686 -2082.6258 -2082.6258 12192.008 -12192.008
470 1853.9148 -2083.4249 -2083.4249 13244.632 -13244.632
480 1853.6885 -2083.2159 -2083.2159 14116.299 -14116.299
490 1915.2224 -2087.1642 -2087.1642 14632.565 -14632.565
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
Loop time of 0.224752 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
519 1936.7625 -2213.3032 -2213.3032 9913.4596 -9913.4596
Loop time of 0.0457649 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
510 1834.5516 -2082.0916 -2082.0916 13945.662 -13945.662
520 1805.8538 -2080.48 -2080.48 11915.304 -11915.304
530 1719.5829 -2075.0416 -2075.0416 10641.83 -10641.83
540 1700.9425 -2073.9843 -2073.9843 10638.084 -10638.084
550 1721.0296 -2075.3479 -2075.3479 10855.732 -10855.732
560 1792.256 -2080.0028 -2080.0028 10718.277 -10718.277
570 1816.469 -2081.5215 -2081.5215 12281.721 -12281.721
580 1898.1645 -2086.8779 -2086.8779 13891.519 -13891.519
590 1909.9896 -2087.7381 -2087.7381 15407.945 -15407.945
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
Loop time of 0.227344 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
620 1905.9376 -2213.3226 -2213.3226 9705.2581 -9705.2581
Loop time of 0.0512102 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
610 1898.495 -2087.6161 -2087.6161 13863.644 -13863.644
620 1873.699 -2086.5202 -2086.5202 11778.817 -11778.817
630 1744.3676 -2078.5837 -2078.5837 11019.865 -11019.865
640 1681.2181 -2074.9263 -2074.9263 9815.9404 -9815.9404
650 1707.9678 -2077.065 -2077.065 10236.708 -10236.708
660 1719.4888 -2078.0855 -2078.0855 10716.295 -10716.295
670 1694.7476 -2076.6002 -2076.6002 10237.649 -10237.649
680 1773.8128 -2081.8591 -2081.8591 12034.22 -12034.22
690 1832.6905 -2085.7381 -2085.7381 12268.403 -12268.403
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
Loop time of 0.22911 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
718 1872.2418 -2213.2732 -2213.2732 9469.3455 -9469.3455
Loop time of 0.047549 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
710 1856.1726 -2087.4734 -2087.4734 12587.6 -12587.6
720 1809.0844 -2084.5719 -2084.5719 11962.825 -11962.825
730 1813.7498 -2085.1228 -2085.1228 12275.918 -12275.918
740 1778.4404 -2083.0339 -2083.0339 12609.945 -12609.945
750 1793.7621 -2084.2846 -2084.2846 12022.021 -12022.021
760 1756.218 -2082.0146 -2082.0146 11970.105 -11970.105
770 1788.1399 -2084.3038 -2084.3038 11486.204 -11486.204
780 1752.5386 -2082.1061 -2082.1061 11773.768 -11773.768
790 1737.5719 -2081.2139 -2081.2139 12812.397 -12812.397
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
Loop time of 0.227638 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
817 1760.5292 -2213.2818 -2213.2818 8701.2542 -8701.2542
Loop time of 0.0444729 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
810 1824.7855 -2084.3929 -2084.3929 13668.719 -13668.719
820 1712.4425 -2078.6074 -2078.6074 12847.66 -12847.66
830 1875.2236 -2083.5586 -2083.5586 12721.192 -12721.192
840 1802.2145 -2083.7392 -2083.7392 11989.282 -11989.282
850 1820.2177 -2085.1324 -2085.1324 11057.193 -11057.193
860 1730.3595 -2080.5914 -2080.5914 11507.405 -11507.405
870 1809.9784 -2081.2823 -2081.2823 12298.894 -12298.894
880 1803.9222 -2081.5723 -2081.5723 11947.359 -11947.359
890 1757.0085 -2078.7491 -2078.7491 12561.76 -12561.76
900 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
Loop time of 0.227705 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
800 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
810 1806.5101 -2079.1895 -2079.1895 11903.119 -11903.119
820 1785.2438 -2077.8038 -2077.8038 11702.485 -11702.485
830 1781.1685 -2077.5303 -2077.5303 12703.961 -12703.961
840 1863.47 -2082.9537 -2082.9537 13361.794 -13361.794
850 1879.7765 -2084.0849 -2084.0849 14480.503 -14480.503
860 1906.2551 -2086.0185 -2086.0185 14752.263 -14752.263
870 1882.1344 -2084.7545 -2084.7545 15091.996 -15091.996
880 1868.6595 -2084.3355 -2084.3355 14227.917 -14227.917
890 1806.8883 -2080.8098 -2080.8098 13418.625 -13418.625
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
Loop time of 0.226983 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
917 1813.034 -2213.2328 -2213.2328 9058.7627 -9058.7627
Loop time of 0.043222 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
910 1790.47 -2080.925 -2080.925 13187.347 -13187.347
920 1773.8688 -2080.4392 -2080.4392 12634.894 -12634.894
930 1785.9855 -2081.8252 -2081.8252 12561.505 -12561.505
940 1801.3588 -2083.4277 -2083.4277 12028.691 -12028.691
950 1778.6138 -2082.521 -2082.521 12646.355 -12646.355
960 1764.4699 -2082.1518 -2082.1518 11945.626 -11945.626
970 1778.2914 -2083.5962 -2083.5962 11676.59 -11676.59
980 1763.0077 -2083.0977 -2083.0977 12675.07 -12675.07
990 1724.8156 -2081.0275 -2081.0275 12706.385 -12706.385
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
Loop time of 0.227145 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
1019 1789.1021 -2213.3142 -2213.3142 8903.9364 -8903.9364
Loop time of 0.0538819 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
1010 1803.5662 -2086.2788 -2086.2788 12296.832 -12296.832
1020 1721.4631 -2081.4632 -2081.4632 12617.022 -12617.022
1030 1901.5059 -2088.5616 -2088.5616 13322.949 -13322.949
1040 1790.4919 -2088.3943 -2088.3943 11842.661 -11842.661
1050 1728.9375 -2084.1491 -2084.1491 11186.843 -11186.843
1060 1822.9805 -2086.1115 -2086.1115 11654.623 -11654.623
1070 1793.5987 -2086.1655 -2086.1655 11565.879 -11565.879
1080 1774.9684 -2085.0099 -2085.0099 11788.082 -11788.082
1090 1875.45 -2090.5357 -2090.5357 12023.082 -12023.082
1100 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
Loop time of 0.226134 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
1010 1751.5551 -2088.5144 -2088.5144 11418.611 -11418.611
1020 1783.4529 -2091.1906 -2091.1906 11869.563 -11869.563
1030 1724.468 -2087.853 -2087.853 11660.095 -11660.095
1040 1700.0952 -2086.721 -2086.721 10696.55 -10696.55
1050 1760.1423 -2091.0982 -2091.0982 9178.1354 -9178.1354
1060 1644.0734 -2083.7826 -2083.7826 9093.1125 -9093.1125
1070 1613.8056 -2081.9631 -2081.9631 9591.8493 -9591.8493
1080 1709.8502 -2088.2878 -2088.2878 9538.5577 -9538.5577
1090 1676.8021 -2085.9346 -2085.9346 10766.925 -10766.925
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
Loop time of 0.227753 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
1117 1718.403 -2213.2587 -2213.2587 8409.3544 -8409.3544
Loop time of 0.044637 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
1110 1765.1951 -2090.924 -2090.924 10989.261 -10989.261
1120 1739.4922 -2088.58 -2088.58 11689.558 -11689.558
1130 1727.0447 -2086.942 -2086.942 12283.035 -12283.035
1140 1785.7915 -2089.784 -2089.784 11818.431 -11818.431
1150 1809.8869 -2090.1546 -2090.1546 10879.76 -10879.76
1160 1744.4121 -2084.5197 -2084.5197 11286.034 -11286.034
1170 1757.7394 -2084.0004 -2084.0004 11548.282 -11548.282
1180 1821.8601 -2086.7401 -2086.7401 11282.746 -11282.746
1190 1801.9718 -2084.0004 -2084.0004 11879.914 -11879.914
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
Loop time of 0.231579 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
1220 1778.413 -2213.2935 -2213.2935 8826.8778 -8826.8778
Loop time of 0.0571249 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
1210 1779.9735 -2080.1523 -2080.1523 11767.914 -11767.914
1220 1761.523 -2077.9508 -2077.9508 12102.479 -12102.479
1230 1799.751 -2079.6111 -2079.6111 11976.738 -11976.738
1240 1852.8341 -2082.3812 -2082.3812 12122.449 -12122.449
1250 1835.3624 -2080.6598 -2080.6598 12594.439 -12594.439
1260 1822.3142 -2079.3754 -2079.3754 12980.571 -12980.571
1270 1824.7898 -2079.2048 -2079.2048 13133.515 -13133.515
1280 1835.3097 -2079.6291 -2079.6291 13141.016 -13141.016
1290 1918.3152 -2084.9315 -2084.9315 12831.552 -12831.552
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
Loop time of 0.231616 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
1320 1872.0268 -2213.3016 -2213.3016 9471.4837 -9471.4837
Loop time of 0.0559161 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
1310 1842.2091 -2079.9447 -2079.9447 11930.547 -11930.547
1320 1839.1324 -2079.8702 -2079.8702 11520.211 -11520.211
1330 1781.5944 -2076.2294 -2076.2294 12517.772 -12517.772
1340 1808.2791 -2078.1377 -2078.1377 12331.797 -12331.797
1350 1825.5011 -2079.4214 -2079.4214 12959.817 -12959.817
1360 1805.1617 -2078.2612 -2078.2612 12283.097 -12283.097
1370 1794.2198 -2077.7174 -2077.7174 11854.379 -11854.379
1380 1856.0315 -2081.9959 -2081.9959 12222.656 -12222.656
1390 1830.6929 -2080.5837 -2080.5837 12676.219 -12676.219
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
Loop time of 0.231967 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
1419 1787.3453 -2213.3099 -2213.3099 8888.2838 -8888.2838
Loop time of 0.0533779 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1787.3453 -2083.1407 -2083.1407 12644.184 -12644.184
1410 1858.6264 -2088.1699 -2088.1699 13665.536 -13665.536
1420 1836.7078 -2087.1342 -2087.1342 13718.627 -13718.627
1430 1761.5946 -2082.6238 -2082.6238 13729.715 -13729.715
1440 1825.9335 -2087.3258 -2087.3258 13009.414 -13009.414
1450 1817.7629 -2087.2906 -2087.2906 12876.965 -12876.965
1460 1773.2189 -2084.9022 -2084.9022 12124.77 -12124.77
1470 1742.8153 -2083.4385 -2083.4385 11686.602 -11686.602
1480 1741.4145 -2083.843 -2083.843 11494.225 -11494.225
1490 1765.3668 -2085.8995 -2085.8995 11215.781 -11215.781
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
Loop time of 0.227673 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
1517 1760.2197 -2213.245 -2213.245 8696.1847 -8696.1847
Loop time of 0.0443079 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1760.2197 -2088.1491 -2088.1491 12985.172 -12985.172
1510 1927.1878 -2099.7308 -2099.7308 12023.236 -12023.236
1520 1616.4053 -2079.8776 -2079.8776 12507.037 -12507.037
1530 1598.2599 -2079.1598 -2079.1598 11597.301 -11597.301
1540 1792.8199 -2092.3519 -2092.3519 10302.629 -10302.629
1550 1633.2272 -2082.1258 -2082.1258 11028.733 -11028.733
1560 1596.4787 -2079.8411 -2079.8411 11401.206 -11401.206
1570 1803.3749 -2093.4571 -2093.4571 11211.847 -11211.847
1580 1632.0154 -2081.9939 -2081.9939 13381.635 -13381.635
1590 1718.3971 -2087.372 -2087.372 14772.258 -14772.258
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
Loop time of 0.227694 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
1618 2048.734 -2213.2799 -2213.2799 10685.447 -10685.447
Loop time of 0.038959 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
1610 1699.675 -2080.9037 -2080.9037 11840.386 -11840.386
1620 1817.4828 -2081.4111 -2081.4111 13490.885 -13490.885
1630 1813.0686 -2081.5266 -2081.5266 13881.909 -13881.909
1640 1779.9893 -2079.3276 -2079.3276 13857.386 -13857.386
1650 1937.4396 -2087.3853 -2087.3853 13788.514 -13788.514
1660 1762.8309 -2083.9296 -2083.9296 12151.903 -12151.903
1670 1791.277 -2082.2407 -2082.2407 12210.144 -12210.144
1680 1803.435 -2081.2765 -2081.2765 12398.317 -12398.317
1690 1802.7286 -2080.2585 -2080.2585 12311.1 -12311.1
1700 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
Loop time of 0.228129 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
1610 1818.7567 -2079.2051 -2079.2051 12961.247 -12961.247
1620 1853.2617 -2080.4774 -2080.4774 13334.998 -13334.998
1630 1845.6923 -2079.1003 -2079.1003 14024.126 -14024.126
1640 1842.4692 -2078.142 -2078.142 13972.69 -13972.69
1650 1932.9485 -2083.4976 -2083.4976 13927.397 -13927.397
1660 1891.8513 -2080.3519 -2080.3519 14382.688 -14382.688
1670 1871.3356 -2078.7396 -2078.7396 15250.018 -15250.018
1680 1889.0458 -2079.7669 -2079.7669 14923.552 -14923.552
1690 1896.2267 -2080.2296 -2080.2296 13037.903 -13037.903
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
Loop time of 0.228841 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
1716 1836.5539 -2213.2588 -2213.2588 9221.7377 -9221.7377
Loop time of 0.0428541 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
1710 1859.5138 -2078.0746 -2078.0746 12410.243 -12410.243
1720 1819.1932 -2075.6335 -2075.6335 12724.601 -12724.601
1730 1813.3698 -2075.501 -2075.501 12702.894 -12702.894
1740 1840.4368 -2077.5556 -2077.5556 13145.533 -13145.533
1750 1872.195 -2079.983 -2079.983 13220.848 -13220.848
1760 1847.9633 -2078.804 -2078.804 13870.064 -13870.064
1770 1887.8505 -2081.9384 -2081.9384 15041.963 -15041.963
1780 1967.1648 -2087.8474 -2087.8474 14594.014 -14594.014
1790 1866.7002 -2082.0986 -2082.0986 13615.248 -13615.248
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
Loop time of 0.232462 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
1819 1761.77 -2213.2705 -2213.2705 8712.9668 -8712.9668
Loop time of 0.043287 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
1810 1703.4947 -2073.1063 -2073.1063 12008.391 -12008.391
1820 1780.1034 -2078.8985 -2078.8985 11424.159 -11424.159
1830 1792.3191 -2080.4109 -2080.4109 11527.375 -11527.375
1840 1740.7982 -2077.6542 -2077.6542 13041.565 -13041.565
1850 1860.8658 -2086.1706 -2086.1706 14356.817 -14356.817
1860 1942.1014 -2092.2204 -2092.2204 14527.618 -14527.618
1870 1830.8975 -2085.683 -2085.683 15024.292 -15024.292
1880 1809.0262 -2085.0269 -2085.0269 14356.631 -14356.631
1890 1832.6706 -2087.3315 -2087.3315 13353.932 -13353.932
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
Loop time of 0.227046 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
1917 1791.352 -2213.2561 -2213.2561 8912.2973 -8912.2973
Loop time of 0.0440671 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
1910 1839.8996 -2088.5949 -2088.5949 13946.912 -13946.912
1920 1728.8047 -2084.4404 -2084.4404 13398.47 -13398.47
1930 1844.6379 -2087.8523 -2087.8523 12606.037 -12606.037
1940 1750.4698 -2084.9552 -2084.9552 12830.245 -12830.245
1950 1777.4189 -2083.7326 -2083.7326 12890.868 -12890.868
1960 1757.0139 -2081.0743 -2081.0743 12928.49 -12928.49
1970 1815.4975 -2082.2189 -2082.2189 12590.606 -12590.606
1980 1820.5692 -2083.6914 -2083.6914 11259.175 -11259.175
1990 1760.8482 -2081.178 -2081.178 12204.966 -12204.966
2000 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
Loop time of 0.225181 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
1910 1835.8382 -2083.7475 -2083.7475 13543.202 -13543.202
1920 1838.6207 -2084.1142 -2084.1142 13995.434 -13995.434
1930 1844.8228 -2084.7395 -2084.7395 14254.28 -14254.28
1940 1809.1821 -2082.6216 -2082.6216 14113.256 -14113.256
1950 1866.6498 -2086.6639 -2086.6639 13152.916 -13152.916
1960 1854.176 -2086.1617 -2086.1617 11993.967 -11993.967
1970 1710.438 -2077.0061 -2077.0061 12356.799 -12356.799
1980 1713.8796 -2077.4442 -2077.4442 12066.558 -12066.558
1990 1830.1984 -2085.2536 -2085.2536 11224.423 -11224.423
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
Loop time of 0.227497 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
2018 1745.1241 -2213.2723 -2213.2723 8595.2359 -8595.2359
Loop time of 0.0472109 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
2010 1764.5303 -2081.1092 -2081.1092 12533.707 -12533.707
2020 1803.9081 -2083.7299 -2083.7299 12751.448 -12751.448
2030 1839.3617 -2086.0949 -2086.0949 12814.216 -12814.216
2040 1868.2548 -2088.0926 -2088.0926 13020.533 -13020.533
2050 1793.5586 -2083.3252 -2083.3252 13251.553 -13251.553
2060 1775.5342 -2082.3028 -2082.3028 12783.678 -12783.678
2070 1851.6766 -2087.482 -2087.482 12508.389 -12508.389
2080 1855.9094 -2087.9994 -2087.9994 12382.735 -12382.735
2090 1728.9486 -2079.9079 -2079.9079 12119.774 -12119.774
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
Loop time of 0.224497 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
2119 1750.5079 -2213.2837 -2213.2837 8634.903 -8634.903
Loop time of 0.0529981 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
Loop time of 7.15221 on 1 procs for 19 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.35367 (18.9266)
Dynamics time (%) = 4.56775 (63.8649)
Quench time (%) = 0.957592 (13.3888)
Other time (%) = 0.0734553 (1.02703)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 98
Dangerous builds = 0

12
examples/prd/log.prd.9Jan12.linux.4 Normal file
View File

@ -0,0 +1,12 @@
LAMMPS (10 Jan 2012)
Running on 4 partitions of processors
Step CPU Clock Event Correlated Coincident Replica
100 0.000 0 0 0 0 0
200 0.507 400 1 0 4 1
700 2.190 2100 2 0 2 3
900 2.991 2600 3 0 1 3
1400 4.674 4300 4 0 1 2
1500 4.963 4400 5 1 1 2
1800 6.052 5300 6 0 2 3
2100 7.149 6200 7 0 1 3
Loop time of 7.15226 on 4 procs for 2000 steps with 511 atoms

170
examples/reax/log.reax.rdx.9Jan12.linux.1 Normal file
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LAMMPS (10 Jan 2012)
# REAX potential for RDX system
# this run is equivalent to GRASP testreax
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 10.0 0 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reax.rdx
dump 1 all custom 1 dump.reax.rdx id type q xs ys zs
run 100
Memory usage per processor = 2.21676 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -2047.6193 -2047.6193 1411.6115 -3290.6584 -45.555509 38.801279 0 64.431331 0 -49.368043 0 -12.014532 -10.833851 1332.1957 -252.57917 0 177.96195
1 0.17729257 -2047.6351 -2047.6245 1302.8598 -3290.4955 -45.636967 38.789181 0 64.424892 0 -49.375516 0 -12.04864 -10.816863 1332.1526 -252.58938 0 177.96112
2 0.61943411 -2047.6752 -2047.6383 1021.8468 -3290.0429 -45.863414 38.754281 0 64.405628 0 -49.396435 0 -12.141947 -10.769089 1332.0375 -252.68399 0 178.02512
3 1.1359535 -2047.7292 -2047.6615 668.22012 -3289.3948 -46.188349 38.700785 0 64.374192 0 -49.426931 0 -12.271547 -10.698951 1331.8843 -252.79663 0 178.08872
4 1.5763627 -2047.7893 -2047.6954 329.5292 -3288.6685 -46.553602 38.635308 0 64.332347 0 -49.462048 0 -12.409557 -10.617427 1331.7273 -252.93214 0 178.15899
5 1.8972502 -2047.7352 -2047.6221 52.254945 -3287.9703 -46.905822 38.565966 0 64.283217 0 -49.496945 0 -12.531215 -10.535327 1331.5878 -253.02457 0 178.29196
6 2.1428043 -2047.7867 -2047.6589 -150.27778 -3287.3774 -47.205572 38.501034 0 64.230854 0 -49.527561 0 -12.618827 -10.461575 1331.4716 -253.12871 0 178.32949
7 2.3931301 -2047.8411 -2047.6984 -279.56888 -3286.9394 -47.428766 38.447638 0 64.179608 0 -49.550828 0 -12.662327 -10.402552 1331.3774 -253.19307 0 178.33125
8 2.7163824 -2047.7765 -2047.6145 -341.77191 -3286.6841 -47.564114 38.410694 0 64.133562 0 -49.564645 0 -12.658017 -10.362104 1331.3036 -253.15871 0 178.36736
9 3.1373572 -2047.8482 -2047.6612 -345.75021 -3286.6236 -47.609801 38.392337 0 64.096348 0 -49.567835 0 -12.607134 -10.341756 1331.2528 -253.21491 0 178.37536
10 3.6258172 -2047.9367 -2047.7206 -299.3677 -3286.7584 -47.5708 38.391799 0 64.070905 0 -49.560094 0 -12.51448 -10.341008 1331.2332 -253.20696 0 178.3191
11 4.0774819 -2047.9388 -2047.6957 -152.67834 -3287.0738 -47.45798 38.405762 0 64.061833 0 -49.542022 0 -12.387756 -10.444213 1331.253 -252.96545 0 178.2118
12 4.4059883 -2048.0651 -2047.8025 -19.83339 -3287.3785 -47.299275 38.429479 0 64.069944 0 -49.51478 0 -12.231965 -10.541991 1331.1623 -252.9065 0 178.14616
13 4.5696709 -2048.1163 -2047.8438 89.031131 -3287.5907 -47.120628 38.456875 0 64.093723 0 -49.48086 0 -12.061365 -10.590477 1330.9268 -252.7704 0 178.02071
14 4.5292629 -2048.1509 -2047.8809 184.99361 -3287.7342 -46.945908 38.481855 0 64.133676 0 -49.443844 0 -11.894586 -10.630355 1330.6213 -252.58485 0 177.84597
15 4.3080728 -2048.0187 -2047.7618 259.08141 -3287.8584 -46.79998 38.499221 0 64.190345 0 -49.408019 0 -11.75291 -10.654408 1330.3442 -252.24881 0 177.67006
16 4.0054984 -2047.9866 -2047.7478 295.1452 -3288.0045 -46.706741 38.505347 0 64.264076 0 -49.377843 0 -11.656714 -10.645964 1330.1788 -252.10538 0 177.56229
17 3.7365454 -2048.023 -2047.8002 308.28727 -3288.1892 -46.685034 38.498597 0 64.355208 0 -49.357284 0 -11.619855 -10.67973 1330.1723 -251.94333 0 177.42537
18 3.5553598 -2048.0383 -2047.8263 262.77689 -3288.3259 -46.749698 38.479152 0 64.463687 0 -49.349 0 -11.649122 -10.663445 1330.2579 -251.80554 0 177.30362
19 3.4492979 -2048.0654 -2047.8598 175.19312 -3288.3269 -46.902897 38.448826 0 64.589134 0 -49.353904 0 -11.74029 -10.637384 1330.3505 -251.75396 0 177.26146
20 3.4854377 -2048.066 -2047.8582 475.16845 -3288.1127 -47.135109 38.410455 0 64.729982 0 -49.370838 0 -11.882918 -10.574723 1330.3482 -251.72077 0 177.24238
21 3.6644743 -2048.0339 -2047.8154 322.43945 -3287.4815 -47.439791 38.338957 0 64.842336 0 -49.391187 0 -12.037419 -10.466406 1330.0588 -251.68721 0 177.22946
22 3.7684691 -2047.9822 -2047.7575 -6.4225926 -3286.5042 -47.785354 38.23892 0 64.931012 0 -49.412517 0 -12.18909 -10.349541 1329.517 -251.64384 0 177.21539
23 3.6581662 -2047.8835 -2047.6654 -366.17001 -3285.4261 -48.131073 38.126581 0 65.022116 0 -49.434818 0 -12.338703 -10.204547 1328.9001 -251.59067 0 177.19368
24 3.3424229 -2047.8405 -2047.6413 -634.89161 -3284.5564 -48.439646 38.02081 0 65.137469 0 -49.458852 0 -12.489944 -10.132405 1328.4467 -251.53413 0 177.16585
25 2.9320147 -2047.7876 -2047.6128 -806.23487 -3284.0314 -48.692929 37.939159 0 65.294101 0 -49.484737 0 -12.641981 -10.06839 1328.2377 -251.45345 0 177.11436
26 2.5498383 -2047.7333 -2047.5813 -856.30568 -3283.8979 -48.882631 37.893307 0 65.497388 0 -49.511409 0 -12.78991 -10.016311 1328.2835 -251.45234 0 177.14302
27 2.2896564 -2047.6894 -2047.5529 -792.15035 -3284.1089 -49.006436 37.886438 0 65.73897 0 -49.536216 0 -12.923848 -9.9792782 1328.5226 -251.52391 0 177.24116
28 2.1953279 -2047.7602 -2047.6293 -649.34235 -3284.5477 -49.064843 37.913247 0 65.998645 0 -49.55526 0 -13.030316 -9.9596855 1328.8432 -251.58997 0 177.23246
29 2.2746812 -2047.7191 -2047.5835 -480.5386 -3285.0694 -49.059624 37.962277 0 66.248359 0 -49.564229 0 -13.094927 -9.9590662 1329.1204 -251.59207 0 177.28922
30 2.5137626 -2047.6832 -2047.5333 -338.78448 -3285.5463 -48.993796 38.019695 0 66.458461 0 -49.559587 0 -13.105556 -9.9777667 1329.255 -251.57907 0 177.34571
31 2.8705252 -2047.7918 -2047.6207 -261.4326 -3285.905 -48.87173 38.073096 0 66.605317 0 -49.539679 0 -13.055347 -10.014584 1329.2051 -251.52496 0 177.23603
32 3.2635131 -2047.7823 -2047.5877 -239.85838 -3286.144 -48.698989 38.114232 0 66.67803 0 -49.505443 0 -12.944463 -10.100635 1328.9976 -251.29263 0 177.11402
33 3.5790915 -2047.919 -2047.7057 -272.81371 -3286.2675 -48.486653 38.140456 0 66.681928 0 -49.460524 0 -12.779189 -10.214915 1328.661 -250.91112 0 176.71745
34 3.7157859 -2047.8509 -2047.6294 -366.24634 -3286.3002 -48.249737 38.154448 0 66.636284 0 -49.41103 0 -12.572509 -10.300515 1328.2382 -250.45877 0 176.41292
35 3.6401724 -2047.9476 -2047.7306 -462.29763 -3286.3612 -48.000983 38.162509 0 66.567443 0 -49.364907 0 -12.344936 -10.377699 1327.8584 -250.05056 0 175.96424
36 3.4154586 -2047.8414 -2047.6378 -506.67101 -3286.5886 -47.754199 38.172106 0 66.502916 0 -49.330405 0 -12.121629 -10.440348 1327.6678 -249.70257 0 175.75356
37 3.1648925 -2047.9481 -2047.7594 -462.33322 -3287.0652 -47.526179 38.189107 0 66.463757 0 -49.314208 0 -11.926014 -10.513399 1327.7612 -249.57666 0 175.55953
38 2.999693 -2047.8782 -2047.6993 -339.366 -3287.7646 -47.336728 38.215402 0 66.459891 0 -49.319815 0 -11.777148 -10.552379 1328.134 -249.54474 0 175.60793
39 2.9638638 -2047.9555 -2047.7788 -159.8588 -3288.5819 -47.203458 38.247999 0 66.488681 0 -49.346668 0 -11.685525 -10.572352 1328.711 -249.73922 0 175.72588
40 3.0282685 -2047.891 -2047.7104 30.336594 -3289.3528 -47.139173 38.279831 0 66.53636 0 -49.390316 0 -11.653427 -10.563935 1329.3595 -250.00754 0 176.0405
41 3.1316157 -2047.966 -2047.7793 185.76175 -3289.9063 -47.148769 38.302051 0 66.582153 0 -49.443584 0 -11.675677 -10.5402 1329.9335 -250.49665 0 176.42744
42 3.2200391 -2047.8987 -2047.7067 267.78306 -3290.1078 -47.228237 38.306942 0 66.604604 0 -49.498297 0 -11.742793 -10.506057 1330.3082 -250.80732 0 176.77199
43 3.2603167 -2047.9772 -2047.7828 248.89514 -3289.8951 -47.364766 38.29047 0 66.588416 0 -49.546987 0 -11.844256 -10.467422 1330.412 -251.24021 0 177.09073
44 3.2199017 -2047.8506 -2047.6587 110.3257 -3289.2994 -47.537875 38.253998 0 66.529827 0 -49.584198 0 -11.971713 -10.380021 1330.2453 -251.43013 0 177.32356
45 3.0619734 -2047.8547 -2047.6722 -136.38229 -3288.4791 -47.719419 38.204799 0 66.439217 0 -49.607162 0 -12.117604 -10.288427 1329.917 -251.59234 0 177.38832
46 2.8063562 -2047.7324 -2047.5651 -401.33261 -3287.7047 -47.875914 38.1548 0 66.335706 0 -49.615969 0 -12.280201 -10.218262 1329.6327 -251.61481 0 177.45426
47 2.5140356 -2047.7803 -2047.6305 -614.67224 -3287.1803 -47.981301 38.118597 0 66.237922 0 -49.612786 0 -12.453199 -10.213521 1329.5324 -251.60413 0 177.37592
48 2.2367481 -2047.7358 -2047.6025 -757.57038 -3286.955 -48.021555 38.110214 0 66.16373 0 -49.600718 0 -12.623438 -10.225255 1329.6121 -251.56506 0 177.36915
49 2.041479 -2047.6985 -2047.5768 -793.66653 -3287.0103 -47.986996 38.139067 0 66.122819 0 -49.58293 0 -12.77354 -10.254916 1329.811 -251.40199 0 177.23938
50 1.9909741 -2047.6767 -2047.558 -711.0059 -3287.2859 -47.870332 38.206887 0 66.114307 0 -49.561739 0 -12.88419 -10.302905 1330.0428 -251.40886 0 177.27323
51 2.0753438 -2047.6523 -2047.5286 -519.0659 -3287.7104 -47.667065 38.306663 0 66.127013 0 -49.538213 0 -12.937431 -10.368198 1330.2339 -251.52519 0 177.42666
52 2.1888895 -2047.7509 -2047.6204 -244.326 -3288.2254 -47.379502 38.424005 0 66.141153 0 -49.512409 0 -12.920435 -10.447817 1330.3529 -251.75808 0 177.57475
53 2.1985535 -2047.7359 -2047.6048 82.46493 -3288.7964 -47.022454 38.540573 0 66.132021 0 -49.484195 0 -12.829283 -10.536326 1330.4209 -251.87569 0 177.71493
54 2.0482615 -2047.7193 -2047.5972 431.56152 -3289.4009 -46.627524 38.63823 0 66.075701 0 -49.454205 0 -12.67156 -10.625721 1330.4921 -252.02296 0 177.87758
55 1.8981294 -2047.7216 -2047.6084 264.22498 -3290.0167 -46.241953 38.70287 0 65.95608 0 -49.424474 0 -12.467678 -10.705843 1330.6221 -252.13237 0 177.98632
56 1.8184602 -2047.7486 -2047.6402 647.6024 -3290.793 -45.897967 38.76022 0 65.818825 0 -49.406506 0 -12.280617 -10.768739 1330.9975 -252.33899 0 178.16065
57 1.8375171 -2047.8239 -2047.7143 974.19507 -3291.5734 -45.654424 38.8027 0 65.661285 0 -49.403355 0 -12.140626 -10.80466 1331.5525 -252.71345 0 178.44959
58 2.0619167 -2047.7443 -2047.6214 1141.4638 -3292.155 -45.559075 38.823968 0 65.479062 0 -49.415742 0 -12.067764 -10.807349 1332.1523 -252.87824 0 178.68343
59 2.491011 -2047.8459 -2047.6974 1100.4717 -3292.3483 -45.632858 38.819861 0 65.267782 0 -49.441542 0 -12.065671 -10.776125 1332.6386 -253.19647 0 178.88883
60 3.0218387 -2047.8023 -2047.6221 885.14837 -3292.0396 -45.863086 38.789338 0 65.025617 0 -49.476197 0 -12.121867 -10.716178 1332.8811 -253.48777 0 179.20626
61 3.5161409 -2047.9077 -2047.6981 569.87371 -3291.2191 -46.209889 38.735187 0 64.755495 0 -49.513989 0 -12.21484 -10.636903 1332.8127 -253.79563 0 179.37923
62 3.8551967 -2047.8533 -2047.6234 221.83559 -3289.9812 -46.6204 38.664151 0 64.4663 0 -49.549588 0 -12.323532 -10.549157 1332.4468 -254.04704 0 179.6404
63 3.969202 -2047.9294 -2047.6928 -114.65266 -3288.4988 -47.042415 38.586152 0 64.172045 0 -49.579068 0 -12.433308 -10.462933 1331.8713 -254.29573 0 179.75335
64 3.8725443 -2047.8511 -2047.6202 -407.91586 -3286.9903 -47.432296 38.512738 0 63.889333 0 -49.60021 0 -12.536943 -10.386089 1331.2258 -254.36295 0 179.82988
65 3.6778717 -2047.9141 -2047.6948 -633.55766 -3285.6754 -47.757612 38.455001 0 63.633986 0 -49.612211 0 -12.631728 -10.32412 1330.6616 -254.56434 0 179.90077
66 3.5381635 -2047.8363 -2047.6254 -769.36047 -3284.7314 -47.996593 38.421432 0 63.418348 0 -49.615167 0 -12.715509 -10.280419 1330.3022 -254.62752 0 179.9883
67 3.5435881 -2047.9253 -2047.714 -806.13068 -3284.2528 -48.137126 38.416068 0 63.249463 0 -49.609505 0 -12.7834 -10.256664 1330.209 -254.68782 0 179.92752
68 3.6196623 -2047.9443 -2047.7285 -677.92385 -3284.2362 -48.17559 38.437561 0 63.132312 0 -49.595623 0 -12.826804 -10.356944 1330.3687 -254.53024 0 179.83857
69 3.6930058 -2048.0947 -2047.8746 -541.29535 -3284.4018 -48.129689 38.479947 0 63.060994 0 -49.573374 0 -12.827407 -10.432156 1330.518 -254.54815 0 179.75888
70 3.7978262 -2048.011 -2047.7846 -398.03835 -3284.608 -48.012566 38.532982 0 63.022244 0 -49.543287 0 -12.778329 -10.464772 1330.5391 -254.32484 0 179.62647
71 3.9049821 -2048.0816 -2047.8488 -255.77523 -3284.8125 -47.838119 38.584921 0 63.003598 0 -49.506582 0 -12.675929 -10.509738 1330.4258 -254.17081 0 179.41775
72 3.9503233 -2048.0102 -2047.7747 -132.79647 -3285.028 -47.624717 38.624864 0 62.99425 0 -49.465536 0 -12.525709 -10.551349 1330.2378 -253.90761 0 179.23577
73 3.8982748 -2048.0032 -2047.7708 -44.325756 -3285.31 -47.394039 38.644829 0 62.988146 0 -49.423629 0 -12.341526 -10.553364 1330.0799 -253.67153 0 178.97796
74 3.7933986 -2048.0378 -2047.8117 31.904217 -3285.7498 -47.167665 38.641193 0 62.986417 0 -49.385397 0 -12.141849 -10.579722 1330.0858 -253.33758 0 178.61084
75 3.7314315 -2047.9104 -2047.688 98.594 -3286.3824 -46.968769 38.614932 0 62.996306 0 -49.355843 0 -11.951856 -10.592807 1330.3254 -252.96171 0 178.36638
76 3.7377793 -2048.0027 -2047.7799 188.23802 -3287.1675 -46.819484 38.57132 0 63.030317 0 -49.339493 0 -11.793827 -10.641562 1330.7882 -252.72211 0 178.09146
77 3.7586551 -2047.9569 -2047.7328 241.61191 -3287.9092 -46.743553 38.518687 0 63.102985 0 -49.339044 0 -11.682774 -10.64531 1331.3039 -252.41247 0 177.84998
78 3.7787566 -2047.9821 -2047.7568 258.25252 -3288.4589 -46.752001 38.465602 0 63.223888 0 -49.354844 0 -11.628931 -10.602746 1331.7318 -252.40341 0 177.79737
79 3.7949437 -2048.0074 -2047.7811 266.35348 -3288.7502 -46.841249 38.418669 0 63.394683 0 -49.384407 0 -11.635872 -10.562349 1331.9993 -252.39336 0 177.74739
80 3.7467427 -2047.9462 -2047.7229 225.47962 -3288.7606 -46.997709 38.381051 0 63.608793 0 -49.422504 0 -11.700043 -10.431202 1332.0713 -252.49254 0 177.79726
81 3.5749391 -2047.9376 -2047.7245 397.10221 -3288.6473 -47.191948 38.351879 0 63.849007 0 -49.462597 0 -11.815328 -10.358351 1332.0874 -252.64052 0 177.89019
82 3.3005858 -2047.8072 -2047.6104 371.82332 -3288.4052 -47.404754 38.316556 0 64.072501 0 -49.495217 0 -11.958963 -10.303741 1332.0402 -252.75561 0 178.08699
83 3.00685 -2047.7858 -2047.6065 554.36777 -3288.0688 -47.614613 38.274048 0 64.258389 0 -49.515085 0 -12.116246 -10.255566 1331.9409 -252.64573 0 177.95693
84 2.7814293 -2047.7659 -2047.6001 377.10491 -3287.5649 -47.809819 38.209321 0 64.370995 0 -49.515964 0 -12.257814 -10.21733 1331.7083 -252.33868 0 177.64992
85 2.6237727 -2047.744 -2047.5875 205.8225 -3286.952 -47.973334 38.131931 0 64.419988 0 -49.499068 0 -12.373924 -10.192152 1331.3595 -251.8514 0 177.18647
86 2.5162531 -2047.7232 -2047.5732 -97.79976 -3286.2825 -48.093853 38.051473 0 64.423119 0 -49.467754 0 -12.453925 -10.181067 1330.9043 -251.25564 0 176.63261
87 2.438659 -2047.6925 -2047.5472 -377.43146 -3285.6731 -48.161976 37.986938 0 64.416287 0 -49.429178 0 -12.496499 -10.18388 1330.4084 -250.61954 0 176.06005
88 2.4253045 -2047.7594 -2047.6148 -560.63873 -3285.2537 -48.172484 37.955847 0 64.433812 0 -49.391358 0 -12.503053 -10.199111 1329.957 -250.13311 0 175.54677
89 2.5131483 -2047.7368 -2047.587 -594.36125 -3285.1387 -48.123167 37.968582 0 64.49941 0 -49.361182 0 -12.476024 -10.224336 1329.639 -249.75309 0 175.23267
90 2.6678279 -2047.73 -2047.571 -443.01207 -3285.3945 -48.014399 38.024282 0 64.621004 0 -49.342673 0 -12.417475 -10.291001 1329.5228 -249.44266 0 175.00454
91 2.7829303 -2047.8153 -2047.6494 -185.84175 -3285.9582 -47.855269 38.110388 0 64.787888 0 -49.336089 0 -12.327323 -10.326664 1329.5818 -249.45431 0 174.96246
92 2.7474533 -2047.7576 -2047.5938 125.24779 -3286.765 -47.658197 38.205824 0 64.972581 0 -49.338799 0 -12.207685 -10.344488 1329.8127 -249.46001 0 175.02546
93 2.5760387 -2047.7183 -2047.5647 360.75263 -3287.7263 -47.44309 38.287039 0 65.135759 0 -49.346624 0 -12.063299 -10.392454 1330.2017 -249.62368 0 175.25258
94 2.3495578 -2047.8453 -2047.7052 643.22508 -3288.6903 -47.238388 38.340263 0 65.249195 0 -49.356564 0 -11.905609 -10.470861 1330.6654 -249.71872 0 175.28031
95 2.1549105 -2047.8079 -2047.6794 768.40446 -3289.386 -47.080039 38.353077 0 65.286179 0 -49.365418 0 -11.742286 -10.490704 1331.0014 -249.68309 0 175.29902
96 2.0852557 -2047.7863 -2047.6619 758.26302 -3289.6912 -46.989293 38.322588 0 65.241408 0 -49.372205 0 -11.588329 -10.519428 1331.1237 -249.62256 0 175.30908
97 2.1514528 -2047.8847 -2047.7564 599.9129 -3289.537 -46.977191 38.256185 0 65.13318 0 -49.378038 0 -11.461659 -10.528962 1330.9686 -249.52307 0 175.16331
98 2.3137715 -2047.8632 -2047.7252 339.3287 -3288.9826 -47.040482 38.1696 0 64.998693 0 -49.385742 0 -11.383585 -10.51446 1330.5698 -249.44332 0 175.14886
99 2.5238613 -2047.9039 -2047.7534 45.38466 -3288.1876 -47.166007 38.083372 0 64.882885 0 -49.398728 0 -11.373776 -10.473963 1330.0404 -249.3169 0 175.00647
100 2.767748 -2047.8632 -2047.6981 -203.1842 -3287.3672 -47.334883 38.017687 0 64.825454 0 -49.419582 0 -11.445973 -10.427316 1329.5397 -249.29485 0 175.0438
Loop time of 0.398233 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.391123 (98.2146)
Neigh time (%) = 0.000715971 (0.179787)
Comm time (%) = 0.000524521 (0.131712)
Outpt time (%) = 0.00567675 (1.42548)
Other time (%) = 0.000192881 (0.0484341)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1110 ave 1110 max 1110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1110
Ave neighs/atom = 52.8571
Neighbor list builds = 10
Dangerous builds = 0

170
examples/reax/log.reax.rdx.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# REAX potential for RDX system
# this run is equivalent to GRASP testreax
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 10.0 0 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reax.rdx
dump 1 all custom 1 dump.reax.rdx id type q xs ys zs
run 100
Memory usage per processor = 2.43838 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -2047.6191 -2047.6191 1411.6115 -3290.6584 -45.555509 38.801279 0 64.431331 0 -49.368043 0 -12.014532 -10.833851 1332.1957 -252.57915 0 177.9621
1 0.17729259 -2047.6352 -2047.6246 1302.8596 -3290.4955 -45.636967 38.789181 0 64.424892 0 -49.375516 0 -12.04864 -10.816863 1332.1526 -252.5894 0 177.96103
2 0.61943409 -2047.6752 -2047.6383 1021.8468 -3290.0429 -45.863414 38.754281 0 64.405628 0 -49.396435 0 -12.141947 -10.769089 1332.0375 -252.68399 0 178.02512
3 1.1359535 -2047.7292 -2047.6615 668.22019 -3289.3948 -46.188349 38.700785 0 64.374192 0 -49.426931 0 -12.271547 -10.698951 1331.8843 -252.79663 0 178.08872
4 1.5763627 -2047.7893 -2047.6954 329.52932 -3288.6685 -46.553602 38.635308 0 64.332347 0 -49.462048 0 -12.409557 -10.617427 1331.7273 -252.93214 0 178.15898
5 1.8972502 -2047.7352 -2047.6221 52.255014 -3287.9703 -46.905822 38.565966 0 64.283217 0 -49.496945 0 -12.531215 -10.535327 1331.5878 -253.02457 0 178.29196
6 2.1428044 -2047.7867 -2047.6589 -150.27775 -3287.3774 -47.205572 38.501034 0 64.230854 0 -49.527561 0 -12.618827 -10.461575 1331.4716 -253.12871 0 178.32949
7 2.3931301 -2047.8411 -2047.6984 -279.56892 -3286.9394 -47.428766 38.447638 0 64.179608 0 -49.550828 0 -12.662327 -10.402552 1331.3774 -253.19307 0 178.33125
8 2.7163825 -2047.7765 -2047.6145 -341.77195 -3286.6841 -47.564114 38.410694 0 64.133562 0 -49.564645 0 -12.658017 -10.362104 1331.3036 -253.15871 0 178.36735
9 3.1373573 -2047.8482 -2047.6612 -345.7503 -3286.6236 -47.609801 38.392337 0 64.096348 0 -49.567835 0 -12.607134 -10.341756 1331.2528 -253.21491 0 178.37536
10 3.6258172 -2047.9367 -2047.7206 -299.36779 -3286.7584 -47.5708 38.391799 0 64.070905 0 -49.560094 0 -12.51448 -10.341008 1331.2332 -253.20696 0 178.3191
11 4.0774819 -2047.9388 -2047.6957 -152.6784 -3287.0738 -47.45798 38.405762 0 64.061833 0 -49.542022 0 -12.387756 -10.444213 1331.253 -252.96545 0 178.2118
12 4.4059882 -2048.0651 -2047.8025 -19.833359 -3287.3785 -47.299275 38.429479 0 64.069944 0 -49.51478 0 -12.231965 -10.541991 1331.1623 -252.9065 0 178.14616
13 4.5696707 -2048.1163 -2047.8438 89.031246 -3287.5907 -47.120628 38.456875 0 64.093723 0 -49.48086 0 -12.061365 -10.590477 1330.9268 -252.7704 0 178.02071
14 4.5292628 -2048.1509 -2047.8809 184.99379 -3287.7342 -46.945908 38.481855 0 64.133676 0 -49.443844 0 -11.894586 -10.630355 1330.6213 -252.58485 0 177.84597
15 4.3080728 -2048.0187 -2047.7618 259.08159 -3287.8584 -46.79998 38.499221 0 64.190345 0 -49.408019 0 -11.75291 -10.654408 1330.3442 -252.24881 0 177.67006
16 4.0054984 -2047.9866 -2047.7478 295.14534 -3288.0045 -46.706741 38.505347 0 64.264076 0 -49.377843 0 -11.656714 -10.645964 1330.1788 -252.10538 0 177.56229
17 3.7365454 -2048.023 -2047.8002 308.28732 -3288.1892 -46.685034 38.498596 0 64.355208 0 -49.357284 0 -11.619855 -10.67973 1330.1723 -251.94333 0 177.42537
18 3.5553597 -2048.0383 -2047.8263 262.77683 -3288.3259 -46.749698 38.479152 0 64.463687 0 -49.349 0 -11.649121 -10.663445 1330.2579 -251.80554 0 177.30362
19 3.4492979 -2048.0654 -2047.8598 175.19297 -3288.3269 -46.902897 38.448826 0 64.589134 0 -49.353904 0 -11.74029 -10.637384 1330.3505 -251.75396 0 177.26146
20 3.4854376 -2048.066 -2047.8582 475.16825 -3288.1127 -47.135109 38.410455 0 64.729981 0 -49.370838 0 -11.882918 -10.574723 1330.3482 -251.72077 0 177.24238
21 3.6644742 -2048.0339 -2047.8154 322.43925 -3287.4815 -47.439791 38.338957 0 64.842336 0 -49.391187 0 -12.037419 -10.466406 1330.0588 -251.68721 0 177.22946
22 3.7684689 -2047.9822 -2047.7575 -6.4227685 -3286.5042 -47.785354 38.23892 0 64.931012 0 -49.412517 0 -12.18909 -10.349541 1329.517 -251.64384 0 177.21539
23 3.6581659 -2047.8835 -2047.6654 -366.17008 -3285.4261 -48.131073 38.126581 0 65.022116 0 -49.434818 0 -12.338703 -10.204547 1328.9001 -251.59067 0 177.19368
24 3.3424227 -2047.8405 -2047.6413 -634.89159 -3284.5564 -48.439646 38.02081 0 65.137469 0 -49.458852 0 -12.489944 -10.132405 1328.4467 -251.53413 0 177.16585
25 2.9320147 -2047.7876 -2047.6128 -806.23479 -3284.0314 -48.692929 37.939159 0 65.294101 0 -49.484737 0 -12.641981 -10.06839 1328.2377 -251.45345 0 177.11436
26 2.5498382 -2047.7333 -2047.5813 -856.30557 -3283.8979 -48.882631 37.893307 0 65.497388 0 -49.511409 0 -12.78991 -10.016311 1328.2835 -251.45234 0 177.14302
27 2.2896564 -2047.6894 -2047.5529 -792.15027 -3284.1089 -49.006436 37.886438 0 65.73897 0 -49.536216 0 -12.923848 -9.9792782 1328.5226 -251.5239 0 177.24116
28 2.1953279 -2047.7602 -2047.6293 -649.34232 -3284.5477 -49.064843 37.913247 0 65.998645 0 -49.55526 0 -13.030316 -9.9596855 1328.8432 -251.58997 0 177.23246
29 2.2746812 -2047.7191 -2047.5835 -480.53863 -3285.0694 -49.059624 37.962277 0 66.248359 0 -49.564229 0 -13.094927 -9.9590662 1329.1204 -251.59207 0 177.28922
30 2.5137626 -2047.6832 -2047.5333 -338.78457 -3285.5463 -48.993796 38.019695 0 66.458461 0 -49.559587 0 -13.105556 -9.9777667 1329.255 -251.57907 0 177.34571
31 2.8705252 -2047.7918 -2047.6207 -261.43271 -3285.905 -48.87173 38.073096 0 66.605317 0 -49.539679 0 -13.055347 -10.014584 1329.2051 -251.52496 0 177.23603
32 3.263513 -2047.7823 -2047.5877 -239.85847 -3286.144 -48.698989 38.114232 0 66.67803 0 -49.505443 0 -12.944463 -10.100635 1328.9976 -251.29263 0 177.11402
33 3.5790914 -2047.919 -2047.7057 -272.81375 -3286.2675 -48.486653 38.140456 0 66.681928 0 -49.460524 0 -12.779188 -10.214915 1328.661 -250.91112 0 176.71745
34 3.7157858 -2047.8509 -2047.6294 -366.24629 -3286.3002 -48.249737 38.154448 0 66.636284 0 -49.41103 0 -12.572509 -10.300515 1328.2382 -250.45877 0 176.41292
35 3.6401723 -2047.9476 -2047.7306 -462.2975 -3286.3612 -48.000982 38.162509 0 66.567443 0 -49.364907 0 -12.344936 -10.377699 1327.8584 -250.05056 0 175.96424
36 3.4154586 -2047.8414 -2047.6378 -506.67084 -3286.5886 -47.754199 38.172106 0 66.502916 0 -49.330405 0 -12.121629 -10.440348 1327.6678 -249.70257 0 175.75356
37 3.1648925 -2047.9481 -2047.7594 -462.33305 -3287.0652 -47.526179 38.189107 0 66.463757 0 -49.314208 0 -11.926014 -10.513399 1327.7612 -249.57666 0 175.55953
38 2.999693 -2047.8782 -2047.6993 -339.36587 -3287.7646 -47.336728 38.215402 0 66.459891 0 -49.319815 0 -11.777148 -10.552379 1328.134 -249.54474 0 175.60793
39 2.9638638 -2047.9555 -2047.7788 -159.85872 -3288.5819 -47.203458 38.247999 0 66.488682 0 -49.346668 0 -11.685525 -10.572352 1328.711 -249.73922 0 175.72588
40 3.0282684 -2047.891 -2047.7104 30.336596 -3289.3528 -47.139173 38.279831 0 66.53636 0 -49.390316 0 -11.653427 -10.563935 1329.3595 -250.00754 0 176.0405
41 3.1316156 -2047.966 -2047.7793 185.76169 -3289.9063 -47.148769 38.302051 0 66.582153 0 -49.443584 0 -11.675677 -10.5402 1329.9335 -250.49665 0 176.42744
42 3.220039 -2047.8987 -2047.7067 267.78296 -3290.1078 -47.228237 38.306942 0 66.604604 0 -49.498297 0 -11.742793 -10.506057 1330.3082 -250.80732 0 176.77199
43 3.2603167 -2047.9772 -2047.7828 248.89503 -3289.8951 -47.364766 38.29047 0 66.588416 0 -49.546987 0 -11.844256 -10.467422 1330.412 -251.24021 0 177.09073
44 3.2199017 -2047.8506 -2047.6587 110.32559 -3289.2994 -47.537875 38.253998 0 66.529827 0 -49.584198 0 -11.971713 -10.380021 1330.2453 -251.43013 0 177.32356
45 3.0619735 -2047.8547 -2047.6722 -136.38215 -3288.4791 -47.719419 38.204799 0 66.439217 0 -49.607162 0 -12.117605 -10.288427 1329.917 -251.59234 0 177.38832
46 2.8063563 -2047.7324 -2047.5651 -401.33272 -3287.7047 -47.875914 38.1548 0 66.335706 0 -49.615969 0 -12.280201 -10.218262 1329.6327 -251.61481 0 177.45425
47 2.5140356 -2047.7803 -2047.6305 -614.67234 -3287.1803 -47.981301 38.118597 0 66.237922 0 -49.612786 0 -12.453199 -10.213521 1329.5324 -251.60413 0 177.37591
48 2.2367481 -2047.7358 -2047.6025 -757.57047 -3286.955 -48.021555 38.110214 0 66.16373 0 -49.600718 0 -12.623438 -10.225255 1329.6121 -251.56506 0 177.36915
49 2.041479 -2047.6985 -2047.5768 -793.6666 -3287.0103 -47.986997 38.139067 0 66.122819 0 -49.58293 0 -12.77354 -10.254916 1329.811 -251.40199 0 177.23938
50 1.9909741 -2047.6767 -2047.558 -711.00594 -3287.2859 -47.870332 38.206887 0 66.114307 0 -49.561739 0 -12.88419 -10.302905 1330.0428 -251.40886 0 177.27323
51 2.0753437 -2047.6523 -2047.5286 -519.06591 -3287.7104 -47.667065 38.306663 0 66.127013 0 -49.538213 0 -12.937431 -10.368198 1330.2339 -251.52519 0 177.42666
52 2.1888893 -2047.7509 -2047.6204 -244.32599 -3288.2254 -47.379502 38.424005 0 66.141153 0 -49.512409 0 -12.920435 -10.447817 1330.3529 -251.75808 0 177.57475
53 2.1985534 -2047.7359 -2047.6048 82.464963 -3288.7964 -47.022454 38.540573 0 66.132021 0 -49.484195 0 -12.829283 -10.536326 1330.4209 -251.87569 0 177.71493
54 2.0482615 -2047.7193 -2047.5972 431.56158 -3289.4009 -46.627524 38.63823 0 66.0757 0 -49.454205 0 -12.67156 -10.625721 1330.4921 -252.02296 0 177.87758
55 1.8981294 -2047.7216 -2047.6084 264.22506 -3290.0167 -46.241953 38.70287 0 65.95608 0 -49.424474 0 -12.467678 -10.705843 1330.6221 -252.13237 0 177.98632
56 1.8184602 -2047.7486 -2047.6402 647.6025 -3290.793 -45.897966 38.76022 0 65.818824 0 -49.406506 0 -12.280617 -10.768739 1330.9975 -252.33899 0 178.16065
57 1.837517 -2047.8239 -2047.7143 974.19518 -3291.5734 -45.654424 38.8027 0 65.661285 0 -49.403355 0 -12.140626 -10.80466 1331.5525 -252.71345 0 178.44959
58 2.0619166 -2047.7443 -2047.6214 1141.4639 -3292.155 -45.559075 38.823968 0 65.479061 0 -49.415742 0 -12.067763 -10.807349 1332.1523 -252.87824 0 178.68344
59 2.491011 -2047.8459 -2047.6974 1100.4717 -3292.3483 -45.632858 38.819861 0 65.267782 0 -49.441542 0 -12.06567 -10.776125 1332.6386 -253.19647 0 178.88883
60 3.0218388 -2047.8023 -2047.6221 885.1484 -3292.0396 -45.863086 38.789338 0 65.025617 0 -49.476197 0 -12.121867 -10.716178 1332.8811 -253.48777 0 179.20626
61 3.516141 -2047.9077 -2047.6981 569.87375 -3291.2191 -46.209889 38.735187 0 64.755495 0 -49.513989 0 -12.21484 -10.636903 1332.8127 -253.79563 0 179.37924
62 3.8551967 -2047.8533 -2047.6234 221.83563 -3289.9812 -46.6204 38.664151 0 64.4663 0 -49.549588 0 -12.323532 -10.549157 1332.4468 -254.04704 0 179.6404
63 3.969202 -2047.9294 -2047.6928 -114.65261 -3288.4988 -47.042415 38.586152 0 64.172045 0 -49.579068 0 -12.433308 -10.462933 1331.8713 -254.29573 0 179.75335
64 3.8725443 -2047.8511 -2047.6202 -407.91583 -3286.9903 -47.432296 38.512738 0 63.889332 0 -49.60021 0 -12.536943 -10.386089 1331.2258 -254.36295 0 179.82988
65 3.6778718 -2047.9141 -2047.6948 -633.55767 -3285.6754 -47.757613 38.455001 0 63.633986 0 -49.612211 0 -12.631728 -10.32412 1330.6616 -254.56434 0 179.90077
66 3.5381634 -2047.8363 -2047.6254 -769.36054 -3284.7314 -47.996593 38.421432 0 63.418348 0 -49.615167 0 -12.715509 -10.280419 1330.3022 -254.62752 0 179.9883
67 3.5435879 -2047.9253 -2047.714 -806.1308 -3284.2528 -48.137126 38.416068 0 63.249463 0 -49.609505 0 -12.7834 -10.256664 1330.209 -254.68782 0 179.92752
68 3.6196621 -2047.9443 -2047.7285 -677.92402 -3284.2362 -48.17559 38.437561 0 63.132312 0 -49.595623 0 -12.826804 -10.356944 1330.3687 -254.53024 0 179.83857
69 3.6930057 -2048.0947 -2047.8746 -541.29551 -3284.4018 -48.129689 38.479947 0 63.060994 0 -49.573374 0 -12.827407 -10.432156 1330.518 -254.54815 0 179.75888
70 3.7978261 -2048.011 -2047.7846 -398.03848 -3284.608 -48.012566 38.532982 0 63.022244 0 -49.543287 0 -12.778329 -10.464772 1330.5391 -254.32484 0 179.62647
71 3.9049819 -2048.0816 -2047.8488 -255.77531 -3284.8125 -47.838119 38.584921 0 63.003598 0 -49.506582 0 -12.675928 -10.509738 1330.4258 -254.17081 0 179.41775
72 3.9503231 -2048.0102 -2047.7747 -132.79648 -3285.028 -47.624717 38.624864 0 62.99425 0 -49.465536 0 -12.525709 -10.551349 1330.2378 -253.90761 0 179.23577
73 3.8982747 -2048.0032 -2047.7708 -44.32569 -3285.31 -47.394039 38.644829 0 62.988146 0 -49.423629 0 -12.341525 -10.553364 1330.0799 -253.67153 0 178.97796
74 3.7933987 -2048.0378 -2047.8117 31.904332 -3285.7498 -47.167665 38.641193 0 62.986417 0 -49.385397 0 -12.141849 -10.579722 1330.0858 -253.33758 0 178.61084
75 3.7314316 -2047.9104 -2047.688 98.59413 -3286.3824 -46.968769 38.614932 0 62.996306 0 -49.355843 0 -11.951856 -10.592807 1330.3254 -252.96171 0 178.36638
76 3.7377794 -2048.0027 -2047.7799 188.23812 -3287.1675 -46.819484 38.57132 0 63.030317 0 -49.339493 0 -11.793827 -10.641562 1330.7882 -252.72211 0 178.09146
77 3.7586551 -2047.9569 -2047.7328 241.61195 -3287.9092 -46.743553 38.518687 0 63.102985 0 -49.339044 0 -11.682774 -10.64531 1331.3039 -252.41247 0 177.84998
78 3.7787567 -2047.9821 -2047.7568 258.25244 -3288.4589 -46.752001 38.465602 0 63.223888 0 -49.354844 0 -11.628931 -10.602746 1331.7318 -252.40341 0 177.79737
79 3.7949438 -2048.0074 -2047.7811 266.35329 -3288.7502 -46.841249 38.418669 0 63.394683 0 -49.384407 0 -11.635871 -10.562349 1331.9993 -252.39336 0 177.74739
80 3.7467427 -2047.9462 -2047.7229 225.47946 -3288.7606 -46.997709 38.381051 0 63.608793 0 -49.422504 0 -11.700043 -10.431202 1332.0713 -252.49254 0 177.79726
81 3.574939 -2047.9376 -2047.7245 397.10207 -3288.6473 -47.191948 38.351879 0 63.849007 0 -49.462597 0 -11.815328 -10.358351 1332.0874 -252.64052 0 177.89019
82 3.3005856 -2047.8072 -2047.6104 371.82326 -3288.4052 -47.404754 38.316556 0 64.072502 0 -49.495217 0 -11.958963 -10.303741 1332.0402 -252.75561 0 178.08699
83 3.0068499 -2047.7858 -2047.6065 554.36779 -3288.0688 -47.614613 38.274048 0 64.258389 0 -49.515085 0 -12.116247 -10.255566 1331.9409 -252.64573 0 177.95693
84 2.7814292 -2047.7659 -2047.6001 377.10503 -3287.5649 -47.809819 38.209321 0 64.370995 0 -49.515964 0 -12.257814 -10.21733 1331.7083 -252.33868 0 177.64992
85 2.6237725 -2047.744 -2047.5875 205.82268 -3286.952 -47.973334 38.131931 0 64.419989 0 -49.499067 0 -12.373924 -10.192152 1331.3595 -251.85139 0 177.18647
86 2.5162529 -2047.7232 -2047.5732 -97.799561 -3286.2825 -48.093852 38.051473 0 64.423119 0 -49.467754 0 -12.453925 -10.181067 1330.9043 -251.25564 0 176.63261
87 2.4386589 -2047.6925 -2047.5472 -377.43129 -3285.6731 -48.161976 37.986938 0 64.416287 0 -49.429178 0 -12.496499 -10.18388 1330.4084 -250.61954 0 176.06005
88 2.4253044 -2047.7594 -2047.6148 -560.63864 -3285.2537 -48.172484 37.955847 0 64.433812 0 -49.391358 0 -12.503053 -10.199111 1329.957 -250.13311 0 175.54677
89 2.5131483 -2047.7368 -2047.587 -594.36124 -3285.1387 -48.123167 37.968582 0 64.49941 0 -49.361182 0 -12.476024 -10.224337 1329.639 -249.75309 0 175.23267
90 2.6678279 -2047.73 -2047.571 -443.01215 -3285.3945 -48.014399 38.024282 0 64.621004 0 -49.342673 0 -12.417475 -10.291001 1329.5228 -249.44266 0 175.00454
91 2.7829303 -2047.8153 -2047.6494 -185.84186 -3285.9582 -47.855268 38.110388 0 64.787888 0 -49.336089 0 -12.327323 -10.326664 1329.5818 -249.45431 0 174.96246
92 2.7474533 -2047.7576 -2047.5938 125.24771 -3286.765 -47.658196 38.205824 0 64.97258 0 -49.338799 0 -12.207685 -10.344488 1329.8127 -249.46001 0 175.02546
93 2.5760389 -2047.7183 -2047.5647 360.75259 -3287.7263 -47.44309 38.287039 0 65.135759 0 -49.346624 0 -12.063299 -10.392454 1330.2017 -249.62368 0 175.25258
94 2.349558 -2047.8453 -2047.7052 643.22514 -3288.6903 -47.238388 38.340263 0 65.249195 0 -49.356564 0 -11.905609 -10.470861 1330.6654 -249.71872 0 175.28031
95 2.1549106 -2047.8079 -2047.6794 768.40457 -3289.386 -47.080039 38.353077 0 65.286178 0 -49.365418 0 -11.742286 -10.490704 1331.0014 -249.68309 0 175.29902
96 2.0852558 -2047.7863 -2047.6619 758.26315 -3289.6912 -46.989293 38.322588 0 65.241408 0 -49.372205 0 -11.588329 -10.519428 1331.1237 -249.62256 0 175.30908
97 2.1514528 -2047.8847 -2047.7564 599.91301 -3289.537 -46.977191 38.256185 0 65.13318 0 -49.378038 0 -11.461659 -10.528962 1330.9686 -249.52308 0 175.16331
98 2.3137715 -2047.8632 -2047.7252 339.32873 -3288.9826 -47.040482 38.1696 0 64.998693 0 -49.385742 0 -11.383585 -10.51446 1330.5698 -249.44332 0 175.14886
99 2.5238614 -2047.9038 -2047.7534 45.384585 -3288.1876 -47.166008 38.083372 0 64.882885 0 -49.398728 0 -11.373776 -10.473963 1330.0404 -249.31689 0 175.0065
100 2.7677482 -2047.8632 -2047.6981 -203.18437 -3287.3672 -47.334883 38.017687 0 64.825454 0 -49.419582 0 -11.445973 -10.427316 1329.5397 -249.29485 0 175.0438
Loop time of 0.307552 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.180175 (58.5835)
Neigh time (%) = 0.000226915 (0.073781)
Comm time (%) = 0.118801 (38.6279)
Outpt time (%) = 0.00818455 (2.66119)
Other time (%) = 0.000164986 (0.0536448)
Nlocal: 5.25 ave 14 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 433 max 282 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 305 ave 784 max 0 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 1220
Ave neighs/atom = 58.0952
Neighbor list builds = 10
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# REAX potential for TATB system
# this run is equivalent to GRASP testtatb
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
384 atoms
# N.B. to match reax/c, set hbnewflag = 1
# reax args: hbcut hbnewflag tripflag precision
#pair_style reax 10.0 1 1 1.0e-6
pair_style reax 10.0 0 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 6.71068 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44977.462 -44977.462 350844.92 -65892.012 9.4831588 606.70862 0 2045.5187 5.3787493 -424.41614 -3566.6607 -444.25112 -517.90927 25281.328 -6401.2462 0 4320.6163
1 1.5362501 -44979.21 -44977.456 351524.29 -65893.77 10.413172 606.81524 0 2045.169 5.3782621 -424.33557 -3567.2748 -444.23842 -517.93353 25281.228 -6401.4158 0 4320.7547
2 6.1403173 -44984.431 -44977.421 353564.02 -65899.051 13.208842 607.13469 0 2044.1214 5.3768107 -424.09328 -3569.1161 -444.20034 -518.00645 25280.931 -6402.1947 0 4321.4587
3 13.798172 -44993.225 -44977.472 356972.83 -65907.867 17.887012 607.66575 0 2042.3809 5.3744256 -423.68764 -3572.1806 -444.13698 -518.12843 25280.439 -6403.6029 0 4322.6319
4 24.486471 -45005.439 -44977.484 361762.22 -65920.24 24.475564 608.40641 0 2039.9553 5.3711579 -423.11592 -3576.4623 -444.04851 -518.30012 25279.759 -6405.6457 0 4324.4065
5 38.17262 -45021.065 -44977.486 367944.3 -65936.199 33.013132 609.35384 0 2036.8556 5.3670795 -422.37437 -3581.9521 -443.93515 -518.52248 25278.899 -6408.1748 0 4326.6035
6 54.814793 -45040.073 -44977.494 375525.26 -65955.782 43.548646 610.50446 0 2033.0959 5.3622834 -421.45833 -3588.6378 -443.79722 -518.79674 25277.871 -6411.253 0 4329.27
7 74.361854 -45062.562 -44977.667 384488.13 -65979.036 56.14069 611.85396 0 2028.6932 5.3568834 -420.36227 -3596.6686 -443.63511 -519.12443 25276.688 -6414.8934 0 4332.4254
8 96.753115 -45088.135 -44977.676 394820.42 -66006.012 70.856555 613.39723 0 2023.6676 5.3510125 -419.07997 -3605.6963 -443.44928 -519.50737 25275.366 -6419.1771 0 4336.1499
9 121.91206 -45116.368 -44977.187 406680.23 -66036.769 87.771046 615.12844 0 2018.7397 5.3448206 -417.60463 -3616.0503 -443.24033 -519.94764 25273.922 -6423.9836 0 4340.3202
10 149.75446 -45148.169 -44977.202 419448.39 -66071.364 106.96367 617.0409 0 2012.5569 5.3384682 -415.92921 -3627.326 -443.00894 -520.44754 25272.379 -6429.3963 0 4345.0239
11 180.18901 -45182.93 -44977.217 433126.49 -66109.859 128.51816 619.12702 0 2005.8371 5.3321158 -414.04636 -3639.6783 -442.75323 -521.00943 25270.759 -6435.3914 0 4350.234
12 213.10176 -45220.694 -44977.407 447323.77 -66152.305 152.51815 621.3781 0 1998.6206 5.3259063 -411.94884 -3653.2385 -442.47944 -521.6355 25269.085 -6442.0018 0 4355.9869
13 248.35364 -45260.832 -44977.299 461500.69 -66198.742 179.04268 623.78402 0 1990.9591 5.319936 -409.62972 -3667.4942 -442.18305 -522.32744 25267.385 -6449.2213 0 4362.2744
14 285.77131 -45303.58 -44977.329 474776.64 -66249.179 208.15938 626.33277 0 1982.9202 5.3142108 -407.08274 -3682.8223 -441.87093 -523.08579 25265.687 -6457.0627 0 4369.1104
15 325.13312 -45348.553 -44977.364 485994.64 -66303.581 239.9165 629.00982 0 1974.5949 5.308582 -404.30252 -3699.0373 -441.54152 -523.9091 25264.018 -6465.5361 0 4376.5068
16 366.14805 -45395.423 -44977.41 493592.79 -66361.841 274.33138 631.79729 0 1966.107 5.3026576 -401.28492 -3716.0758 -441.19624 -524.7927 25262.409 -6474.6458 0 4384.4666
17 408.43184 -45443.752 -44977.466 495609.06 -66423.751 311.37652 634.67308 0 1957.6248 5.2956906 -398.02733 -3733.8675 -440.83661 -525.72714 25260.887 -6484.3971 0 4392.9975
18 451.48082 -45492.968 -44977.535 489764.64 -66488.965 350.96361 637.60998 0 1949.3723 5.2864539 -394.52899 -3752.336 -440.46434 -526.69643 25259.48 -6494.7901 0 4402.1008
19 494.65084 -45542.334 -44977.616 473698.87 -66556.967 392.9281 640.57527 0 1941.6376 5.2731328 -390.79122 -3771.3986 -440.08124 -527.67642 25258.211 -6505.7958 0 4411.7515
20 537.15237 -45590.95 -44977.71 445393.52 -66627.054 437.01837 643.53106 0 1934.773 5.253285 -386.81774 -3790.967 -439.68929 -528.63394 25257.103 -6517.4601 0 4421.9934
21 578.07545 -45637.77 -44977.81 403759.03 -66698.343 482.89589 646.43599 0 1929.1799 5.2239444 -382.61485 -3810.9481 -439.2906 -529.52762 25256.17 -6529.7387 0 4432.7876
22 616.45505 -45681.684 -44977.908 349235.78 -66769.835 530.15196 649.24824 0 1925.2752 5.1819278 -378.19171 -3831.2452 -438.88741 -530.31106 25255.425 -6542.6417 0 4444.1461
23 651.3754 -45721.632 -44977.989 284158.42 -66840.508 578.34298 651.92981 0 1923.441 5.1243532 -373.56051 -3851.7589 -438.48202 -530.9385 25254.87 -6556.0745 0 4455.9825
24 682.06338 -45756.047 -44977.37 211816.16 -66909.459 627.03832 654.45076 0 1923.9682 5.0492645 -368.73671 -3872.421 -437.32012 -531.38912 25254.506 -6569.9969 0 4468.2626
25 708.05182 -45785.744 -44977.397 138937.28 -66976.018 675.86583 656.79217 0 1927.0098 4.9561644 -363.73915 -3893.0659 -436.84675 -531.60529 25254.329 -6584.4458 0 4481.0237
Loop time of 5.25044 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 5.19548 (98.9532)
Neigh time (%) = 0.049526 (0.943273)
Comm time (%) = 0.00251365 (0.047875)
Outpt time (%) = 0.00154328 (0.0293934)
Other time (%) = 0.00137615 (0.0262102)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286819 ave 286819 max 286819 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286819
Ave neighs/atom = 746.924
Neighbor list builds = 5
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# REAX potential for TATB system
# this run is equivalent to GRASP testtatb
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
384 atoms
# N.B. to match reax/c, set hbnewflag = 1
# reax args: hbcut hbnewflag tripflag precision
#pair_style reax 10.0 1 1 1.0e-6
pair_style reax 10.0 0 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 3.32015 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44977.462 -44977.462 350844.92 -65892.012 9.4831588 606.70862 0 2045.5187 5.3787493 -424.41614 -3566.6607 -444.25112 -517.90927 25281.328 -6401.2462 0 4320.6162
1 1.5362501 -44979.21 -44977.456 351524.29 -65893.77 10.413172 606.81524 0 2045.169 5.3782621 -424.33557 -3567.2748 -444.23842 -517.93353 25281.228 -6401.4158 0 4320.7547
2 6.1403173 -44984.431 -44977.421 353564.02 -65899.051 13.208842 607.13469 0 2044.1214 5.3768107 -424.09328 -3569.1161 -444.20034 -518.00645 25280.931 -6402.1946 0 4321.4586
3 13.798172 -44993.227 -44977.474 356972.84 -65907.867 17.887012 607.66575 0 2042.3809 5.3744256 -423.68764 -3572.1806 -444.13698 -518.12843 25280.439 -6403.6023 0 4322.6293
4 24.486471 -45005.435 -44977.48 361762.21 -65920.24 24.475564 608.40641 0 2039.9553 5.3711579 -423.11592 -3576.4623 -444.04851 -518.30012 25279.759 -6405.6475 0 4324.4118
5 38.17262 -45021.065 -44977.485 367944.3 -65936.199 33.013132 609.35384 0 2036.8556 5.3670795 -422.37437 -3581.9521 -443.93515 -518.52248 25278.899 -6408.1767 0 4326.6058
6 54.814793 -45040.073 -44977.494 375525.32 -65955.782 43.548646 610.50446 0 2033.0959 5.3622834 -421.45833 -3588.6378 -443.79722 -518.79674 25277.871 -6411.2257 0 4329.2423
7 74.361854 -45062.564 -44977.668 384488.09 -65979.036 56.140691 611.85396 0 2028.6932 5.3568834 -420.36227 -3596.6686 -443.63511 -519.12443 25276.688 -6414.9073 0 4332.4375
8 96.753115 -45088.134 -44977.676 394820.42 -66006.012 70.856556 613.39723 0 2023.6676 5.3510125 -419.07997 -3605.6963 -443.44928 -519.50737 25275.366 -6419.1799 0 4336.1531
9 121.91206 -45116.369 -44977.188 406680.24 -66036.769 87.771047 615.12844 0 2018.7397 5.3448206 -417.60463 -3616.0503 -443.24033 -519.94764 25273.922 -6423.9806 0 4340.3169
10 149.75446 -45148.169 -44977.202 419448.39 -66071.364 106.96367 617.0409 0 2012.5569 5.3384682 -415.92921 -3627.326 -443.00894 -520.44754 25272.379 -6429.3956 0 4345.0232
11 180.18901 -45182.93 -44977.217 433126.48 -66109.859 128.51816 619.12702 0 2005.8371 5.3321158 -414.04636 -3639.6783 -442.75323 -521.00943 25270.759 -6435.3945 0 4350.2375
12 213.10176 -45220.695 -44977.407 447323.77 -66152.305 152.51815 621.3781 0 1998.6206 5.3259063 -411.94884 -3653.2385 -442.47944 -521.6355 25269.085 -6441.9986 0 4355.9832
13 248.35364 -45260.832 -44977.299 461500.69 -66198.742 179.04268 623.78402 0 1990.9591 5.319936 -409.62972 -3667.4942 -442.18305 -522.32744 25267.385 -6449.2215 0 4362.2749
14 285.77131 -45303.579 -44977.329 474776.65 -66249.179 208.15938 626.33277 0 1982.9202 5.3142108 -407.08274 -3682.8223 -441.87093 -523.08579 25265.687 -6457.0635 0 4369.1116
15 325.13312 -45348.553 -44977.365 485994.64 -66303.581 239.9165 629.00982 0 1974.5949 5.308582 -404.30252 -3699.0373 -441.54152 -523.9091 25264.018 -6465.536 0 4376.5062
16 366.14805 -45395.422 -44977.409 493592.8 -66361.841 274.33139 631.79729 0 1966.107 5.3026576 -401.28492 -3716.0758 -441.19624 -524.7927 25262.409 -6474.6448 0 4384.4661
17 408.43184 -45443.752 -44977.466 495609.06 -66423.751 311.37652 634.67308 0 1957.6248 5.2956906 -398.02733 -3733.8675 -440.83661 -525.72714 25260.887 -6484.3969 0 4392.9974
18 451.48082 -45492.968 -44977.535 489764.65 -66488.965 350.96362 637.60998 0 1949.3723 5.2864539 -394.52899 -3752.336 -440.46434 -526.69643 25259.479 -6494.7885 0 4402.0997
19 494.65084 -45542.336 -44977.618 473698.76 -66556.967 392.9281 640.57527 0 1941.6376 5.2731328 -390.79122 -3771.3986 -440.08124 -527.67642 25258.211 -6505.8243 0 4411.7778
20 537.15237 -45590.952 -44977.712 445393.41 -66627.054 437.01837 643.53106 0 1934.773 5.253285 -386.81774 -3790.967 -439.68929 -528.63394 25257.103 -6517.4882 0 4422.0193
21 578.07544 -45637.772 -44977.812 403758.92 -66698.343 482.89589 646.43599 0 1929.1799 5.2239444 -382.61485 -3810.9481 -439.2906 -529.52762 25256.17 -6529.7678 0 4432.8145
22 616.45505 -45681.684 -44977.908 349235.78 -66769.835 530.15195 649.24824 0 1925.2752 5.1819278 -378.19171 -3831.2452 -438.88741 -530.31106 25255.425 -6542.6395 0 4444.1437
23 651.3754 -45721.632 -44977.989 284158.41 -66840.508 578.34297 651.92981 0 1923.441 5.1243533 -373.56052 -3851.7589 -438.48202 -530.9385 25254.87 -6556.0746 0 4455.9826
24 682.06338 -45756.047 -44977.37 211816.14 -66909.459 627.03831 654.45076 0 1923.9682 5.0492645 -368.73671 -3872.421 -437.32012 -531.38912 25254.506 -6569.9982 0 4468.2638
25 708.05182 -45785.744 -44977.396 138937.27 -66976.018 675.86581 656.79217 0 1927.0098 4.9561644 -363.73915 -3893.0659 -436.84675 -531.60529 25254.329 -6584.4438 0 4481.0217
Loop time of 2.44196 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 2.37349 (97.1962)
Neigh time (%) = 0.0108814 (0.445599)
Comm time (%) = 0.0543768 (2.22677)
Outpt time (%) = 0.00227308 (0.0930843)
Other time (%) = 0.000935674 (0.0383165)
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79731 ave 79731 max 79731 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 318924
Ave neighs/atom = 830.531
Neighbor list builds = 5
Dangerous builds = 0

78
examples/reax/log.reaxc.rdx.9Jan12.linux.1 Normal file
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LAMMPS (10 Jan 2012)
# REAX potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
21 atoms
pair_style reax/c NULL
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
dump 1 all atom 10 dump.reax.rdx
run 100
Memory usage per processor = 3.36981 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -2047.6192 -2047.6192 1411.6059 -3290.6584 -45.555509 38.801279 0 64.431326 0 -49.368043 0 -12.014532 -10.833851 1332.1957 -252.57895 0 177.96181
10 3.6250746 -2047.8374 -2047.6213 -299.29788 -3286.7577 -47.570889 38.391844 0 64.071067 0 -49.560103 0 -12.514519 -10.341012 1331.2323 -253.18347 0 178.39505
20 3.4851966 -2047.9794 -2047.7716 475.20344 -3288.1123 -47.134454 38.410334 0 64.72975 0 -49.370822 0 -11.882226 -10.574851 1330.3468 -251.63641 0 177.24484
30 2.5132745 -2047.7704 -2047.6205 -340.63099 -3285.5229 -48.991864 38.019618 0 66.457332 0 -49.559786 0 -13.10045 -9.9781232 1329.2274 -251.73644 0 177.41485
40 3.0232311 -2047.9594 -2047.7792 21.700614 -3289.2578 -47.147547 38.279866 0 66.537178 0 -49.390314 0 -11.652525 -10.56356 1329.2708 -250.11063 0 176.07519
50 1.990721 -2047.738 -2047.6193 -714.43544 -3287.2234 -47.871139 38.207269 0 66.115851 0 -49.561576 0 -12.880091 -10.303605 1329.9753 -251.47217 0 177.27559
60 3.0207655 -2047.8057 -2047.6256 877.22909 -3291.9702 -45.868842 38.789238 0 65.02199 0 -49.476448 0 -12.119935 -10.715769 1332.8197 -253.50299 0 179.21763
70 3.7979867 -2048.0143 -2047.7878 -407.76315 -3284.4652 -48.020673 38.534105 0 63.022006 0 -49.542841 0 -12.774251 -10.465485 1330.3969 -254.29695 0 179.59816
80 3.7164824 -2047.8611 -2047.6396 220.95831 -3288.6586 -46.999324 38.381564 0 63.615152 0 -49.422698 0 -11.696876 -10.432264 1331.9644 -252.44099 0 177.82845
90 2.6654591 -2047.8079 -2047.649 -449.08758 -3285.2642 -48.012804 38.024045 0 64.608148 0 -49.343129 0 -12.394068 -10.291747 1329.3842 -249.5516 0 175.03318
100 2.7731308 -2047.8848 -2047.7195 -235.73754 -3287.2634 -47.364088 38.017482 0 64.838745 0 -49.418546 0 -11.472543 -10.400448 1329.4671 -249.31631 0 175.02711
Loop time of 0.270813 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.262195 (96.8178)
Neigh time (%) = 0.000696182 (0.257071)
Comm time (%) = 0.000518322 (0.191395)
Outpt time (%) = 0.000496149 (0.183207)
Other time (%) = 0.00690722 (2.55055)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1110 ave 1110 max 1110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1110
Ave neighs/atom = 52.8571
Neighbor list builds = 10
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# REAX potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
21 atoms
pair_style reax/c NULL
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
dump 1 all atom 10 dump.reax.rdx
run 100
Memory usage per processor = 3.59354 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -2047.6192 -2047.6192 1411.6051 -3290.6584 -45.555509 38.801279 0 64.431326 0 -49.368043 0 -12.014532 -10.833851 1332.1957 -252.57908 0 177.96194
10 3.6250762 -2047.8374 -2047.6213 -299.29972 -3286.7577 -47.57089 38.391844 0 64.071067 0 -49.560102 0 -12.51452 -10.341012 1331.2323 -253.18355 0 178.39513
20 3.4851578 -2047.9794 -2047.7716 475.17542 -3288.1123 -47.134473 38.41033 0 64.729741 0 -49.370823 0 -11.882237 -10.574847 1330.3468 -251.63847 0 177.24689
30 2.5132467 -2047.7703 -2047.6205 -340.63046 -3285.5228 -48.991897 38.019619 0 66.457326 0 -49.559777 0 -13.10048 -9.9781237 1329.2273 -251.73031 0 177.40874
40 3.0231761 -2047.9594 -2047.7792 21.718473 -3289.258 -47.147503 38.279849 0 66.537175 0 -49.390313 0 -11.652462 -10.563562 1329.2708 -250.10599 0 176.07056
50 1.9907242 -2047.738 -2047.6193 -714.56947 -3287.2233 -47.871115 38.207252 0 66.115812 0 -49.561573 0 -12.880072 -10.303609 1329.9752 -251.48697 0 177.29036
60 3.0206213 -2047.8057 -2047.6256 877.19514 -3291.9699 -45.868872 38.78924 0 65.021919 0 -49.476435 0 -12.119954 -10.715774 1332.8194 -253.49604 0 179.21072
70 3.798014 -2048.0143 -2047.7879 -407.80527 -3284.4655 -48.020645 38.534105 0 63.022071 0 -49.542845 0 -12.774261 -10.465486 1330.3971 -254.30899 0 179.61016
80 3.7164646 -2047.8611 -2047.6396 221.02437 -3288.6587 -46.999336 38.381581 0 63.615247 0 -49.422692 0 -11.696912 -10.432265 1331.9645 -252.43638 0 177.82386
90 2.6655168 -2047.8079 -2047.649 -449.21506 -3285.2638 -48.012928 38.024019 0 64.608125 0 -49.343135 0 -12.394116 -10.29172 1329.3841 -249.56135 0 175.04292
100 2.7731053 -2047.8848 -2047.7195 -235.88371 -3287.2633 -47.364007 38.017457 0 64.83867 0 -49.418529 0 -11.472482 -10.400466 1329.467 -249.32842 0 175.0392
Loop time of 0.210253 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.136896 (65.1102)
Neigh time (%) = 0.000205219 (0.0976055)
Comm time (%) = 0.0463336 (22.037)
Outpt time (%) = 0.000781 (0.371457)
Other time (%) = 0.0260371 (12.3837)
Nlocal: 5.25 ave 14 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 433 max 282 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 305 ave 784 max 0 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 1220
Ave neighs/atom = 58.0952
Neighbor list builds = 10
Dangerous builds = 0

95
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LAMMPS (10 Jan 2012)
# REAX potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
# if hbnewflag = 1 in in.reax.tatb
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z
run 25
Memory usage per processor = 8.50974 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -47407.4 -47407.4 249533.35 -65892.012 9.483159 606.70862 0 2045.5184 5.3787493 -424.41614 -5996.6006 -444.25112 -517.90927 25281.328 -6401.2431 0 4320.6153
1 2.4332294 -47410.179 -47407.401 250303.62 -65894.23 11.188327 606.77952 0 2045.2545 5.3782483 -424.20811 -5998.425 -444.22639 -517.92742 25280.913 -6401.5055 0 4320.8291
2 9.719183 -47418.501 -47407.405 252619.32 -65900.894 16.319614 606.99197 0 2044.4649 5.3767549 -423.58231 -6003.8944 -444.15229 -517.98203 25279.673 -6402.2928 0 4321.4704
3 21.816439 -47432.319 -47407.412 256494.31 -65912.035 24.924111 607.34524 0 2043.1547 5.3742985 -422.53369 -6012.9969 -444.02917 -518.07354 25277.617 -6403.6081 0 4322.5423
4 38.655246 -47451.552 -47407.422 261949.4 -65927.703 37.079442 607.83813 0 2041.3331 5.3709282 -421.05398 -6025.7115 -443.85758 -518.20275 25274.761 -6405.4367 0 4324.0303
5 60.136545 -47476.29 -47407.635 268995.54 -65947.966 52.892364 608.46906 0 2039.0123 5.3667131 -419.13195 -6042.208 -443.63837 -518.37073 25271.128 -6407.8009 0 4325.9567
6 86.130606 -47505.982 -47407.651 277678.33 -65972.908 72.496623 609.23614 0 2036.2075 5.3617422 -416.75373 -6062.0407 -443.37265 -518.57893 25266.749 -6410.7149 0 4328.3358
7 116.47568 -47540.882 -47407.907 287978.35 -66002.626 96.049867 610.13724 0 2032.9371 5.3561245 -413.90333 -6085.5888 -443.0619 -518.82915 25261.658 -6414.1742 0 4331.1631
8 150.96906 -47579.59 -47407.236 300164.71 -66037.227 123.72947 611.17009 0 2029.9242 5.3499872 -410.56323 -6112.3014 -442.70796 -519.12351 25255.9 -6418.2017 0 4334.4616
9 189.37675 -47623.461 -47407.259 313657.42 -66076.819 155.7255 612.33235 0 2025.8058 5.3434729 -406.71536 -6142.3156 -442.31046 -519.46452 25249.523 -6422.808 0 4338.2423
10 231.43585 -47671.519 -47407.301 328587.18 -66121.512 192.23538 613.62172 0 2021.2961 5.3367337 -402.34181 -6175.5187 -441.8774 -519.85491 25242.583 -6427.9982 0 4342.5105
11 276.83946 -47723.386 -47407.332 344707.79 -66171.401 233.45314 615.03589 0 2016.4265 5.3299208 -397.42613 -6211.7372 -441.40653 -520.29759 25235.142 -6433.7718 0 4347.2661
12 325.24124 -47778.682 -47407.37 361650.64 -66226.56 279.55812 616.57246 0 2011.2344 5.3231669 -391.95462 -6250.8019 -440.9072 -520.79541 25227.269 -6440.1511 0 4352.532
13 376.251 -47836.96 -47407.413 378838.11 -66287.031 330.7004 618.22869 0 2005.7662 5.3165582 -385.91779 -6292.4987 -440.38084 -521.35077 25219.034 -6447.1716 0 4358.344
14 429.43118 -47897.722 -47407.462 395422.86 -66352.796 386.98376 620.00107 0 2000.0824 5.310092 -379.312 -6336.5797 -439.83211 -521.96502 25210.516 -6454.8598 0 4364.7296
15 484.29023 -47960.407 -47407.517 410219.6 -66423.764 448.4463 621.88466 0 1994.2638 5.3036142 -372.14102 -6382.7634 -439.26609 -522.63766 25201.793 -6463.2125 0 4371.6866
16 540.27239 -48024.381 -47407.579 421649.2 -66499.738 515.03894 623.87223 0 1988.4216 5.2967339 -364.4175 -6430.7367 -438.68817 -523.36508 25192.949 -6472.2394 0 4379.226
17 596.74424 -48088.964 -47407.691 427724.02 -66580.383 586.60295 625.9532 0 1982.7078 5.2887159 -356.16421 -6480.1998 -438.10393 -524.13903 25184.064 -6481.9624 0 4387.3713
18 652.97945 -48153.246 -47407.772 426140.07 -66665.188 662.8485 628.11261 0 1977.327 5.2783594 -347.41486 -6530.7092 -437.51898 -524.94491 25175.22 -6492.3572 0 4396.1002
19 708.14772 -48216.32 -47407.863 414483.76 -66753.439 743.33761 630.33041 0 1972.545 5.2638935 -338.21443 -6581.929 -436.93886 -525.76007 25166.493 -6503.4912 0 4405.4828
20 761.31745 -48277.121 -47407.962 390656.7 -66844.203 827.47653 632.5816 0 1968.689 5.2429366 -328.6187 -6633.4776 -436.36881 -526.55296 25157.953 -6515.3569 0 4415.5146
21 811.48466 -48334.789 -47408.357 353426.81 -66936.342 914.52388 634.8376 0 1966.1348 5.2125915 -318.69323 -6685.2728 -435.81367 -527.28375 25149.662 -6527.9293 0 4426.1746
22 857.60827 -48386.919 -47407.83 302318.37 -67028.575 1003.62 637.06904 0 1965.2746 5.1697369 -308.51151 -6736.3658 -434.60389 -527.92872 25141.674 -6541.1739 0 4437.4328
23 898.73555 -48433.1 -47407.059 240278.84 -67119.589 1093.8368 639.2496 0 1966.4695 5.1115298 -298.15265 -6786.38 -433.44406 -528.43404 25134.029 -6555.126 0 4449.3299
24 934.08592 -48471.379 -47404.979 169550.89 -67208.178 1184.2453 641.36027 0 1969.9934 5.0360099 -287.6986 -6835.3943 -430.80657 -528.78009 25126.757 -6569.608 0 4461.6943
25 963.21976 -48503.674 -47404.014 97838.888 -67293.361 1273.9734 643.39191 0 1976.3578 4.9426402 -277.2317 -6883.3292 -429.31805 -528.89112 25119.879 -6584.7276 0 4474.6396
Loop time of 4.3855 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 3.96553 (90.4236)
Neigh time (%) = 0.0494721 (1.12808)
Comm time (%) = 0.00237727 (0.0542075)
Outpt time (%) = 0.00166726 (0.0380176)
Other time (%) = 0.366458 (8.35613)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286932 ave 286932 max 286932 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286932
Ave neighs/atom = 747.219
Neighbor list builds = 5
Dangerous builds = 0

95
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LAMMPS (10 Jan 2012)
# REAX potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
# if hbnewflag = 1 in in.reax.tatb
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 1
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
dump 1 all custom 100 dump.reax.tatb id type q x y z
run 25
Memory usage per processor = 4.61908 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -47407.4 -47407.4 249533.35 -65892.012 9.483159 606.70862 0 2045.5184 5.3787493 -424.41614 -5996.6006 -444.25112 -517.90927 25281.328 -6401.2431 0 4320.6153
1 2.4332294 -47410.179 -47407.401 250303.62 -65894.23 11.188327 606.77952 0 2045.2545 5.3782483 -424.20811 -5998.425 -444.22639 -517.92742 25280.913 -6401.5055 0 4320.8291
2 9.719183 -47418.501 -47407.405 252619.32 -65900.894 16.319614 606.99197 0 2044.4649 5.3767549 -423.58231 -6003.8944 -444.15229 -517.98203 25279.673 -6402.2928 0 4321.4704
3 21.816439 -47432.319 -47407.412 256494.31 -65912.035 24.924111 607.34524 0 2043.1547 5.3742985 -422.53369 -6012.9969 -444.02917 -518.07354 25277.617 -6403.6081 0 4322.5423
4 38.655246 -47451.552 -47407.422 261949.4 -65927.703 37.079442 607.83813 0 2041.3331 5.3709282 -421.05398 -6025.7115 -443.85758 -518.20275 25274.761 -6405.4367 0 4324.0303
5 60.136545 -47476.29 -47407.635 268995.54 -65947.966 52.892364 608.46906 0 2039.0123 5.3667131 -419.13195 -6042.208 -443.63837 -518.37073 25271.128 -6407.8009 0 4325.9567
6 86.130606 -47505.982 -47407.651 277678.33 -65972.908 72.496623 609.23614 0 2036.2075 5.3617422 -416.75373 -6062.0407 -443.37265 -518.57893 25266.749 -6410.715 0 4328.3359
7 116.47568 -47540.882 -47407.907 287978.35 -66002.626 96.049867 610.13724 0 2032.9371 5.3561245 -413.90333 -6085.5888 -443.0619 -518.82915 25261.658 -6414.1742 0 4331.1631
8 150.96906 -47579.59 -47407.236 300164.71 -66037.227 123.72947 611.17009 0 2029.9242 5.3499872 -410.56323 -6112.3014 -442.70796 -519.12351 25255.9 -6418.2017 0 4334.4616
9 189.37675 -47623.461 -47407.259 313657.42 -66076.819 155.7255 612.33235 0 2025.8058 5.3434729 -406.71536 -6142.3156 -442.31046 -519.46452 25249.523 -6422.808 0 4338.2423
10 231.43585 -47671.519 -47407.301 328587.18 -66121.512 192.23538 613.62172 0 2021.2961 5.3367337 -402.34181 -6175.5187 -441.8774 -519.85491 25242.583 -6427.9982 0 4342.5106
11 276.83946 -47723.386 -47407.332 344707.79 -66171.401 233.45314 615.03589 0 2016.4265 5.3299208 -397.42613 -6211.7372 -441.40653 -520.29759 25235.142 -6433.7718 0 4347.2662
12 325.24124 -47778.682 -47407.37 361650.64 -66226.56 279.55812 616.57246 0 2011.2344 5.3231669 -391.95462 -6250.8019 -440.9072 -520.79541 25227.269 -6440.1511 0 4352.532
13 376.251 -47836.96 -47407.413 378838.11 -66287.031 330.7004 618.22869 0 2005.7662 5.3165582 -385.91779 -6292.4987 -440.38084 -521.35077 25219.034 -6447.1716 0 4358.344
14 429.43118 -47897.722 -47407.462 395422.86 -66352.796 386.98376 620.00107 0 2000.0824 5.310092 -379.312 -6336.5797 -439.83211 -521.96502 25210.516 -6454.8598 0 4364.7296
15 484.29023 -47960.407 -47407.517 410219.6 -66423.764 448.4463 621.88466 0 1994.2638 5.3036142 -372.14102 -6382.7634 -439.26609 -522.63766 25201.793 -6463.2125 0 4371.6866
16 540.27239 -48024.381 -47407.579 421649.2 -66499.738 515.03894 623.87223 0 1988.4216 5.2967339 -364.4175 -6430.7367 -438.68817 -523.36508 25192.949 -6472.2395 0 4379.226
17 596.74424 -48088.964 -47407.691 427724.02 -66580.383 586.60295 625.9532 0 1982.7078 5.2887159 -356.16421 -6480.1998 -438.10393 -524.13903 25184.064 -6481.9625 0 4387.3713
18 652.97945 -48153.246 -47407.772 426140.07 -66665.188 662.8485 628.11261 0 1977.327 5.2783594 -347.41486 -6530.7092 -437.51898 -524.94491 25175.22 -6492.3573 0 4396.1003
19 708.14772 -48216.32 -47407.863 414483.76 -66753.439 743.33761 630.33041 0 1972.545 5.2638935 -338.21443 -6581.929 -436.93886 -525.76007 25166.493 -6503.4912 0 4405.4827
20 761.31745 -48277.121 -47407.962 390656.71 -66844.203 827.47653 632.5816 0 1968.689 5.2429366 -328.6187 -6633.4776 -436.36881 -526.55296 25157.953 -6515.353 0 4415.5107
21 811.48466 -48334.789 -47408.357 353426.83 -66936.342 914.52388 634.8376 0 1966.1348 5.2125915 -318.69323 -6685.2728 -435.81367 -527.28375 25149.662 -6527.9205 0 4426.1658
22 857.60827 -48386.919 -47407.831 302318.32 -67028.575 1003.62 637.06904 0 1965.2746 5.1697369 -308.51151 -6736.3658 -434.60389 -527.92872 25141.674 -6541.191 0 4437.4499
23 898.73556 -48433.1 -47407.059 240278.95 -67119.589 1093.8368 639.2496 0 1966.4695 5.1115298 -298.15265 -6786.38 -433.44406 -528.43404 25134.029 -6555.088 0 4449.2919
24 934.08594 -48471.379 -47404.979 169550.81 -67208.178 1184.2453 641.36027 0 1969.9934 5.0360099 -287.6986 -6835.3943 -430.80657 -528.78009 25126.757 -6569.631 0 4461.7172
25 963.21978 -48503.674 -47404.014 97838.961 -67293.361 1273.9734 643.39191 0 1976.3578 4.9426402 -277.2317 -6883.3292 -429.31805 -528.89112 25119.879 -6584.7034 0 4474.6155
Loop time of 2.19885 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 1.95163 (88.7569)
Neigh time (%) = 0.0107548 (0.489108)
Comm time (%) = 0.0822858 (3.74222)
Outpt time (%) = 0.00185025 (0.0841461)
Other time (%) = 0.152328 (6.92764)
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79756 ave 79756 max 79756 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319024
Ave neighs/atom = 830.792
Neighbor list builds = 5
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.86288 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663195 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690661 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.01162
8600 16738.474 -0.00076532814 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.0003765244 0 5269.5216 12.011692
9550 16738.493 -0.0053156165 0 5269.5203 12.011611
9600 16738.549 -0.026814372 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589899 0 5269.4979 12.062708
9750 16738.013 0.13550096 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270505 0 5269.5237 11.395098
9900 16738.489 -0.00024984559 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395077
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.137668 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00791883 (5.75212)
Neigh time (%) = 0.0309033 (22.4477)
Comm time (%) = 0.0089097 (6.47187)
Outpt time (%) = 0.015656 (11.3723)
Other time (%) = 0.0742803 (53.956)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

306
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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.82479 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722853e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554428 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550084 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270545 0 5269.5237 11.395098
9900 16738.489 -0.00024984574 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.196736 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0025723 (1.30749)
Neigh time (%) = 0.010328 (5.24968)
Comm time (%) = 0.0892789 (45.3801)
Outpt time (%) = 0.0199543 (10.1427)
Other time (%) = 0.0746023 (37.92)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

306
examples/rigid/log.rigid.poems.9Jan12.linux.1 Normal file
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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.9398 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384278
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699139
1200 21815.003 45.317413 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064079
1300 20780.781 217.36508 0 3680.8286 6.0538613
1350 20558.971 254.36484 0 3680.8601 -3.6773928
1400 21485.029 99.812897 0 3680.6511 -16.185475
1450 21771.107 52.159622 0 3680.6775 -2.4756668
1500 21520.948 93.50391 0 3680.3286 2.1023576
1550 21351.418 121.68135 0 3680.2511 5.5159926
1600 20778.805 216.92181 0 3680.0559 15.089192
1650 21477.637 100.21848 0 3679.8247 -1.1045589
1700 18501.336 596.47967 0 3680.0357 -15.679718
1750 18563.641 587.34804 0 3681.2882 33.532242
1800 19110.182 494.82394 0 3679.8543 18.024056
1850 21364.187 119.23612 0 3679.9339 2.5290785
1900 20146.615 322.15055 0 3679.9197 5.7314455
1950 20692.672 231.25319 0 3680.0319 4.2977815
2000 20943.904 189.11228 0 3679.7629 -22.6447
2050 19667.984 401.84213 0 3679.8394 3.6248494
2100 20280.339 299.77895 0 3679.8354 7.480669
2150 19181.64 483.55835 0 3680.4983 22.624694
2200 21300.479 130.65196 0 3680.7318 4.7093384
2250 20486.287 266.74857 0 3681.1297 -8.6495123
2300 18651.575 572.50504 0 3681.1009 -5.261082
2350 21514.238 95.495372 0 3681.2017 -9.3698609
2400 21465.082 103.76223 0 3681.2758 -29.530492
2450 20102.547 331.8625 0 3682.2869 35.630207
2500 20766.689 221.28369 0 3682.3986 -12.4229
2550 20456.257 272.87511 0 3682.2513 -22.515235
2600 21464.354 104.88637 0 3682.2788 -10.110008
2650 20885.777 201.39511 0 3682.358 5.0268371
2700 18576.387 586.63809 0 3682.7026 22.269183
2750 21023.584 178.26789 0 3682.1985 -8.8172166
2800 21363.884 121.51908 0 3682.1664 -6.913586
2850 17264.155 805.16849 0 3682.5276 29.921611
2900 19751.146 390.19286 0 3682.0506 8.8575471
2950 21171.167 153.48579 0 3682.0136 1.9171651
3000 18698.646 565.2524 0 3681.6934 -16.611709
3050 19756.096 389.49951 0 3682.1822 0.79771573
3100 20716.934 229.53125 0 3682.3536 18.675629
3150 21107.033 164.26375 0 3682.1026 6.292817
3200 21194.557 149.62327 0 3682.0495 0.40762301
3250 19019.061 511.83944 0 3681.683 -1.0191767
3300 19904.232 364.91979 0 3682.2917 1.580824
3350 19383.048 452.00672 0 3682.5146 8.9939778
3400 18629.871 577.12591 0 3682.1044 19.393397
3450 20366.419 287.55662 0 3681.9598 6.7676479
3500 20957.937 189.21014 0 3682.1996 9.17515
3550 21807.252 47.635006 0 3682.1771 2.2490841
3600 21690.617 67.029898 0 3682.1327 -1.4725416
3650 21600.202 82.085085 0 3682.1188 -3.9470263
3700 19902.074 365.09934 0 3682.1117 3.5789954
3750 20669.825 237.14074 0 3682.1116 -7.992071
3800 20226.287 311.40404 0 3682.4519 -11.829103
3850 20713.814 230.18758 0 3682.4899 -11.37713
3900 19621.738 411.85323 0 3682.1428 -0.86016858
3950 20828.921 210.87742 0 3682.3643 -1.7978283
4000 21734.525 60.230547 0 3682.6513 3.0013342
4050 19859.621 371.8688 0 3681.8056 19.53421
4100 20748.845 224.82927 0 3682.9701 -0.67873587
4150 19578.269 420.02964 0 3683.0745 4.448634
4200 19142.314 492.92862 0 3683.3143 7.5300212
4250 20189.963 318.02141 0 3683.0152 2.2489634
4300 20569.793 254.7842 0 3683.0831 2.014004
4350 21505.248 99.029749 0 3683.2377 -1.8448103
4400 21795.012 50.799563 0 3683.3016 -3.3446933
4450 21630.638 78.27653 0 3683.3829 0.97935456
4500 20485.622 268.77758 0 3683.0479 9.0931688
4550 21328.202 128.77982 0 3683.4802 6.9392514
4600 20425.456 279.4671 0 3683.7097 14.657178
4650 21734.316 61.575892 0 3683.9619 -6.1228621
4700 20377.517 287.77871 0 3684.0315 -10.350636
4750 21765.762 56.481378 0 3684.1084 -13.686961
4800 21064.967 173.07588 0 3683.9038 -3.5246286
4850 21496.739 100.96272 0 3683.7525 3.4134893
4900 21387.734 118.85944 0 3683.4818 2.7545377
4950 21606.598 82.305575 0 3683.4052 2.7661083
5000 20813.389 211.50552 0 3680.4037 -1.99709
5050 21258.837 140.0257 0 3683.1652 -4.6011608
5100 18840.1 543.32464 0 3683.3413 31.178048
5150 22005.655 16.168882 0 3683.778 -4.3729594
5200 20808.086 215.87951 0 3683.8939 7.4410336
5250 18679.669 570.83153 0 3684.1098 14.191478
5300 19753.173 391.94671 0 3684.1422 -8.5241508
5350 21608.313 82.705694 0 3684.0912 -3.6094817
5400 21488.174 102.68409 0 3684.0464 4.2600964
5450 17518.356 764.26875 0 3683.9947 -0.12243804
5500 21696.071 68.069788 0 3684.0816 -1.5476526
5550 18502.148 599.7684 0 3683.4597 37.379976
5600 18128.267 662.17376 0 3683.5516 16.554047
5650 18537.13 594.3189 0 3683.8406 12.05774
5700 20851.723 208.91824 0 3684.2053 -4.3830301
5750 20941.372 194.08984 0 3684.3185 -0.1943864
5800 20194.472 318.72727 0 3684.4726 5.154744
5850 20856.188 208.56814 0 3684.5994 3.2314482
5900 21125.245 164.07233 0 3684.9465 -0.33002911
5950 20138.458 328.54345 0 3684.9532 10.557313
6000 20981.486 188.51066 0 3685.4249 -9.0163197
6050 20822.112 215.14903 0 3685.5011 -18.139995
6100 20076.859 339.70008 0 3685.8432 -3.0307257
6150 19953.615 360.46342 0 3686.066 8.3344429
6200 20903.384 202.40101 0 3686.2984 -0.39424049
6250 21134.826 163.89116 0 3686.3621 -4.1668704
6300 21258.213 143.90658 0 3686.9422 -7.391516
6350 20373.797 291.10416 0 3686.7369 -14.895748
6400 19051.752 510.8571 0 3686.1491 -0.078518196
6450 19649.32 412.61991 0 3687.5065 -1.5921483
6500 20142.923 330.66911 0 3687.8229 6.8022912
6550 19574.327 424.60137 0 3686.9891 11.82743
6600 16105.355 1002.7817 0 3687.0076 17.558797
6650 21537.744 97.953562 0 3687.5775 2.735191
6700 16808.381 887.46461 0 3688.8614 -9.3638392
6750 16391.199 958.16942 0 3690.0359 24.040757
6800 19891.18 371.95843 0 3687.1551 -25.326616
6850 19344.505 464.12314 0 3688.2073 -16.88882
6900 21489.989 106.09106 0 3687.7559 -2.7741331
6950 19023.694 517.19865 0 3687.8143 12.795625
7000 21072.663 175.47912 0 3687.5897 -4.6260178
7050 19697.946 404.85665 0 3687.8476 0.96426982
7100 20684.854 240.16243 0 3687.638 -6.9283531
7150 20888.947 205.87412 0 3687.3653 2.4592293
7200 20709.233 235.52341 0 3687.0622 1.8850608
7250 20644.676 246.05983 0 3686.8391 -1.9432958
7300 19940.501 363.58269 0 3686.9996 8.7916219
7350 20904.854 202.70884 0 3686.8511 1.1932912
7400 19794.615 388.44762 0 3687.5502 4.2494869
7450 20398.713 287.96541 0 3687.7509 1.9565661
7500 14969.907 1195.4664 0 3690.451 61.49775
7550 20048.243 346.41733 0 3687.7911 8.8637262
7600 13724.843 1400.6649 0 3688.1386 -28.102927
7650 17323.581 800.37606 0 3687.6396 17.015401
7700 20781.624 224.2726 0 3687.8767 2.5260419
7750 19629.33 416.31516 0 3687.8702 18.39744
7800 20804.173 220.99571 0 3688.3579 11.409891
7850 20756.856 228.60421 0 3688.0803 -33.84006
7900 21716.444 68.965593 0 3688.3729 -12.291272
7950 19610.154 419.14133 0 3687.5002 1.7759679
8000 18622.409 585.42868 0 3689.1635 26.686729
8050 19777.369 392.63726 0 3688.8654 -22.209128
8100 16497.521 939.24542 0 3688.8322 -42.367659
8150 19446.13 444.3108 0 3685.3324 32.613169
8200 20411.209 286.5915 0 3688.4597 -5.2887315
8250 14328.544 1302.6847 0 3690.7753 15.143982
8300 21405.234 121.47682 0 3689.0157 -4.6378296
8350 15481.055 1109.2428 0 3689.4186 57.85088
8400 14139.682 1332.356 0 3688.9697 -0.1974486
8450 15623.736 1084.5594 0 3688.5155 37.668188
8500 18872.571 543.29677 0 3688.7253 -11.622477
8550 18568.346 594.15647 0 3688.8809 -0.53198127
8600 18857.924 546.26599 0 3689.2533 6.9976522
8650 20422.926 285.18311 0 3689.0041 -2.1124395
8700 15904.428 1038.6394 0 3689.3774 11.108432
8750 17585.096 758.32272 0 3689.172 -13.175342
8800 19561.883 429.1997 0 3689.5135 31.379344
8850 21083.378 174.46783 0 3688.3642 -1.405537
8900 21922.179 35.258703 0 3688.9551 0.92994553
8950 15270.836 1145.5748 0 3690.714 59.72214
9000 21236.73 149.52929 0 3688.9843 3.6894217
9050 20391.028 289.54828 0 3688.053 -12.318301
9100 19963.6 361.58733 0 3688.854 -1.6201635
9150 20852.5 213.26173 0 3688.6783 3.4781812
9200 17559.276 763.58389 0 3690.13 23.653055
9250 20719.763 235.38861 0 3688.6825 -7.2385902
9300 20210.461 320.16875 0 3688.5789 0.71513298
9350 20589.665 256.39159 0 3688.0025 11.766742
9400 21888.845 39.743204 0 3687.884 0.2325157
9450 19995.034 355.22797 0 3687.7336 -30.801824
9500 20562.534 260.81379 0 3687.9028 7.6818244
9550 20724.259 233.42976 0 3687.4729 2.5906906
9600 21156.272 161.92778 0 3687.9731 -3.6794578
9650 15407.774 1117.1504 0 3685.1127 10.296536
9700 20086.616 339.94203 0 3687.7114 6.85039
9750 21017.639 184.92766 0 3687.8675 -4.924906
9800 17788.545 723.17057 0 3687.928 19.866063
9850 21918.073 35.503859 0 3688.516 -1.9119993
9900 17765.237 727.83046 0 3688.7033 19.055502
9950 21306.635 137.72864 0 3688.8345 -5.5977574
10000 21575.787 92.853786 0 3688.8182 -4.0094168
Loop time of 3.45277 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.153845 (4.4557)
Neigh time (%) = 0.0926647 (2.68378)
Comm time (%) = 0.0103235 (0.298993)
Outpt time (%) = 0.0163345 (0.473085)
Other time (%) = 3.1796 (92.0884)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56 ave 56 max 56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 750 ave 750 max 750 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 750
Ave neighs/atom = 9.25926
Neighbor list builds = 990
Dangerous builds = 927

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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.90125 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699149
1200 21815.003 45.317415 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773956
1400 21485.029 99.812922 0 3680.6511 -16.185473
1450 21771.107 52.159608 0 3680.6775 -2.4756674
1500 21520.948 93.503928 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.515995
1600 20778.805 216.92177 0 3680.0559 15.089187
1650 21477.638 100.21835 0 3679.8247 -1.1045756
1700 18501.339 596.47913 0 3680.0357 -15.679677
1750 18563.642 587.34787 0 3681.2882 33.532207
1800 19110.186 494.82333 0 3679.8543 18.024046
1850 21364.191 119.23538 0 3679.9339 2.5291119
1900 20146.628 322.14841 0 3679.9197 5.7313081
1950 20692.671 231.25336 0 3680.0319 4.2977737
2000 20943.904 189.11227 0 3679.7629 -22.645146
2050 19668.063 401.82894 0 3679.8394 3.6252006
2100 20280.448 299.76054 0 3679.8353 7.4807993
2150 19181.869 483.52061 0 3680.4987 22.620257
2200 21300.14 130.70883 0 3680.7322 4.710318
2250 20486.992 266.63125 0 3681.1299 -8.6453582
2300 18653.249 572.22692 0 3681.1018 -5.2639533
2350 21513.474 95.623043 0 3681.2021 -9.3615923
2400 21466.352 103.55115 0 3681.2765 -29.563489
2450 20099.92 332.30226 0 3682.2888 35.75288
2500 20764.233 221.69469 0 3682.4003 -12.472324
2550 20434.265 276.55013 0 3682.261 -22.406554
2600 21466.593 104.51528 0 3682.2808 -10.076416
2650 20808.645 214.25423 0 3682.3618 5.1518496
2700 18565.645 588.3715 0 3682.6457 22.26312
2750 20753.062 223.37556 0 3682.2193 -7.8155982
2800 20986.776 184.39985 0 3682.1958 -7.0608776
2850 16721.211 895.59298 0 3682.4615 33.619161
2900 19294.24 466.43871 0 3682.1454 8.0033435
2950 20471.71 270.09532 0 3682.047 2.5545202
3000 20609.248 247.27073 0 3682.1453 -1.8817723
3050 18576.568 586.31423 0 3682.4089 -1.7806882
3100 19790.767 383.54865 0 3682.0099 -6.0384293
3150 20941.678 191.88039 0 3682.16 4.7195299
3200 20187.734 317.22178 0 3681.8441 7.1381064
3250 19982.327 351.80543 0 3682.1932 -10.356822
3300 19720.165 395.60482 0 3682.299 12.415019
3350 20008.047 347.27468 0 3681.9491 5.0458582
3400 20411.522 280.16521 0 3682.0855 -7.1769483
3450 20046.145 341.27051 0 3682.2947 0.22584972
3500 17937.429 692.9726 0 3682.544 16.131523
3550 18771.683 553.86993 0 3682.4837 -1.5944448
3600 19901.288 364.81878 0 3681.7001 -24.39551
3650 20746.323 224.83374 0 3682.5543 -7.6981313
3700 21681.686 68.935986 0 3682.5503 -5.7316854
3750 21130.966 160.34639 0 3682.174 2.5404231
3800 19573.729 419.87434 0 3682.1625 10.483835
3850 19672.797 403.73028 0 3682.5297 7.9092657
3900 19429.209 444.39996 0 3682.6014 4.6871663
3950 18794.538 550.12554 0 3682.5485 -3.4850598
4000 18356.499 622.71257 0 3682.1291 21.961288
4050 18499.159 599.5728 0 3682.7659 9.7197804
4100 18893.082 533.58148 0 3682.4285 7.1537738
4150 18555.438 590.46012 0 3683.0331 -5.9854705
4200 20095.772 332.86056 0 3682.1558 6.0048046
4250 21395.629 117.09714 0 3683.0352 -12.849296
4300 20642.157 242.80387 0 3683.1634 -7.1285142
4350 16782.008 886.90013 0 3683.9014 59.279202
4400 21722.722 63.477041 0 3683.9307 -6.7708918
4450 21483.705 103.77396 0 3684.3914 -14.801558
4500 18637.223 577.90593 0 3684.1097 -5.399645
4550 21501.072 101.01026 0 3684.5223 -0.2687012
4600 21419.25 114.67746 0 3684.5525 -5.1248351
4650 19532.212 428.88221 0 3684.251 -13.937733
4700 19108.648 500.22789 0 3685.0025 0.72814013
4750 21304.939 134.30984 0 3685.133 -10.419682
4800 21011.564 183.12003 0 3685.0474 -0.21596054
4850 21288.378 137.28914 0 3685.3522 -3.783224
4900 20238.761 312.44314 0 3685.57 -0.89650269
4950 20973.64 190.4195 0 3686.0262 2.3977528
5000 20982.662 188.75492 0 3685.8652 -10.898981
5050 20287.196 304.79028 0 3685.9895 7.9988821
5100 20161.046 325.98224 0 3686.1566 11.304549
5150 20768.1 224.94586 0 3686.2959 -11.679983
5200 20550.091 261.40569 0 3686.4209 -3.8503144
5250 20274.307 307.08369 0 3686.1349 3.2350203
5300 21107.734 168.31547 0 3686.2711 -2.7299125
5350 21575.088 90.511714 0 3686.3597 -23.416041
5400 19335.208 463.98466 0 3686.5193 1.1686111
5450 20334.202 297.13584 0 3686.1696 7.9612042
5500 18596.894 586.39323 0 3685.8756 19.42362
5550 16402.199 953.72484 0 3687.4247 -7.6804149
5600 19716.462 400.17421 0 3686.2512 0.73274328
5650 19794.552 387.60203 0 3686.694 7.4829917
5700 21404.995 119.38491 0 3686.884 1.1256427
5750 21737.498 64.038982 0 3686.9553 0.66497166
5800 21196.338 153.70183 0 3686.4248 -4.0562788
5850 18817.877 550.28735 0 3686.6001 15.517346
5900 20855.92 210.47881 0 3686.4654 -6.7252193
5950 18187.477 655.72108 0 3686.9673 -5.840425
6000 21574.226 91.415225 0 3687.1196 -4.1947877
6050 20647.597 245.36705 0 3686.6333 -4.2710188
6100 20195.663 320.68953 0 3686.6333 1.9183471
6150 19569.943 425.30544 0 3686.9627 -2.0191803
6200 21009.348 185.15969 0 3686.7176 -1.5383241
6250 21311.107 135.08699 0 3686.9382 -8.4198399
6300 18617.034 583.66046 0 3686.4994 11.716969
6350 19818.978 382.62883 0 3685.7919 4.9679172
6400 21403.509 119.46416 0 3686.7156 -1.3369474
6450 16394.437 955.35248 0 3687.7587 22.900909
6500 15570.429 1095.0835 0 3690.155 -24.50813
6550 20905.847 202.70205 0 3687.0099 -5.4533991
6600 20419.664 282.65592 0 3685.9333 -1.0348411
6650 16008.949 1023.4924 0 3691.6506 48.451181
6700 18929.104 531.79459 0 3686.6452 8.487112
6750 20317.67 301.1228 0 3687.4011 -9.6972866
6800 21238.238 147.54216 0 3687.2486 -4.457873
6850 19469.334 441.11845 0 3686.0075 29.322933
6900 20880.087 207.70983 0 3687.7244 -4.1197403
6950 20864.561 210.00891 0 3687.4358 -9.4014401
7000 21701.899 70.744638 0 3687.7278 2.6762921
7050 18936.455 531.70563 0 3687.7815 29.134314
7100 21418.983 118.08942 0 3687.9199 0.64845095
7150 21271.75 142.65664 0 3687.9482 -6.1860835
7200 21584.017 90.531714 0 3687.8679 -15.915843
7250 20478.212 274.65055 0 3687.6858 3.5293379
7300 20787.975 223.07914 0 3687.7416 8.3746157
7350 21169.849 159.84727 0 3688.1554 4.806229
7400 18050.739 679.46766 0 3687.9242 0.1356599
7450 21759.344 61.894907 0 3688.4523 -6.0686382
7500 20115.323 334.36139 0 3686.9153 -3.9834726
7550 21513.687 103.04204 0 3688.6565 -3.6546291
7600 20396.612 289.44922 0 3688.8845 8.3149013
7650 19954.93 363.06299 0 3688.8846 6.7857536
7700 20579.453 259.44475 0 3689.3535 -13.300779
7750 21435.784 117.44734 0 3690.078 -3.5454036
7800 19676.963 410.82634 0 3690.3202 16.17995
7850 22001.763 23.427845 0 3690.3883 -3.2253193
7900 21367.244 128.97238 0 3690.1797 -10.139451
7950 21835.619 51.102569 0 3690.3723 -6.9113133
8000 21081.866 176.87472 0 3690.519 -3.400648
8050 17587.847 759.00567 0 3690.3134 42.149831
8100 20622.874 253.16935 0 3690.3149 -1.0529121
8150 18826.468 552.8081 0 3690.5528 -26.78369
8200 19639.531 417.23576 0 3690.491 11.18475
8250 18736.82 568.57113 0 3691.3744 6.4120512
8300 21628.735 86.117146 0 3690.9062 -15.136564
8350 21300.133 140.75663 0 3690.7788 -1.3028295
8400 20100.75 340.28553 0 3690.4105 2.3621868
8450 20330.628 301.64835 0 3690.0863 -6.9035421
8500 21379.743 126.87873 0 3690.1693 -0.67103323
8550 21693.455 74.592469 0 3690.1683 -6.6175553
8600 20824.252 219.41263 0 3690.1212 1.7682173
8650 20289.679 308.59538 0 3690.2085 11.354028
8700 21803.688 56.071063 0 3690.0191 -2.6145414
8750 21111.316 171.22439 0 3689.777 6.7898851
8800 20775.535 227.17109 0 3689.7603 9.4162984
8850 19043.442 515.72721 0 3689.6343 5.3736614
8900 21157.163 163.34868 0 3689.5426 1.4354174
8950 20978.891 192.95509 0 3689.437 0.96560879
9000 21292.787 140.85118 0 3689.6489 -8.9387525
9050 20239.076 316.1505 0 3689.3299 8.0442974
9100 19869.892 377.60414 0 3689.2529 -7.7929877
9150 21454.531 113.72022 0 3689.4753 -13.322839
9200 17967.414 695.13611 0 3689.705 5.5120587
9250 20511.881 271.10991 0 3689.7567 7.4880289
9300 19920.611 369.49427 0 3689.5961 20.373053
9350 20461.102 279.43877 0 3689.6224 10.339057
9400 20099.827 339.51057 0 3689.4817 6.7892922
9450 19918.317 369.41224 0 3689.1318 10.326641
9500 21020.607 186.56179 0 3689.9963 7.3622937
9550 21179.796 160.20422 0 3690.1702 -1.0782427
9600 21518.982 104.08914 0 3690.5861 -5.3790399
9650 21206.19 156.4724 0 3690.8374 1.6109043
9700 21452.317 115.4785 0 3690.8646 -6.2719599
9750 19577.709 427.73595 0 3690.6875 -5.943044
9800 15600.07 1090.9222 0 3690.9338 12.384319
9850 18256.931 647.85044 0 3690.6723 3.3325276
9900 20351.693 298.44268 0 3690.3914 1.2947227
9950 21085.505 176.1557 0 3690.4065 -6.3748251
10000 18801.541 557.05356 0 3690.6438 -8.7522263
Loop time of 3.73749 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0412061 (1.10251)
Neigh time (%) = 0.0274655 (0.734866)
Comm time (%) = 0.341529 (9.13793)
Outpt time (%) = 0.0218447 (0.584475)
Other time (%) = 3.30544 (88.4402)
Nlocal: 20.25 ave 79 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 68 max 12 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 181.5 ave 722 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 726
Ave neighs/atom = 8.96296
Neighbor list builds = 990
Dangerous builds = 920

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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (fix_poems.cpp:331)
WARNING: More than one fix poems (fix_poems.cpp:331)
WARNING: One or more atoms are time integrated more than once (modify.cpp:240)
Memory usage per processor = 2.2859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15169 0 3764.0939 -1.613454
1550 18147.996 404.12676 0 3764.8668 8.4194769
1600 18615.043 317.42464 0 3764.6548 -2.328898
1650 20120.654 38.887941 0 3764.935 -8.7620212
1700 19450.906 162.98296 0 3765.0025 2.3254683
1750 19374.633 177.37942 0 3765.2744 8.9328782
1800 19424.403 167.93976 0 3765.0514 0.081237835
1850 17936.373 442.81943 0 3764.3699 6.6007243
1900 19982.597 64.405942 0 3764.8868 -2.953039
1950 16216.047 761.87633 0 3764.848 13.993767
2000 18584.36 322.1319 0 3763.68 7.1655723
2050 20107.967 41.025515 0 3764.723 -0.31095875
2100 20002.359 60.588285 0 3764.7288 -6.7919218
2150 16949.463 626.65155 0 3765.4411 3.5099746
2200 20010.951 58.808709 0 3764.5403 -10.862337
2250 18982.724 247.0099 0 3762.3292 -0.53785372
2300 18401.404 354.86011 0 3762.5276 1.0917872
2350 19390.477 172.95029 0 3763.7793 -3.3527625
2400 16082.495 786.07427 0 3764.3141 -16.195237
2450 18871.033 268.63511 0 3763.2709 11.187102
2500 19687.13 117.79738 0 3763.5622 4.3929264
2550 18873.431 268.30382 0 3763.3836 -5.6531376
2600 17014.989 612.51599 0 3763.44 6.3265978
2650 18779.234 286.24534 0 3763.8812 2.3814839
2700 19733.494 108.84054 0 3763.1912 -0.28455721
2750 19487.299 154.68388 0 3763.4429 -1.5938513
2800 18419.252 351.12627 0 3762.0988 20.847774
2850 18788.886 283.58089 0 3763.0043 3.0280372
2900 20110.801 39.005938 0 3763.2284 0.0030136934
2950 15582.268 877.76573 0 3763.3708 16.827059
3000 17927.524 442.93443 0 3762.8463 4.0702273
3050 19054.272 234.78929 0 3763.3582 7.6784952
3100 19318.656 185.86832 0 3763.3972 3.4909968
3150 19336.244 182.13325 0 3762.9192 -19.24283
3200 18983.457 247.36835 0 3762.8233 -5.7526831
3250 19674.232 119.66794 0 3763.0442 1.9423166
3300 16157.209 769.95841 0 3762.0342 2.80189
3350 19030.029 239.07461 0 3763.1541 7.0444034
3400 15352.517 920.23705 0 3763.2957 26.469475
3450 19113.998 223.38478 0 3763.0139 5.4622379
3500 15355.047 921.10005 0 3764.6272 12.744088
3550 18453.302 345.84221 0 3763.1203 4.3303151
3600 15805.132 835.73363 0 3762.6098 -19.192108
3650 19366.655 176.75046 0 3763.168 3.6029674
3700 17926.815 443.58998 0 3763.3705 6.3106911
3750 18145.089 402.96409 0 3763.1657 -1.4495144
3800 17128.054 590.66146 0 3762.5233 1.3740587
3850 19650.661 123.98432 0 3762.9956 -3.6403709
3900 13651.635 1236.4269 0 3764.5075 1.8197344
3950 19607.542 131.80571 0 3762.8321 -5.2300693
4000 15976.222 803.9711 0 3762.5308 5.8844711
4050 17251.262 568.38221 0 3763.0604 -27.565001
4100 18718.869 296.1222 0 3762.5795 0.24957933
4150 18981.941 247.56533 0 3762.7396 8.9334676
4200 18058.249 418.65815 0 3762.7784 -9.7406053
4250 17840.27 458.9852 0 3762.7389 -1.2566229
4300 16801.487 651.25038 0 3762.6368 20.311604
4350 19284.648 191.5548 0 3762.786 3.8849247
4400 18089.637 412.4593 0 3762.392 -0.16156227
4450 18109.553 409.19646 0 3762.8174 -6.6744782
4500 18559.157 325.84529 0 3762.7262 -3.7834397
4550 19417.817 167.1903 0 3763.0824 -1.9438809
4600 19940.102 70.544215 0 3763.1558 -6.5714777
4650 17531.219 516.03395 0 3762.5561 16.825376
4700 18330.28 368.15762 0 3762.6539 -5.8154827
4750 18059.26 418.88115 0 3763.1886 6.9154907
4800 18230.172 387.09769 0 3763.0554 -5.8764301
4850 15352.316 920.35111 0 3763.3726 -14.150721
4900 17901.178 447.18401 0 3762.217 12.995669
4950 17096.795 596.75363 0 3762.8268 6.9584988
5000 18233.348 386.97511 0 3763.521 -8.6953829
5050 19238.643 200.76564 0 3763.4773 -0.95923788
5100 18851.592 272.21836 0 3763.2539 6.6015785
5150 17618.203 500.9924 0 3763.6226 6.4089848
5200 19510.809 150.29265 0 3763.4053 -1.138488
5250 17991.038 431.73878 0 3763.4124 0.9206177
5300 16496.992 709.42568 0 3764.4241 8.328767
5350 16683.15 674.66196 0 3764.1342 -12.119189
5400 19197.624 208.27759 0 3763.3932 1.8895925
5450 16776.936 656.25236 0 3763.0923 8.3324322
5500 18314.437 372.39317 0 3763.9556 0.87158511
5550 18678.675 304.31808 0 3763.3319 8.1494425
5600 18772.959 286.93218 0 3763.406 -1.3023432
5650 15494.947 894.36223 0 3763.7968 -10.336527
5700 18507.481 336.45923 0 3763.7704 -3.8746687
5750 17082.667 600.40729 0 3763.8641 42.148906
5800 19845.873 88.449333 0 3763.611 1.7380604
5850 17992.679 431.95872 0 3763.9363 -12.928704
5900 19680.707 119.00911 0 3763.5844 -0.79613571
5950 19914.393 75.816066 0 3763.6667 5.5342994
6000 19142.271 218.80112 0 3763.6661 7.4018805
6050 17025.724 611.14107 0 3764.053 -6.1043602
6100 18966.612 250.76138 0 3763.0969 1.1322144
6150 17451.81 531.32734 0 3763.144 -6.5894955
6200 16334.478 739.3296 0 3764.233 -27.518822
6250 18790.228 283.56338 0 3763.2353 -7.8911412
6300 18163.654 399.45237 0 3763.092 -0.20584174
6350 18674.03 305.36153 0 3763.5151 -10.44952
6400 19677.482 119.8165 0 3763.7947 4.767842
6450 19606.353 133.20697 0 3764.0132 3.1402747
6500 18685.174 303.25291 0 3763.4703 1.219211
6550 18842.997 274.29542 0 3763.7394 -3.0675196
6600 18984.844 247.94633 0 3763.6582 3.2871433
6650 19270.874 194.75275 0 3763.4332 2.0520948
6700 16730.98 665.42234 0 3763.752 24.63305
6750 18240.959 385.54575 0 3763.5012 9.3542656
6800 19212.072 205.42671 0 3763.2178 -4.7707967
6850 19428.264 165.41827 0 3763.2449 -5.9896144
6900 16510.385 705.90782 0 3763.3866 -4.5120114
6950 18469.724 342.72852 0 3763.0477 1.5930349
7000 19023.531 240.06714 0 3762.9432 0.97630625
7050 19981.38 63.051871 0 3763.3075 1.1975773
7100 18884.497 266.0407 0 3763.1698 5.014732
7150 20007.363 58.305336 0 3763.3725 -3.8475432
7200 19060.008 233.74726 0 3763.3784 -7.355987
7250 19587.118 136.14609 0 3763.3902 -0.071525055
7300 18255.08 382.9175 0 3763.4878 8.3070642
7350 19840.127 89.391828 0 3763.4894 3.0925365
7400 19081.218 229.96717 0 3763.5261 -0.088491483
7450 19495.919 153.12566 0 3763.481 7.3486168
7500 18103.878 410.89471 0 3763.4647 8.253657
7550 18818.034 278.46924 0 3763.2904 -6.6529064
7600 16900.909 634.03412 0 3763.8321 24.447016
7650 19309.193 187.4356 0 3763.2121 5.0831969
7700 17040.81 608.00812 0 3763.7136 -4.5789647
7750 19420.333 167.12363 0 3763.4815 4.3678178
7800 19164.248 214.10676 0 3763.0416 0.12405627
7850 19137.03 219.31269 0 3763.2071 -6.7131335
7900 19606.78 132.67382 0 3763.5591 -4.5096484
7950 18593.444 319.64585 0 3762.8763 -4.9001288
8000 19288.423 191.51728 0 3763.4475 3.8370068
8050 19132.57 220.46289 0 3763.5314 -1.3284232
8100 17510.857 520.52922 0 3763.2806 -4.6183989
8150 18356.887 364.17504 0 3763.5986 4.3938444
8200 19553.346 142.51623 0 3763.5063 0.93248057
8250 17919.922 444.70362 0 3763.2076 7.3984984
8300 17268.822 564.38824 0 3762.3182 24.155843
8350 19389.272 172.63516 0 3763.241 5.9225389
8400 17896.652 449.19012 0 3763.3849 0.63394353
8450 18315.977 371.4271 0 3763.2746 -33.234548
8500 16047.998 796.54623 0 3768.3978 51.901492
8550 19188.248 210.03454 0 3763.4138 -1.5401941
8600 17951.392 433.85317 0 3758.185 26.657038
8650 18678.909 304.65925 0 3763.7164 -0.5735548
8700 18473.965 342.61835 0 3763.7231 -0.39588258
8750 17278.537 562.78121 0 3762.5102 16.884408
8800 19997.623 60.585822 0 3763.8494 -2.7220886
8850 17720.683 482.98842 0 3764.5963 13.298184
8900 19450.503 162.05753 0 3764.0025 -5.0266355
8950 20065.748 48.178324 0 3764.0575 -3.298456
9000 18411.075 354.70332 0 3764.1617 2.5439463
9050 19835.128 90.878715 0 3764.0505 -2.4322016
9100 19486.363 155.54042 0 3764.1261 -5.332552
9150 19203.984 207.95102 0 3764.2443 3.1640673
9200 18048.222 421.26909 0 3763.5324 23.881772
9250 19682.985 119.25528 0 3764.2524 1.533906
9300 19857.159 86.947891 0 3764.1996 -4.5024234
9350 20060.359 49.452616 0 3764.3338 -1.493574
9400 19561.395 141.85818 0 3764.3387 -3.1573118
9450 19134.008 221.07861 0 3764.4133 -0.60832086
9500 18369.624 362.74228 0 3764.5244 -0.37049085
9550 18146.354 404.01981 0 3764.4558 10.150467
9600 15002.89 991.64237 0 3769.9553 51.550272
9650 18607.005 318.66284 0 3764.4045 3.3985276
9700 18489.496 340.51647 0 3764.4972 2.941698
9750 19635.157 128.29122 0 3764.4315 -14.101437
9800 18284.554 378.61 0 3764.6385 -7.2125841
9850 17756.297 476.00442 0 3764.2076 -4.4238573
9900 18996.512 246.68301 0 3764.5557 -5.0986512
9950 19432.438 165.78467 0 3764.3843 -3.7163888
10000 19336.629 183.60921 0 3764.4664 -0.93973872
Loop time of 3.69311 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.113802 (3.08147)
Neigh time (%) = 0.0713954 (1.93321)
Comm time (%) = 0.0130091 (0.352253)
Outpt time (%) = 0.0163274 (0.442104)
Other time (%) = 3.47857 (94.191)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69 ave 69 max 69 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 636 ave 636 max 636 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 636
Ave neighs/atom = 7.85185
Neighbor list builds = 991
Dangerous builds = 933

310
examples/rigid/log.rigid.poems2.9Jan12.linux.4 Normal file
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LAMMPS (10 Jan 2012)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (fix_poems.cpp:331)
WARNING: More than one fix poems (fix_poems.cpp:331)
WARNING: One or more atoms are time integrated more than once (modify.cpp:240)
Memory usage per processor = 2.24533 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47586 0 3765.6103 -17.92346
1500 19223.687 204.15182 0 3764.0939 -1.613452
1550 18147.996 404.12678 0 3764.8668 8.4194792
1600 18615.043 317.42471 0 3764.6548 -2.3288881
1650 20120.654 38.887882 0 3764.935 -8.7620352
1700 19450.908 162.98242 0 3765.0025 2.3254787
1750 19374.63 177.37994 0 3765.2744 8.9328764
1800 19424.404 167.93955 0 3765.0514 0.081221207
1850 17936.104 442.8692 0 3764.3699 6.6014634
1900 19982.594 64.406495 0 3764.8868 -2.9529141
1950 16215.626 761.95548 0 3764.8491 13.995806
2000 18584.494 322.10724 0 3763.6801 7.1652003
2050 20107.964 41.026031 0 3764.723 -0.31084595
2100 20002.303 60.598606 0 3764.7288 -6.7920431
2150 16950.12 626.52975 0 3765.4408 3.5077027
2200 20010.956 58.807784 0 3764.5404 -10.861982
2250 18982.743 247.00649 0 3762.3293 -0.53838506
2300 18401.159 354.90522 0 3762.5273 1.0923853
2350 19390.592 172.92882 0 3763.7792 -3.3521232
2400 16078.693 786.77936 0 3764.3151 -16.207246
2450 18869.645 268.89132 0 3763.27 11.210758
2500 19689.703 117.31993 0 3763.5612 4.3700595
2550 18867.605 269.38371 0 3763.3847 -5.673697
2600 17024.852 610.68855 0 3763.4389 6.2927269
2650 18723.802 296.52976 0 3763.9005 2.4475504
2700 19752.355 105.40597 0 3763.2494 -0.38635488
2750 19524.414 147.78984 0 3763.4221 -1.5733395
2800 17840.968 459.3254 0 3763.2085 29.661669
2850 18887.52 265.43414 0 3763.1231 3.7534553
2900 20160.325 29.79531 0 3763.1888 2.8076367
2950 17931.673 442.25832 0 3762.9386 4.1038365
3000 19003.992 243.57426 0 3762.832 3.5213285
3050 18907.933 261.70341 0 3763.1725 6.1845639
3100 19086.668 229.05632 0 3763.6245 -1.7059047
3150 19524.328 148.10446 0 3763.7208 -13.257029
3200 19888.015 80.720451 0 3763.6863 -5.9850932
3250 18329.653 367.80596 0 3762.1862 2.5356842
3300 17774.857 472.07926 0 3763.7194 26.05786
3350 18586.91 322.11111 0 3764.1316 5.7227572
3400 18142.722 404.27409 0 3764.0373 22.972948
3450 19641.028 126.721 0 3763.9484 4.4124099
3500 19716.345 112.83226 0 3764.0073 3.0970704
3550 19750.966 106.4596 0 3764.0458 -1.2020093
3600 19385.115 174.22116 0 3764.0572 -0.30312978
3650 19806.188 96.296016 0 3764.1086 1.3884533
3700 19632.503 128.4744 0 3764.1231 5.4783086
3750 19984.029 63.34637 0 3764.0924 -7.6169503
3800 19391.726 173.11834 0 3764.1788 -5.5199774
3850 19701.864 115.6328 0 3764.1262 -4.613059
3900 19071.277 232.53842 0 3764.2563 0.60414949
3950 19543.806 144.70463 0 3763.9279 3.9673805
4000 17072.153 601.63639 0 3763.1462 14.038181
4050 19472.634 157.9704 0 3764.0138 0.075484598
4100 19458.162 160.55562 0 3763.919 1.7856979
4150 19028.89 239.83121 0 3763.6997 11.420854
4200 20109.582 39.912078 0 3763.9088 -2.4825779
4250 19501.856 151.85318 0 3763.308 4.4374703
4300 19953.632 68.83941 0 3763.9565 -1.9144758
4350 19109.358 225.03756 0 3763.8075 0.43487388
4400 19762.511 104.29295 0 3764.0171 2.7984598
4450 19722.718 111.70804 0 3764.0632 2.2845927
4500 19915.846 75.911584 0 3764.0312 4.1625614
4550 19884.847 81.607953 0 3763.987 2.0252211
4600 18612.632 317.21746 0 3764.0011 5.1726513
4650 19078.336 230.90268 0 3763.9279 5.205472
4700 19715.75 112.95427 0 3764.019 4.3237781
4750 19742.684 107.93515 0 3763.9878 2.1485577
4800 19197.053 208.91261 0 3763.9225 -2.943785
4850 19760.387 104.71117 0 3764.0421 -4.0934577
4900 17998.47 431.02848 0 3764.0784 13.811824
4950 19604.398 133.53703 0 3763.9811 -5.5636088
5000 19232.029 202.51843 0 3764.0053 -1.8269075
5050 19715.235 112.97181 0 3763.9412 1.7390053
5100 19398.744 171.53062 0 3763.8906 3.3491974
5150 19314.84 187.15985 0 3763.982 2.8628327
5200 19694.326 116.88381 0 3763.9813 0.87055141
5250 19863.902 85.505146 0 3764.0056 -0.59127781
5300 18854.279 272.69199 0 3764.2251 0.97585642
5350 20102.125 41.375281 0 3763.9911 3.4442258
5400 18613.294 317.12781 0 3764.0342 9.5393349
5450 19559.083 141.5345 0 3763.5869 3.6962703
5500 17569.068 510.18672 0 3763.7179 13.24936
5550 19270.914 194.90196 0 3763.5898 3.8986118
5600 19498.122 153.15583 0 3763.9191 -3.4776966
5650 19777.463 101.36242 0 3763.8555 -11.848632
5700 19084.468 229.69625 0 3763.8569 1.2585904
5750 18724.734 296.2904 0 3763.8337 2.6582121
5800 19386.427 173.81408 0 3763.8932 4.2211994
5850 19803.648 96.837994 0 3764.1802 1.3140639
5900 19673.781 120.82275 0 3764.1155 -2.5154465
5950 19736.953 109.09143 0 3764.0827 -2.2181212
6000 19790.274 99.158109 0 3764.0237 -3.68098
6050 19545.34 144.53706 0 3764.0444 0.39182955
6100 17986.935 433.2002 0 3764.114 10.030916
6150 19723.117 111.58597 0 3764.015 2.7481914
6200 19196.262 209.2757 0 3764.139 -4.1838898
6250 19595.664 135.40327 0 3764.2299 -4.9572417
6300 20066.143 48.26479 0 3764.2173 -2.0440702
6350 19658.915 123.66551 0 3764.2054 6.3983302
6400 16099.375 783.30808 0 3764.6738 10.626182
6450 18777.763 287.09552 0 3764.4591 -4.455207
6500 16707.737 670.37041 0 3764.3958 13.941367
6550 19762.607 104.62762 0 3764.3696 0.16306805
6600 19257.046 198.21098 0 3764.3305 -5.4407238
6650 19832.195 91.712241 0 3764.3409 -1.9458256
6700 19850.998 88.250674 0 3764.3614 5.8183659
6750 19413.067 169.26039 0 3764.2728 6.1295075
6800 19765.494 103.96165 0 3764.2383 -3.7688435
6850 16858.457 642.54223 0 3764.4787 4.5079169
6900 19982.921 63.847652 0 3764.3885 -9.1345046
6950 19913.352 76.606013 0 3764.2639 -2.5724183
7000 19224.043 204.40946 0 3764.4174 8.8267535
7050 19611.945 132.75353 0 3764.5952 -1.2121033
7100 18439.385 350.13652 0 3764.8375 -10.124288
7150 19682.442 120.04202 0 3764.9386 -3.6256683
7200 19422.224 168.10408 0 3764.8122 0.82487728
7250 18329.588 370.25204 0 3764.6202 11.648525
7300 19708.59 114.99145 0 3764.7304 0.046523759
7350 19816.323 95.213196 0 3764.9026 -0.47763944
7400 17665.439 493.59617 0 3764.9737 -0.91038002
7450 19566.729 141.55672 0 3765.0251 -5.4595222
7500 19814.753 95.678399 0 3765.077 2.7766353
7550 18372.821 362.40112 0 3764.7753 14.250033
7600 19501.443 153.75428 0 3765.1326 7.1710143
7650 19668.707 122.7639 0 3765.117 -7.9237216
7700 19679.165 120.74844 0 3765.0382 -2.2087708
7750 19318.592 187.36213 0 3764.8791 5.2470406
7800 18421.715 352.99021 0 3764.419 9.1913905
7850 18895.708 265.3653 0 3764.5705 5.549395
7900 19577.99 139.06024 0 3764.614 -9.4076317
7950 19740.609 109.09893 0 3764.7672 -9.8961255
8000 18940.832 256.98999 0 3764.5514 3.9687427
8050 18969.072 252.07733 0 3764.8685 -4.0865115
8100 18105.878 411.85769 0 3764.798 6.9985575
8150 17720.026 483.41227 0 3764.8985 -9.9691828
8200 19228.141 204.22365 0 3764.9906 4.5129102
8250 18208.089 392.95005 0 3764.8183 -1.1095191
8300 17975.092 435.94429 0 3764.665 17.753982
8350 18763.356 290.24792 0 3764.9434 2.4934075
8400 20081.591 46.079041 0 3764.8922 -1.2146918
8450 19112.458 225.50295 0 3764.847 -4.35039
8500 19307.507 189.3956 0 3764.86 5.0874862
8550 19181.088 212.75782 0 3764.8111 0.25341129
8600 18801.701 282.9206 0 3764.7171 -11.907333
8650 18881.312 268.25685 0 3764.7961 7.0176888
8700 15686.277 860.48983 0 3765.356 21.424289
8750 18618.866 316.47733 0 3764.4154 -4.6552691
8800 18339.56 368.23406 0 3764.4489 2.6401219
8850 19445.679 163.71793 0 3764.7697 -2.4895575
8900 19121.794 223.5113 0 3764.5842 -5.0630299
8950 14402.118 1099.2335 0 3766.2923 -7.4933486
9000 19175.071 213.69795 0 3764.637 -5.6657242
9050 19412.386 169.60603 0 3764.4924 -12.723782
9100 18455.972 346.68851 0 3764.4611 9.1721288
9150 19954.848 69.041959 0 3764.3841 -0.91356236
9200 19613.768 132.03036 0 3764.2097 4.9013519
9250 15254.687 939.82439 0 3764.7665 11.510878
9300 19048.696 236.62627 0 3764.1625 0.67464829
9350 18952.271 254.3769 0 3764.0568 8.2625973
9400 17082.985 600.49483 0 3764.0105 -9.9046787
9450 16757.345 660.90075 0 3764.1128 21.116304
9500 19841.884 89.284407 0 3763.7073 -0.64193305
9550 19304.212 189.00596 0 3763.86 -12.873723
9600 16227.696 759.23524 0 3764.3641 11.721944
9650 17820.924 463.01451 0 3763.1857 3.9496789
9700 19354.393 179.78068 0 3763.9275 -2.6872013
9750 13935.985 1183.7739 0 3764.5119 10.647433
9800 19587.907 136.31855 0 3763.7087 5.5549859
9850 19080.946 230.80379 0 3764.3124 -4.0577518
9900 19455.883 161.42232 0 3764.3637 -1.6117009
9950 18749.317 292.29982 0 3764.3955 3.9849608
10000 18721.798 297.49023 0 3764.4899 1.6710415
Loop time of 3.89194 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0295593 (0.7595)
Neigh time (%) = 0.0209811 (0.539092)
Comm time (%) = 0.258437 (6.6403)
Outpt time (%) = 0.0221968 (0.570326)
Other time (%) = 3.56077 (91.4908)
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 16 ave 33 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 162.75 ave 371 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 651
Ave neighs/atom = 8.03704
Neighbor list builds = 993
Dangerous builds = 949

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 2.37454 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346
50 300 -8237.7876 0 -8184.1576 13746.642 19678.792
75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233
100 300 -8245.8191 0 -8192.189 9038.4055 19770.872
Loop time of 0.243427 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 0.228408 (93.8302)
Neigh time (%) = 0.00815201 (3.34885)
Comm time (%) = 0.0018518 (0.76072)
Outpt time (%) = 6.10352e-05 (0.0250733)
Other time (%) = 0.0049541 (2.03515)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2122 ave 2122 max 2122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45975 ave 45975 max 45975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45975
Ave neighs/atom = 24.0455
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 2.37645 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
100 300 -8260.7953 0 -8225.0549 3177.3605 19809.773
200 298.50746 -8257.8441 0 -8222.2815 1696.64 19926.446
300 296.80999 -8250.2343 0 -8214.8739 -338.92466 20051.103
400 306.47135 -8245.2265 0 -8208.7151 9.7606112 20134.594
500 298.68843 -8240.244 0 -8204.6599 722.49284 20161.098
600 302.37622 -8230.4652 0 -8194.4417 4007.3859 20279.478
700 300 -8222.0223 0 -8186.2819 6769.4135 20405.698
800 303.21952 -8210.998 0 -8174.874 8152.7988 20510.204
900 297.74338 -8197.2403 0 -8161.7687 10764.828 20634.767
1000 300 -8180.7508 0 -8145.0104 14227.468 20760.551
1100 305.89822 -8166.6544 0 -8130.2113 18078.278 20875.344
1200 295.27459 -8152.0699 0 -8116.8924 21328.094 21001.128
1300 300 -8141.732 0 -8105.9916 22799.705 21115.921
1400 300 -8130.0647 0 -8094.3243 23526.574 21246.59
1500 300 -8125.4387 0 -8089.6983 22002.546 21356.499
1600 300 -8128.9533 0 -8093.2128 18328.671 21485.946
1700 300 -8151.4563 0 -8115.7159 11511.304 21600.74
1800 300 -8160.1502 0 -8124.4098 7547.562 21724.081
1900 309.29943 -8153.7122 0 -8116.8639 8409.7432 21858.414
2000 307.15092 -8160.675 0 -8124.0826 5894.1343 21976.871
2100 308.54207 -8156.5601 0 -8119.802 4916.8536 22095.327
2200 300 -8157.4804 0 -8121.74 2411.8958 22217.448
2300 300 -8162.7297 0 -8126.9893 -128.11671 22334.684
2400 300 -8166.1396 0 -8130.3991 -1504.9194 22459.246
2500 300 -8169.094 0 -8133.3536 -119.96486 22578.925
2600 304.76063 -8162.5898 0 -8126.2822 2246.5398 22714.478
2700 308.04872 -8167.1208 0 -8130.4215 77.151948 22834.156
2800 300 -8167.1381 0 -8131.3977 -2885.907 22951.392
2900 308.65071 -8164.1796 0 -8127.4086 -7537.8706 23075.955
3000 302.42612 -8159.1684 0 -8123.139 -9974.9028 23189.527
Loop time of 7.54227 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 6.83641 (90.6412)
Neigh time (%) = 0.450643 (5.9749)
Comm time (%) = 0.0600526 (0.796214)
Outpt time (%) = 0.0466561 (0.618595)
Other time (%) = 0.148517 (1.96913)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2104 ave 2104 max 2104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 44986 ave 44986 max 44986 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 44986
Ave neighs/atom = 23.5282
Neighbor list builds = 221
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 2.27477 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346
50 300 -8239.0761 0 -8185.446 13404.703 19669.87
75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549
100 300 -8250.5856 0 -8196.9555 6735.754 19818.526
Loop time of 0.0705068 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.0616967 (87.5046)
Neigh time (%) = 0.00212312 (3.01122)
Comm time (%) = 0.00468183 (6.64025)
Outpt time (%) = 0.000109732 (0.155633)
Other time (%) = 0.00189543 (2.68829)
Nlocal: 478 ave 490 max 468 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1033.75 ave 1043 max 1021 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 11508.8 ave 12218 max 10874 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 46035
Ave neighs/atom = 24.0769
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 2.27477 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
100 298.90147 -8254.2464 0 -8218.6368 1673.5647 19875.172
200 292.67105 -8257.6816 0 -8222.8143 597.02209 19851.638
300 304.83817 -8252.3996 0 -8216.0828 -1766.9124 19972.145
400 304.67912 -8245.8917 0 -8209.5938 984.88656 20123.442
500 304.19559 -8240.3464 0 -8204.1061 858.95575 20228.779
600 300 -8228.866 0 -8193.1256 3277.69 20298.36
700 301.21369 -8221.8851 0 -8186.0001 5982.9806 20420.849
800 292.95939 -8207.7529 0 -8172.8512 9954.3357 20536.518
900 301.91087 -8196.792 0 -8160.8239 12198.791 20621.333
1000 304.47104 -8183.7675 0 -8147.4944 16413.662 20759.329
1100 309.51789 -8171.7638 0 -8134.8895 19823.617 20871.68
1200 300 -8162.1479 0 -8126.4075 21358.891 21002.349
1300 306.82902 -8154.9346 0 -8118.3806 19922.78 21112.258
1400 302.84766 -8146.0057 0 -8109.926 20387.683 21245.369
1500 300 -8136.5305 0 -8100.7901 19767.587 21371.153
1600 300 -8133.8687 0 -8098.1282 16820.721 21487.167
1700 300 -8138.1712 0 -8102.4307 13421.303 21603.182
1800 300 -8156.4639 0 -8120.7235 8511.6435 21732.63
1900 300 -8171.1239 0 -8135.3835 5041.7586 21849.865
2000 300 -8163.4848 0 -8127.7444 3694.8641 21970.765
2100 308.72044 -8171.8831 0 -8135.1038 970.54577 22092.885
2200 302.52995 -8169.1085 0 -8133.0666 52.192359 22216.227
2300 300 -8170.9512 0 -8135.2107 -1542.8185 22335.905
2400 300 -8172.0501 0 -8136.3097 -2043.706 22458.025
2500 308.89262 -8175.1797 0 -8138.3798 -3806.7013 22581.367
2600 308.78531 -8173.0575 0 -8136.2705 -3040.4487 22705.93
2700 309.91867 -8169.3099 0 -8132.3878 -3733.9914 22819.502
2800 300 -8170.4846 0 -8134.7442 -3811.1294 22953.834
2900 298.97302 -8165.3476 0 -8129.7295 -4051.2587 23075.955
3000 299.96914 -8161.4805 0 -8125.7437 -2883.9458 23201.739
Loop time of 2.15711 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 1.80975 (83.8969)
Neigh time (%) = 0.116127 (5.38344)
Comm time (%) = 0.13217 (6.12716)
Outpt time (%) = 0.0456018 (2.11403)
Other time (%) = 0.0534638 (2.47849)
Nlocal: 478 ave 512 max 446 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 1006 ave 1055 max 967 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 11265.2 ave 12221 max 10346 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 45061
Ave neighs/atom = 23.5675
Neighbor list builds = 223
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 2.35723 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346
50 300 -7292.2273 0 -7246.508 7558.4629 19680.84
75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503
100 300 -7297.4174 0 -7251.698 1627.881 19767.928
Loop time of 0.208741 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.195505 (93.659)
Neigh time (%) = 0.00704098 (3.37307)
Comm time (%) = 0.00166225 (0.796324)
Outpt time (%) = 5.8651e-05 (0.0280975)
Other time (%) = 0.0044744 (2.14352)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39444 ave 39444 max 39444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39444
Ave neighs/atom = 23.0937
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 2.35723 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
100 290.32156 -7309.73 0 -7280.2463 -5963.004 19831.09
200 290.76236 -7306.4805 0 -7276.952 -7421.6375 19919.327
300 293.25821 -7304.1086 0 -7274.3267 -11013.42 20035.976
400 293.84766 -7299.0985 0 -7269.2567 -7886.1633 20097.992
500 291.74499 -7299.9751 0 -7270.3468 -5636.1333 20137.736
600 303.46664 -7291.5162 0 -7260.6975 -1010.2257 20269.626
700 300 -7287.9569 0 -7257.4903 -2205.2748 20391.564
800 300 -7280.4222 0 -7249.9555 -2876.2467 20512.915
900 292.92463 -7272.7361 0 -7242.9881 -1776.974 20633.545
1000 307.93499 -7265.1866 0 -7233.9141 -1238.6225 20750.781
1100 300.17079 -7260.1229 0 -7229.6389 -1843.002 20881.45
1200 302.06128 -7255.9277 0 -7225.2517 -1889.3058 21004.792
1300 300 -7259.2664 0 -7228.7998 -3186.0907 21111.036
1400 300 -7265.444 0 -7234.9774 -6109.5646 21244.148
1500 308.79162 -7271.0073 0 -7239.6478 -6107.0978 21361.383
1600 300 -7275.2324 0 -7244.7658 -8519.8045 21492.052
1700 309.22602 -7278.5756 0 -7247.172 -13752.852 21610.509
1800 300 -7284.3068 0 -7253.8402 -14337.648 21720.418
1900 299.75827 -7283.413 0 -7252.9709 -14463.157 21846.202
2000 297.70312 -7274.9007 0 -7244.6674 -20480.857 21978.092
2100 304.09482 -7269.8328 0 -7238.9503 -19791.258 22092.885
2200 299.66443 -7269.2566 0 -7238.8241 -16602.972 22216.227
2300 299.27231 -7268.2781 0 -7237.8853 -15847.311 22337.126
2400 300.69324 -7259.5316 0 -7228.9946 -14598.831 22462.91
2500 297.44581 -7258.0006 0 -7227.7934 -17846.994 22581.367
2600 300 -7253.3731 0 -7222.9065 -18557.919 22710.815
2700 305.12651 -7253.1648 0 -7222.1775 -20331.834 22824.387
2800 294.14063 -7249.1464 0 -7219.2748 -17541.566 22952.613
2900 307.30441 -7249.4895 0 -7218.281 -17450.515 23071.07
3000 304.44871 -7244.9559 0 -7214.0374 -15842.46 23199.297
Loop time of 6.44215 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 5.84485 (90.7281)
Neigh time (%) = 0.366316 (5.68623)
Comm time (%) = 0.0535274 (0.830892)
Outpt time (%) = 0.04369 (0.678189)
Other time (%) = 0.133776 (2.07657)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1879 ave 1879 max 1879 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38632 ave 38632 max 38632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38632
Ave neighs/atom = 22.6183
Neighbor list builds = 209
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
timestep 0.001
run 100
Memory usage per processor = 2.26254 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582
50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062
75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777
100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395
Loop time of 0.0606166 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.0526265 (86.8186)
Neigh time (%) = 0.00232816 (3.84079)
Comm time (%) = 0.00390279 (6.43849)
Outpt time (%) = 0.000118196 (0.194989)
Other time (%) = 0.00164098 (2.70714)
Nlocal: 427 ave 435 max 419 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 780.25 ave 792 max 769 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 9878.75 ave 10203 max 9534 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 39515
Ave neighs/atom = 23.1352
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 100 dump.shear
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
reset_timestep 0
run 3000
Memory usage per processor = 2.26254 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
100 309.43345 -7305.7349 0 -7274.3103 -4898.9067 19876.383
200 292.09158 -7308.3924 0 -7278.7289 -9672.4555 19871.139
300 297.20209 -7303.4054 0 -7273.2229 -10458.509 20026.545
400 301.76624 -7298.9615 0 -7268.3155 -8311.9182 20057.341
500 296.6739 -7299.7346 0 -7269.6058 -6648.1941 20142.621
600 301.5451 -7294.6131 0 -7263.9896 -4525.1055 20268.839
700 297.72688 -7285.6963 0 -7255.4605 -1774.5536 20391.147
800 309.01491 -7279.9489 0 -7248.5668 -394.2912 20501.655
900 307.05599 -7273.2334 0 -7242.0502 8.1721666 20633.545
1000 299.45693 -7266.8728 0 -7236.4613 -2338.8876 20759.329
1100 300 -7259.9532 0 -7229.4865 -3092.0664 20875.344
1200 300 -7258.5089 0 -7228.0423 -5092.1152 20997.464
1300 300 -7261.2914 0 -7230.8248 -5743.4972 21124.47
1400 300 -7266.0446 0 -7235.578 -7828.4242 21233.157
1500 307.13101 -7271.165 0 -7239.9741 -11309.87 21360.162
1600 300 -7273.2378 0 -7242.7712 -13366.956 21484.725
1700 301.7588 -7270.2824 0 -7239.6372 -14195.725 21609.288
1800 300 -7271.2595 0 -7240.7929 -11929.424 21736.293
1900 307.50197 -7274.3144 0 -7243.0859 -14024.738 21852.308
2000 300 -7267.9904 0 -7237.5238 -19598.421 21965.88
2100 300.69536 -7264.7536 0 -7234.2163 -20295.562 22090.443
2200 301.08099 -7267.9694 0 -7237.393 -22833.972 22223.554
2300 291.66065 -7261.6554 0 -7232.0357 -23125.705 22343.232
2400 298.88457 -7257.9563 0 -7227.603 -25049.249 22470.237
2500 304.37073 -7253.7601 0 -7222.8496 -25545.14 22589.915
2600 300 -7246.4222 0 -7215.9556 -25051.428 22710.815
2700 300 -7243.8917 0 -7213.4251 -28923.111 22826.829
2800 300 -7239.3939 0 -7208.9273 -28323.168 22958.719
2900 304.87485 -7235.3221 0 -7204.3604 -26726.42 23072.291
3000 300 -7233.1367 0 -7202.6701 -27373.287 23200.518
Loop time of 1.84879 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 1.5564 (84.1845)
Neigh time (%) = 0.0949981 (5.13839)
Comm time (%) = 0.107428 (5.81072)
Outpt time (%) = 0.0408981 (2.21215)
Other time (%) = 0.0490716 (2.65425)
Nlocal: 427 ave 441 max 411 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 777.25 ave 826 max 727 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 9559.25 ave 10062 max 9128 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 38237
Ave neighs/atom = 22.387
Neighbor list builds = 210
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d SRD test: big + small particles
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with sigma 1.0
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 diameter 1.0
100 settings made for diameter
group big type 1
100 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
run 1000
Memory usage per processor = 2.74779 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.54272 0 0.88288 -0.041088
1000 1.8791467 -0.97185784 0 0.8884974 0.61487656
Loop time of 0.0159652 on 1 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00843024 (52.8038)
Neigh time (%) = 0.0026598 (16.6599)
Comm time (%) = 0.0019424 (12.1664)
Outpt time (%) = 1.00136e-05 (0.0627212)
Other time (%) = 0.00292277 (18.3071)
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 88 ave 88 max 88 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 459 ave 459 max 459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 459
Ave neighs/atom = 4.59
Neighbor list builds = 129
Dangerous builds = 0
unfix 1
unfix 2
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 21316 atoms
set type 2 mass 0.01
21316 settings made for mass
set type 2 diameter 0.0
21316 settings made for diameter
group small type 2
21316 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 6700 atoms, new total = 14716
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
fix 3 all enforce2d
# diagnostics
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
thermo 100
dump 1 all atom 250 dump.srd.mixture
run 5000
SRD info:
SRD/big particles = 14616 100
big particle diameter max/min = 0.88 0.88
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 4.86648
SRD viscosity = 0.463448
big/SRD mass density ratio = 2.12808
WARNING: Fix srd grid size > 1/4 of big particle diameter (fix_srd.cpp:2718)
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
Memory usage per processor = 12.0447 Mbytes
Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0
100 1.1596877 3969 0.00179671 -0.88368702 0.26440384 0.85824544 7578 83 83 0 0 12996 3311 0.90986343 0
200 1.2193121 3969 0.001834514 -0.93715195 0.26996708 0.70474789 7511 90 90 0 0 12996 3299 0.93333115 0
300 0.99964232 3969 -0.00024687038 -1.0259753 -0.036329445 0.17545201 7647 91 91 0 0 12996 3304 0.92248322 0
400 1.0499322 3969 0.00055095426 -0.95835442 0.081078429 0.36186511 7386 108 108 0 0 12996 3287 0.93178952 0
500 1.0774128 3969 0.00085873911 -0.94026661 0.12637205 0.44079381 7472 85 85 0 1 12996 3294 0.92990791 0
600 1.0713454 3969 0.00045284139 -0.99399184 0.066640139 0.10369128 7656 83 83 0 0 12996 3283 0.9442218 0
700 0.98148416 3969 0.00027332701 -0.93144651 0.040222802 0.40064794 7616 68 68 0 1 12996 3291 0.92556298 0
800 1.038835 3969 0.00026382768 -0.98962177 0.038824881 0.26546656 7518 100 100 0 1 12996 3313 0.92639077 0
900 1.0976069 3969 0.0005211042 -1.0099451 0.076685694 0.28307539 7658 91 91 0 0 12996 3300 0.95182154 0
1000 1.0541417 3969 0.00060061674 -0.95521356 0.088386759 0.61226289 7577 78 78 0 1 12996 3279 0.93137952 0
1100 1.0332458 3969 0.00050159758 -0.94909829 0.073815099 0.6685224 7581 79 79 0 0 12996 3295 0.94032764 0
1200 0.89438281 3969 -0.00096584613 -1.0275729 -0.14213392 0.37403554 7576 96 96 0 0 12996 3281 0.93102063 0
1300 1.0211539 3969 2.286332e-05 -1.0075778 0.0033645662 0.56342549 7660 94 94 0 0 12996 3302 0.92477424 0
1400 0.99883891 3969 0.00024046091 -0.9534643 0.035386228 0.5689857 7634 82 82 0 0 12996 3288 0.94186158 0
1500 0.93938218 3969 -0.00014395945 -0.95117343 -0.021185072 0.53463026 7632 87 87 0 0 12996 3293 0.95231047 0
1600 1.2197277 3969 0.0011523527 -1.0379502 0.16958023 0.3478121 7659 82 82 0 0 12996 3301 0.9451025 0
1700 0.96932134 3969 -0.00064508306 -1.0545586 -0.094930423 0.29578009 7332 92 92 0 0 12996 3284 0.94431043 0
1800 1.0534784 3969 -4.2619236e-05 -1.0492155 -0.0062718467 0.42534773 7647 94 94 0 0 12996 3309 0.93884698 0
1900 1.1715618 3969 0.00031188504 -1.1139492 0.045897003 0.23182966 7624 78 78 0 0 12996 3271 0.93820406 0
2000 0.9840555 3969 -0.00078568321 -1.0898361 -0.11562114 0.24175316 7571 77 77 0 0 12996 3313 0.92926386 0
2100 0.91303589 3969 -0.001459571 -1.118696 -0.21479047 0.27799152 7668 84 84 0 0 12996 3313 0.93483511 0
2200 0.97316562 3969 -0.00087469617 -1.0921543 -0.12872029 0.40701899 7422 96 96 0 0 12996 3297 0.93837781 0
2300 1.1071289 3969 0.00055485995 -1.0144044 0.08165319 0.70028696 7242 86 86 0 0 12996 3293 0.93155673 0
2400 0.95313231 3969 -0.00066790967 -1.0418906 -0.098289587 0.56977108 7370 88 88 0 0 12996 3302 0.93579748 0
2500 1.0789299 3969 -0.00067288654 -1.1671626 -0.099021984 0.1320041 7485 84 84 0 0 12996 3275 0.94791836 0
2600 1.0013882 3969 -0.00086378434 -1.1184888 -0.1271145 0.31303314 7412 82 82 0 0 12996 3277 0.9269671 0
2700 0.99821888 3969 -0.00016681979 -1.0127859 -0.024549201 0.71198483 7543 93 93 0 0 12996 3308 0.93084261 0
2800 1.032743 3969 -0.00066018247 -1.119568 -0.097152452 0.34329585 7442 106 106 0 0 12996 3295 0.92448695 0
2900 1.158581 3969 0.00061952386 -1.055826 0.091169131 0.55199976 7462 85 85 0 0 12996 3291 0.92795242 0
3000 1.0890666 3969 -5.0289217e-05 -1.0855765 -0.0074005612 0.35916031 7412 77 77 0 0 12996 3274 0.94994596 0
3100 0.98273391 3969 -0.00062906795 -1.0654802 -0.09257364 0.32240559 7489 71 71 0 0 12996 3284 0.95127784 0
3200 1.0182699 3969 -0.00092197839 -1.1437655 -0.13567834 0.060449966 7464 94 94 0 1 12996 3278 0.93022375 0
3300 0.92962276 3969 -0.0012252227 -1.1006303 -0.18030378 0.2692969 7449 98 98 0 0 12996 3293 0.92546839 0
3400 1.0270974 3969 -0.00078991522 -1.1330703 -0.11624392 0.28393475 7555 74 74 0 0 12996 3304 0.92199839 0
3500 0.91276883 3969 -0.0012028955 -1.0806592 -0.1770181 0.48380351 7422 100 100 0 0 12996 3281 0.94501126 0
3600 1.1604674 3969 0.00041287296 -1.0881043 0.060758384 0.4937285 7451 78 78 0 0 12996 3321 0.92302575 0
3700 0.92829756 3969 -0.0012843951 -1.1080262 -0.18901158 0.28403593 7502 80 80 0 0 12996 3297 0.92606333 0
3800 0.99862294 3969 -0.00028587151 -1.0307056 -0.042068851 0.57880501 7353 84 84 0 0 12996 3285 0.93847635 0
3900 1.0748889 3969 -0.00039644261 -1.1224805 -0.058340495 0.3117021 7199 95 95 0 0 12996 3290 0.92380848 0
4000 1.1443251 3969 0.00073233367 -1.0251116 0.10777022 0.72975938 7478 90 90 0 0 12996 3300 0.92374817 0
4100 1.0573661 3969 -8.8349019e-05 -1.0597939 -0.013001442 0.62403315 7528 77 77 0 0 12996 3292 0.92800097 0
4200 0.93387975 3969 -0.0012090318 -1.1024621 -0.17792112 0.50858912 7397 80 80 0 0 12996 3303 0.9315765 0
4300 0.99747825 3969 -0.00050121316 -1.061262 -0.073758528 0.63526459 7355 90 90 0 0 12996 3293 0.93486767 0
4400 0.91351004 3969 -0.0013423585 -1.1019164 -0.19754147 0.44962963 7448 94 94 0 0 12996 3283 0.9351589 0
4500 1.112129 3969 -9.3639925e-05 -1.1147878 -0.013780051 0.5084257 7570 77 77 0 0 12996 3287 0.93096727 0
4600 1.0070341 3969 -0.00044065884 -1.0618111 -0.064847355 0.50331376 7503 74 74 0 0 12996 3256 0.93088036 0
4700 1.1678442 3969 0.00045268406 -1.0895488 0.066616986 0.46676039 7514 81 81 0 1 12996 3282 0.91797333 0
4800 1.1647145 3969 0.00063121154 -1.0601783 0.092889091 0.52493522 7437 89 89 0 0 12996 3304 0.93239615 0
4900 1.1545752 3969 -0.00015064108 -1.1651978 -0.022168341 0.098732178 7561 85 85 0 1 12996 3298 0.91920589 0
5000 1.2758575 3969 0.0016719011 -1.017062 0.24603697 0.63374434 7283 77 77 0 0 12996 3281 0.92343378 0
Loop time of 3.1676 on 1 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0429308 (1.35531)
Neigh time (%) = 0.201053 (6.34717)
Comm time (%) = 0.0404043 (1.27555)
Outpt time (%) = 0.223962 (7.07041)
Other time (%) = 2.65925 (83.9516)
Nlocal: 14716 ave 14716 max 14716 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 80 ave 80 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 490 ave 490 max 490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 490
Ave neighs/atom = 0.0332971
Neighbor list builds = 250
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d SRD test: big + small particles
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with sigma 1.0
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
2 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 diameter 1.0
100 settings made for diameter
group big type 1
100 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
run 1000
Memory usage per processor = 2.74723 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.54272 0 0.88288 -0.041088
1000 1.8791467 -0.97185784 0 0.8884974 0.61487657
Loop time of 0.0149925 on 4 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00214541 (14.3099)
Neigh time (%) = 0.000690401 (4.60498)
Comm time (%) = 0.00878567 (58.6005)
Outpt time (%) = 1.81794e-05 (0.121257)
Other time (%) = 0.00335282 (22.3634)
Nlocal: 25 ave 26 max 23 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 47 ave 48 max 46 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 114.75 ave 124 max 100 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 459
Ave neighs/atom = 4.59
Neighbor list builds = 129
Dangerous builds = 0
unfix 1
unfix 2
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 21316 atoms
set type 2 mass 0.01
21316 settings made for mass
set type 2 diameter 0.0
21316 settings made for diameter
group small type 2
21316 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Deleted 6700 atoms, new total = 14716
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
fix 3 all enforce2d
# diagnostics
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
thermo 100
dump 1 all atom 250 dump.srd.mixture
run 5000
SRD info:
SRD/big particles = 14616 100
big particle diameter max/min = 0.88 0.88
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 4.86648
SRD viscosity = 0.463448
big/SRD mass density ratio = 2.12808
WARNING: Fix srd grid size > 1/4 of big particle diameter (fix_srd.cpp:2718)
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
Memory usage per processor = 6.32655 Mbytes
Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
100 1.4044369 3969 0.0030633087 -0.93959598 0.45079651 0.78900114 7464 99 99 0 0 22500 3312 0.93283021 0
200 1.1569395 3969 0.0010544039 -0.99020406 0.15516608 0.50132859 7393 82 82 0 0 22500 3291 0.92342254 0
300 1.0082066 3969 1.5754289e-06 -0.99789266 0.00023184012 0.36859357 7443 90 90 0 0 22500 3298 0.93222633 0
400 1.1459472 3969 0.0010570023 -0.97893929 0.15554845 0.47616067 7327 81 81 0 0 22500 3297 0.91766446 0
500 1.0836955 3969 0.00072569678 -0.966065 0.10679354 0.49205907 7447 89 89 0 0 22500 3258 0.93553253 0
600 0.95868561 3969 -0.00031108604 -0.99487817 -0.045779421 0.3676888 7488 90 90 0 0 22500 3280 0.91061957 0
700 0.98121671 3969 -0.00022225428 -1.0041115 -0.03270694 0.3605398 7393 80 80 0 0 22500 3299 0.90992183 0
800 1.0870893 3969 0.00028589178 -1.0341466 0.042071834 0.3576364 7506 96 96 0 0 22500 3290 0.92887007 0
900 1.087553 3969 8.795578e-05 -1.0637339 0.012943573 0.28026879 7405 82 82 0 0 22500 3301 0.91599453 0
1000 1.0160539 3969 7.5618714e-05 -0.99476531 0.01112805 0.60009776 7334 88 88 0 0 22500 3296 0.92803837 0
1100 0.94619807 3969 -0.00084794884 -1.0615202 -0.12478415 0.36153566 7565 89 89 0 0 22500 3300 0.93685597 0
1200 1.2187057 3969 0.00079088888 -1.0901314 0.11638721 0.34195358 7558 94 94 0 0 22500 3281 0.92133419 0
1300 1.0297116 3969 -6.2029069e-05 -1.0285427 -0.0091281978 0.44490154 7365 76 76 0 0 22500 3273 0.92349253 0
1400 1.0723726 3969 3.8902675e-05 -1.055924 0.0057249176 0.40617642 7524 90 90 0 0 22500 3280 0.92787441 0
1500 1.0661279 3969 -0.00010841884 -1.0714216 -0.015954917 0.49701435 7285 69 69 0 0 22500 3295 0.92862687 0
1600 1.2175256 3969 0.00087968156 -1.0758964 0.12945394 0.64512981 7286 89 89 0 1 22500 3294 0.92600699 0
1700 1.1985014 3969 0.0014648642 -0.970947 0.21556942 1.0479949 7228 85 85 0 0 22500 3268 0.92256981 0
1800 1.2075839 3969 0.00072247447 -1.0891887 0.10631934 0.57872746 7449 87 87 0 0 22500 3288 0.92069976 0
1900 1.2255534 3969 0.00088656095 -1.0828315 0.13046631 0.65685308 7385 76 76 0 0 22500 3291 0.9048111 0
2000 1.291624 3969 0.0012489132 -1.0949177 0.18379006 0.54486534 7460 88 88 0 0 22500 3269 0.92086677 0
2100 1.1111637 3969 8.680692e-05 -1.0872776 0.012774506 0.54623825 7399 79 79 0 0 22500 3283 0.89787043 0
2200 1.1101509 3969 -0.00019790624 -1.1281733 -0.029123882 0.36938914 7394 80 80 0 0 22500 3289 0.92391832 0
2300 0.99008142 3969 -0.0010221939 -1.1306067 -0.15042605 0.49715741 7403 77 77 0 0 22500 3298 0.9032635 0
2400 1.1298599 3969 -0.00028442155 -1.1604168 -0.041855476 0.62622034 7213 99 99 0 0 22500 3279 0.92291152 0
2500 0.96755195 3969 -0.0013882655 -1.1621736 -0.20429715 0.53854953 7302 91 91 0 0 22500 3282 0.9169308 0
2600 0.92289325 3969 -0.0018295583 -1.1829021 -0.2692378 0.48117908 7387 114 114 0 0 22500 3292 0.90278484 0
2700 1.0556828 3969 -0.0010119543 -1.1940452 -0.14891919 0.38438637 7379 77 77 0 0 22500 3290 0.90840462 0
2800 0.96725457 3969 -0.0014988251 -1.1781491 -0.2205671 0.45335869 7311 77 77 0 0 22500 3273 0.91859555 0
2900 1.0133684 3969 -0.0012783239 -1.1913529 -0.18811815 0.47922787 7445 91 91 0 0 22500 3282 0.93217047 0
3000 0.97710883 3969 -0.0011590153 -1.1378984 -0.17056069 0.64470243 7454 90 90 0 0 22500 3294 0.90446012 0
3100 0.85234697 3969 -0.002077265 -1.1495138 -0.30569031 0.55071072 7386 95 95 0 0 22500 3276 0.90586471 0
3200 1.052911 3969 -0.00084248304 -1.1663617 -0.1239798 0.49920749 7410 84 84 0 0 22500 3298 0.94126987 0
3300 1.1427076 3969 0.00052348324 -1.0542447 0.077035793 0.97657677 7268 70 70 0 0 22500 3281 0.93981555 0
3400 1.1749571 3969 -0.00049301879 -1.2357602 -0.072552645 0.2551001 7443 77 77 0 0 22500 3296 0.92174553 0
3500 0.99448585 3969 -0.0015705474 -1.2156628 -0.23112176 0.31069295 7502 97 97 0 0 22500 3271 0.94669984 0
3600 1.0615674 3969 -0.00088670873 -1.1814398 -0.13048806 0.42774035 7386 70 70 0 0 22500 3298 0.91457914 0
3700 0.92549328 3969 -0.0018599812 -1.1899532 -0.27371483 0.36471531 7459 81 81 0 0 22500 3305 0.93382818 0
3800 0.85987993 3969 -0.0018189231 -1.1189538 -0.26767272 0.42802928 7232 75 75 0 0 22500 3304 0.91492738 0
3900 0.92111833 3969 -0.0011824977 -1.0859235 -0.17401636 0.73992354 7351 80 80 0 0 22500 3298 0.94205739 0
4000 0.91817371 3969 -0.0014469814 -1.1219298 -0.21293778 0.64725317 7478 86 86 0 0 22500 3309 0.92689567 0
4100 1.0607641 3969 -0.00061451533 -1.1405885 -0.090432076 0.54575249 7474 87 87 0 0 22500 3306 0.94825937 0
4200 1.1112883 3969 0.00012926229 -1.0811532 0.019022238 0.71771029 7527 67 67 0 1 22500 3285 0.93577595 0
4300 1.3096702 3969 0.00060322354 -1.2078031 0.088770376 0.31006723 7617 88 88 0 0 22500 3291 0.95276158 0
4400 1.2076765 3969 0.001009301 -1.047071 0.14852873 0.83105522 7355 97 97 0 0 22500 3293 0.94207048 0
4500 0.94049473 3969 -0.0011505342 -1.1004024 -0.16931262 0.46258624 7403 78 78 0 0 22500 3275 0.95198657 0
4600 0.8241741 3969 -0.0025714658 -1.1943493 -0.37841691 0.010193689 7604 99 99 0 1 22500 3287 0.94875859 0
4700 0.98678642 3969 -0.0011664864 -1.1485787 -0.17166013 0.16963181 7691 94 94 0 0 22500 3289 0.92141605 0
4800 0.97602307 3969 -0.0010910984 -1.1268289 -0.16056604 0.24433738 7547 85 85 0 0 22500 3287 0.92130755 0
4900 1.0427787 3969 -0.00050976935 -1.1073686 -0.075017657 0.30774039 7563 85 85 0 0 22500 3300 0.92864167 0
5000 1.3048873 3969 0.0015736036 -1.0602669 0.23157151 0.49881308 7529 104 104 0 0 22500 3293 0.91471093 0
Loop time of 1.185 on 4 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0118163 (0.997157)
Neigh time (%) = 0.0523425 (4.41711)
Comm time (%) = 0.077751 (6.56129)
Outpt time (%) = 0.191228 (16.1375)
Other time (%) = 0.851857 (71.887)
Nlocal: 3679 ave 4052 max 3370 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 49 ave 53 max 42 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 120.5 ave 162 max 85 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 482
Ave neighs/atom = 0.0327535
Neighbor list builds = 250
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d SRD only test
units lj
atom_style atomic
atom_modify first empty
dimension 2
# create box with big lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
1 by 1 by 1 MPI processor grid
# add SRD particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 1 region plane
Created 21316 atoms
group empty type 2
0 atoms in group empty
mass 1 0.01
velocity all create 1.0 593849 loop geom
# settings - need dummy empty group to enable no communication
neighbor 0.3 bin
neigh_modify delay 1 every 1 check no
communicate single group empty
# timestep is big and SRD frequency is 1
timestep 0.02
fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
fix 2 all enforce2d
# diagnostics
thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
thermo 100
dump 1 all atom 250 dump.srd.pure
run 5000
SRD info:
SRD/big particles = 21316 0
big particle diameter max/min = 0 1e+20
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 5.37062
SRD viscosity = 0.439647
big/SRD mass density ratio = 0
# of rescaled SRD velocities = 0
ave/max all velocity = 13.2735 24.2873
Memory usage per processor = 4.08603 Mbytes
Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
0 1 0 0.99995309 85.26 0 0 0
100 0.97820615 3969 0.97816026 83.401857 0 0 0
200 0.9609326 3969 0.96088752 81.929113 0 0 0
300 0.94460302 3969 0.9445587 80.536853 0 0 0
400 0.93098293 3969 0.93093925 79.375605 0 0 0
500 0.91803208 3969 0.91798901 78.271415 0 0 0
600 0.90779378 3969 0.90775119 77.398497 0 0 0
700 0.89695247 3969 0.89691039 76.474168 0 0 0
800 0.88637078 3969 0.88632919 75.571972 0 0 0
900 0.87833669 3969 0.87829548 74.886986 0 0 0
1000 0.87030089 3969 0.87026006 74.201854 0 0 0
1100 0.86318709 3969 0.86314659 73.595331 0 0 0
1200 0.85736665 3969 0.85732643 73.099081 0 0 0
1300 0.85147901 3969 0.85143906 72.5971 0 0 0
1400 0.84496088 3969 0.84492124 72.041365 0 0 0
1500 0.83857476 3969 0.83853542 71.496884 0 0 0
1600 0.8336916 3969 0.83365249 71.080546 0 0 0
1700 0.82954371 3969 0.8295048 70.726897 0 0 0
1800 0.82570979 3969 0.82567105 70.400016 0 0 0
1900 0.82189413 3969 0.82185557 70.074693 0 0 0
2000 0.81818525 3969 0.81814687 69.758475 0 0 0
2100 0.81436257 3969 0.81432436 69.432552 0 0 0
2200 0.80997949 3969 0.80994149 69.058851 0 0 0
2300 0.80685831 3969 0.80682045 68.792739 0 0 0
2400 0.80374622 3969 0.80370851 68.527402 0 0 0
2500 0.80103773 3969 0.80100015 68.296477 0 0 0
2600 0.79858358 3969 0.79854611 68.087236 0 0 0
2700 0.79617295 3969 0.7961356 67.881706 0 0 0
2800 0.79312496 3969 0.79308775 67.621834 0 0 0
2900 0.79126456 3969 0.79122744 67.463216 0 0 0
3000 0.78897033 3969 0.78893331 67.26761 0 0 0
3100 0.78632296 3969 0.78628607 67.041895 0 0 0
3200 0.78442284 3969 0.78438604 66.879892 0 0 0
3300 0.78168316 3969 0.78164649 66.646306 0 0 0
3400 0.7788658 3969 0.77882926 66.406098 0 0 0
3500 0.77703408 3969 0.77699762 66.249925 0 0 0
3600 0.77441139 3969 0.77437506 66.026315 0 0 0
3700 0.7723528 3969 0.77231656 65.850799 0 0 0
3800 0.77019626 3969 0.77016013 65.666933 0 0 0
3900 0.76835687 3969 0.76832082 65.510107 0 0 0
4000 0.76701071 3969 0.76697473 65.395333 0 0 0
4100 0.76552115 3969 0.76548523 65.268333 0 0 0
4200 0.76360426 3969 0.76356843 65.104899 0 0 0
4300 0.76173186 3969 0.76169613 64.945259 0 0 0
4400 0.75933463 3969 0.759299 64.74087 0 0 0
4500 0.75806391 3969 0.75802835 64.632529 0 0 0
4600 0.75692832 3969 0.75689281 64.535709 0 0 0
4700 0.75569109 3969 0.75565564 64.430222 0 0 0
4800 0.75446697 3969 0.75443157 64.325854 0 0 0
4900 0.75276753 3969 0.75273221 64.180959 0 0 0
5000 0.75113693 3969 0.75110169 64.041935 0 0 0
Loop time of 8.027 on 1 procs for 5000 steps with 21316 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 5.17779 (64.5047)
Comm time (%) = 0.631268 (7.8643)
Outpt time (%) = 0.325017 (4.04905)
Other time (%) = 1.89293 (23.582)
Nlocal: 21316 ave 21316 max 21316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5000
Dangerous builds = 0

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LAMMPS (10 Jan 2012)
# 2d SRD only test
units lj
atom_style atomic
atom_modify first empty
dimension 2
# create box with big lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
2 by 2 by 1 MPI processor grid
# add SRD particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 1 region plane
Created 21316 atoms
group empty type 2
0 atoms in group empty
mass 1 0.01
velocity all create 1.0 593849 loop geom
# settings - need dummy empty group to enable no communication
neighbor 0.3 bin
neigh_modify delay 1 every 1 check no
communicate single group empty
# timestep is big and SRD frequency is 1
timestep 0.02
fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip
fix 2 all enforce2d
# diagnostics
thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6]
thermo 100
dump 1 all atom 250 dump.srd.pure
run 5000
SRD info:
SRD/big particles = 21316 0
big particle diameter max/min = 0 1e+20
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 5.37062
SRD viscosity = 0.439647
big/SRD mass density ratio = 0
# of rescaled SRD velocities = 0
ave/max all velocity = 13.2735 24.2873
Memory usage per processor = 1.34973 Mbytes
Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6]
0 1 0 0.99995309 85.26 0 0 0
100 0.97718565 3969 0.97713981 83.314849 0 0 0
200 0.95953504 3969 0.95949002 81.809957 0 0 0
300 0.94384163 3969 0.94379735 80.471937 0 0 0
400 0.93018267 3969 0.93013903 79.307374 0 0 0
500 0.9189656 3969 0.91892248 78.351007 0 0 0
600 0.90794939 3969 0.9079068 77.411765 0 0 0
700 0.899123 3969 0.89908081 76.659227 0 0 0
800 0.89045828 3969 0.89041651 75.920473 0 0 0
900 0.88189664 3969 0.88185527 75.190507 0 0 0
1000 0.87511065 3969 0.87506959 74.611934 0 0 0
1100 0.86844868 3969 0.86840794 74.043934 0 0 0
1200 0.86236759 3969 0.86232713 73.52546 0 0 0
1300 0.85644064 3969 0.85640047 73.020129 0 0 0
1400 0.85088468 3969 0.85084476 72.546428 0 0 0
1500 0.84573938 3969 0.8456997 72.107739 0 0 0
1600 0.84169541 3969 0.84165592 71.76295 0 0 0
1700 0.83686816 3969 0.8368289 71.351379 0 0 0
1800 0.83199161 3969 0.83195258 70.935605 0 0 0
1900 0.82774228 3969 0.82770345 70.573307 0 0 0
2000 0.82446049 3969 0.82442181 70.293501 0 0 0
2100 0.82065145 3969 0.82061295 69.968743 0 0 0
2200 0.81761922 3969 0.81758087 69.710215 0 0 0
2300 0.81355286 3969 0.8135147 69.363517 0 0 0
2400 0.81040375 3969 0.81036573 69.095024 0 0 0
2500 0.80651947 3969 0.80648164 68.76385 0 0 0
2600 0.80304949 3969 0.80301181 68.467999 0 0 0
2700 0.80027966 3969 0.80024211 68.231843 0 0 0
2800 0.79726989 3969 0.79723248 67.97523 0 0 0
2900 0.79526953 3969 0.79523222 67.80468 0 0 0
3000 0.79213985 3969 0.79210268 67.537843 0 0 0
3100 0.79008514 3969 0.79004808 67.362659 0 0 0
3200 0.78760949 3969 0.78757254 67.151585 0 0 0
3300 0.78482758 3969 0.78479077 66.9144 0 0 0
3400 0.78225219 3969 0.7822155 66.694822 0 0 0
3500 0.78019518 3969 0.78015858 66.519441 0 0 0
3600 0.7782201 3969 0.77818359 66.351045 0 0 0
3700 0.77626555 3969 0.77622913 66.184401 0 0 0
3800 0.77429464 3969 0.77425832 66.016361 0 0 0
3900 0.7728635 3969 0.77282724 65.894342 0 0 0
4000 0.7712408 3969 0.77120462 65.75599 0 0 0
4100 0.76928811 3969 0.76925202 65.589504 0 0 0
4200 0.76768117 3969 0.76764516 65.452497 0 0 0
4300 0.76576395 3969 0.76572802 65.289034 0 0 0
4400 0.76375476 3969 0.76371893 65.117731 0 0 0
4500 0.76222055 3969 0.76218479 64.986924 0 0 0
4600 0.76007803 3969 0.76004237 64.804252 0 0 0
4700 0.75921155 3969 0.75917594 64.730377 0 0 0
4800 0.75699084 3969 0.75695533 64.541039 0 0 0
4900 0.75590428 3969 0.75586882 64.448399 0 0 0
5000 0.75435525 3969 0.75431986 64.316328 0 0 0
Loop time of 2.18424 on 4 procs for 5000 steps with 21316 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 0.913574 (41.8257)
Comm time (%) = 0.444886 (20.368)
Outpt time (%) = 0.273467 (12.52)
Other time (%) = 0.552312 (25.2862)
Nlocal: 5329 ave 5410 max 5266 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5000
Dangerous builds = 0

7530
examples/tad/log.tad.0.9Jan12.linux.3 Normal file
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